野油菜黄单胞菌感光相关基因功能研究
摘要
光现象对包括细菌在内的所有生命形式具有广泛的影响，比如，细菌的光抑制或光趋性等。同时，光也参与细菌的调控系统，影响细菌致病性。野油菜黄单胞菌（Xcc）是十字花科植物黑腐病的致病菌，通过序列分析发现，Xcc基因组中包含33个编码PAS结构域基因（PAS基因），涉及到了组氨酸激酶（HK）、Hybrid（HK/RR Hybrid）和GGDEF等几大功能类别。PAS结构域是一类重要的信号模块，其结构高度保守、序列差异较大，并能感应光、氧化还原电位、氧、某些小分子物质和细胞能量水平等变化。本研究首先运用三种预测工具对Xcc中的PAS结构域进行了二级结构预测，对有差异的预测结果，我们选取共同二级结构预测区作为最终结果，然后运用clustalX2.0对PAS结构域进行了基于二级结构的聚类分析。首先聚类分析了16个已知功能的PAS结构域，包括1个与电势信号相关、1个与红光信号相关、3个与氧信号相关和11个与蓝光信号相关的结构域，并对这些PAS结构域的氨基酸序列进行了进化分析；然后，将其同Xcc的PAS结构域一并实施了聚类分析。结果显示，16个已知PAS被较好地按照功能归类，从已知的三维结构比对中，我们不仅确证了聚类的结果，同时发现了某类PAS的活性位点和可能活性区域。据此，6个光感应相关类别和1个氧感应相关类别在一并聚类分析中被发现。为了更加深入地了解Xcc中PAS的功能，我们将全部33个PAS基因逐一进行了基因敲除，对所得突变体进行了一系列的检测，包括生长、游动性和致病性等，并将检测结果与聚类分析结果逐一比对，结果大部分相吻合。
通过本研究，我们归纳了基于二级结构分析蛋白结构域功能的高效和准确的方法，在Xcc的PAS结构域分析中，一共发现13个PAS基因与感应或传导光信号相关，编码包括4个HK，5个Hybrid和4个GGDEF蛋白，其中4个（XC_1476、XC_1037、XC_3829和XC_2324与致病性有关。
XC_3829是一GGDEF家族蛋白，对应突变体的致病性仅在弱光照条件下减弱，其蛋白结构中除了一个GGDEF结构域外，还包括两个PAS结构域和一个PAC结构域。在蛋白水平的体外酶活检测中，GGDEF结构域的DGC（Diguanylatecyclase）酶活大部分依赖于上游序列，全长蛋白的酶活在弱蓝光条件下（30μW/cm2）最强，其他光照和黑暗条件下，酶活均较弱。XC_3829的第一个PAS结构域与FMN互作，第二个PAS结构域能够感应光而抑制酶活。因此，两个PAS结构域相互协调地感应光信号，实现了对蛋白功能的精细调控。
Light is an energy source and an ever-present stimulus in environment, whichhas been revealed on most regions of wavelength in some researches on bacteria. Theseinfluences include light inhibition, phototaxis and photosynthesis, even virulence ofbacteria, etc. Xanthomonas campestris pathovar campestris (Xcc) is a cruciferousplant-infecting pathogen, which is the causal agent of black rot. PAS (Per–Arnt–Sim)domains are important signaling modules that monitor changes in light, redox potential,oxygen, small ligands, and overall energy level of a cell. Prokaryotic genome analysiswith bioinformatics methods revealed the presence of PAS proteins in~15%of allsequenced genomes. PAS proteins participated in switching of lights as putativephotoreceptors according to more and more clues. Thirty-three PAS domain-containingproteins (thereafter PAS proteins) were found in Xcc genome and proteome with asystematic analysis via bioinformatics methods. These PAS proteins include8histidinekinases (HK),10response regulators or hybrids (HK/RR hybrid),8GGDEF familyproteins,3transcription regulators,2chemotaxis protein,1phytochrome-like proteinand1methyltransferase.
The revealed PAS domain structures indicated that its general secondary structurewas very conservative, and cofactors frequently interact with helixes. Therefore,secondary structure topology (SST) of PAS domains were firstly predicted with threetools, and merged manually. Afterwards, a comparison alignment on SST of PASdomains was built, meanwhile, other16PAS domains that have been proven to functionas light, oxygen or voltage sensors, were added in the analysis. Three categories (light,oxygen and voltage) of known PAS domains were well clustered on the basis of SSTs,therefore, the six clusters of the full tree were compared with the results of the latermutants tests. The33mutants of PAS genes of Xcc, which include22in-frame deletionsand11insertional mutations, were detected in growth, motility and virulence assays, etc.Thirteen PAS proteins were detected to involve in light sensing or signaling in Xcc,which included4HK,5hybrid and4GGDEF family proteins. Four PAS proteins wereinvolved in virulence of Xcc with interacting with light signals. These results weremuch consistent with clustering analysis.
The protein of XC_3829contains four predicted domains of two PAS, a PAC and aGGDEF, and the two PAS domains involved individually in deferent clusters. Fordetecting functions of PAS domain, the full length and three fragments of the proteinwere expressed as C-terminal His6-tagged fusion, and purified using nickel-affinitychromatography. The purified products were assayed with GTP in enzymatic reactions.The fragment of only GGDEF domain showed very low DGC activity. The DGCactivity of full protein was FMN dependent and was triggered in weak blue lightcondition. The PAS1domain interacted with FMN, and sensed blue light; the PAS2domain can sense light to inhibit the DGC activity. The interaction of the both PASdomains of XC_3829finely manipulates the DGC intensity of XC_3829.
通过本研究，我们归纳了基于二级结构分析蛋白结构域功能的高效和准确的方法，在Xcc的PAS结构域分析中，一共发现13个PAS基因与感应或传导光信号相关，编码包括4个HK，5个Hybrid和4个GGDEF蛋白，其中4个（XC_1476、XC_1037、XC_3829和XC_2324与致病性有关。
XC_3829是一GGDEF家族蛋白，对应突变体的致病性仅在弱光照条件下减弱，其蛋白结构中除了一个GGDEF结构域外，还包括两个PAS结构域和一个PAC结构域。在蛋白水平的体外酶活检测中，GGDEF结构域的DGC（Diguanylatecyclase）酶活大部分依赖于上游序列，全长蛋白的酶活在弱蓝光条件下（30μW/cm2）最强，其他光照和黑暗条件下，酶活均较弱。XC_3829的第一个PAS结构域与FMN互作，第二个PAS结构域能够感应光而抑制酶活。因此，两个PAS结构域相互协调地感应光信号，实现了对蛋白功能的精细调控。
Light is an energy source and an ever-present stimulus in environment, whichhas been revealed on most regions of wavelength in some researches on bacteria. Theseinfluences include light inhibition, phototaxis and photosynthesis, even virulence ofbacteria, etc. Xanthomonas campestris pathovar campestris (Xcc) is a cruciferousplant-infecting pathogen, which is the causal agent of black rot. PAS (Per–Arnt–Sim)domains are important signaling modules that monitor changes in light, redox potential,oxygen, small ligands, and overall energy level of a cell. Prokaryotic genome analysiswith bioinformatics methods revealed the presence of PAS proteins in~15%of allsequenced genomes. PAS proteins participated in switching of lights as putativephotoreceptors according to more and more clues. Thirty-three PAS domain-containingproteins (thereafter PAS proteins) were found in Xcc genome and proteome with asystematic analysis via bioinformatics methods. These PAS proteins include8histidinekinases (HK),10response regulators or hybrids (HK/RR hybrid),8GGDEF familyproteins,3transcription regulators,2chemotaxis protein,1phytochrome-like proteinand1methyltransferase.
The revealed PAS domain structures indicated that its general secondary structurewas very conservative, and cofactors frequently interact with helixes. Therefore,secondary structure topology (SST) of PAS domains were firstly predicted with threetools, and merged manually. Afterwards, a comparison alignment on SST of PASdomains was built, meanwhile, other16PAS domains that have been proven to functionas light, oxygen or voltage sensors, were added in the analysis. Three categories (light,oxygen and voltage) of known PAS domains were well clustered on the basis of SSTs,therefore, the six clusters of the full tree were compared with the results of the latermutants tests. The33mutants of PAS genes of Xcc, which include22in-frame deletionsand11insertional mutations, were detected in growth, motility and virulence assays, etc.Thirteen PAS proteins were detected to involve in light sensing or signaling in Xcc,which included4HK,5hybrid and4GGDEF family proteins. Four PAS proteins wereinvolved in virulence of Xcc with interacting with light signals. These results weremuch consistent with clustering analysis.
The protein of XC_3829contains four predicted domains of two PAS, a PAC and aGGDEF, and the two PAS domains involved individually in deferent clusters. Fordetecting functions of PAS domain, the full length and three fragments of the proteinwere expressed as C-terminal His6-tagged fusion, and purified using nickel-affinitychromatography. The purified products were assayed with GTP in enzymatic reactions.The fragment of only GGDEF domain showed very low DGC activity. The DGCactivity of full protein was FMN dependent and was triggered in weak blue lightcondition. The PAS1domain interacted with FMN, and sensed blue light; the PAS2domain can sense light to inhibit the DGC activity. The interaction of the both PASdomains of XC_3829finely manipulates the DGC intensity of XC_3829.
引文
[1] Onsando J A. Black rot of crucifers, in Diseases of vegetables and oil seed crops. ChaubeH S, et al, eds. Englewood Cliffs, NJ: Prentice Hall,1992,2:243-252.
[2] Chan J W, Goodwin P H. The molecular genetics of virulence of Xanthomonascampestris. Biotechnol Adv,1999,17:489-508.
[3] Vauterin L, Hoste B, Kersters K, et al. Reclassification of Xanthomonas. Int J SystBacteriol,1995,45(472-489).
[4] Schaad N W, Postnikova E, Lacy G H, et al. Reclassification of Xanthomonas campestrispv. citri (ex Hasse1915) Dye1978forms A, B/C/D, and E as X. smithii subsp. citri (exHasse) sp. nov. nom. rev. comb. nov, X. fuscans subsp. aurantifolii (ex Gabriel1989) sp.nov. nom. rev. comb. nov, and X. alfalfae subsp. citrumelo (ex Riker and Jones) Gabrielet al,1989sp. nov. nom. rev. comb. nov; X. campestris pv malvacearum (ex smith1901)Dye1978as X. smithii subsp. smithii nov. comb. nov. nom. nov; X. campestris pv.alfalfae (ex Riker and Jones,1935) dye1978as X. alfalfae subsp. alfalfae (ex Riker et al.,1935) sp. nov. nom. rev; and "var. fuscans" of X. campestris pv. phaseoli (ex Smith,1987) Dye1978as X. fuscans subsp. fuscans sp. nov. Syst Appl Microbiol,2005,28(494-518).
[5] Goncalves E R, Rosato Y B. Phylogenetic analysis of Xanthomonas species based upon16S-23S rDNA intergenic spacer sequences. Int J Syst Evol Microbiol2002,52:355-361.
[6] Alvarez A M. Black rot of crucifers Mechanisms of Resistance to Plant Diseases, ed.Slusarenko A J, Fraser R S S, and van Loon L C. Dordrecht: Kluwer AcademicPublications.2000,21-52.
[7] Gordon C A, Hodges N A, Marriott C. Antibiotic interaction and diffusion throughalginate and exopolysaccharide of cystic fibrosis-derived Pseudomonas aeruginosa. JAntimicrob Chemother,1988,22:667-674.
[8] Costerton J W, Cheng K J, Geesey G G, et al. Bacterial Biofilms in Nature and Disease.Anna Rev Micmbiol,1987,41:435-464.
[9] Katzen F, Ferreiro D U, Oddo C G, et al. Xanthomonas campestris pv. campestris gummutants: effects on xanthan biosynthesis and plant virulence. J Bacteriol,1998,180:1607-1617.
[10] Morris E R, Rees D A, Young G, et al. Order-disorder transition for a bacterialpolysaccharide in solution: a role for polysaccharide conformation in recognitionbetween Xanthomonas pathogen and its plant host. J Mol Biol,1977,110:1-16.
[11] Newman M A, Conrads-Strauch J, Scofield G, et al. Defense-related gene induction inBrassica campestris in response to defined mutants of Xanthomonas campestris withaltered pathogenicity. Mol Plant Microbe Interact,1994,7:553-563.
[12] Vojnov A A, Slater H, Newman M A, et al. Regulation of the synthesis of cyclic glucanin Xanthomonas campestris by a diffusible signal molecule. Arch Microbiol,2001,176:415-420.
[13] Yun M H, Torres P S, El-Oirdi M, et al. Xanthan induces plant susceptibility bysuppressing callose deposition. Plant Physiol,2006,141:178-187.
[14] Xu G W, Gonzalez C F. Evaluation of TN4431-induced protease mutants ofXanthomonas campestris pv. oryzae for growth in plants and pathogenicity.Phytopathology,198979:1210-1215.
[15] Dow J M, Clarke B R, Milligan D E, et al. Extracellular proteases from Xanthomonascampestris pv. campestris, the black rot pathogen. Appl Environ Microbiol,1990,56(10):2994-2998.
[16] Roberts D P, Denny T P, Schell M A. Cloning of the egl gene of Pseudomonassolanacearum and analysis of its role in phytopathogenicity. J Bacteriol,1988,170:1445-1451.
[17] Walker D S, Reeves P, Salmond G P C. The major secreted cellulase, CelV of Erwiniacarotovora subsp. carotovora is an important soft rot virulence factor. Mol PlantMicrobe Interact,1994,7:425-431.
[18] Gough C L, Dow J M, Keen J, et al. Nucleotide sequence of the engXCA gene encodingthe major endoglucanase of Xanthomonas campestris pv. campestris. Gene,1990,89:53-59.
[19] Schr ter K, Flaschel E, Pühler A, et al. Xanthomonas campestris pv. campestris secretesthe endoglucanases ENGXCA and ENGXCB: construction of anendoglucanase-deficient mutant for industrial xanthan production. Appl MicrobiolBiotechnol,2001,55:727-733.
[20] Hsiao Y M, Zheng M H, Hu R M, et al. Regulation of the pehA gene encoding the majorpolygalacturonase of Xanthomonas campestris by Clp and RpfF. Microbiology,2008154:705-713.
[21] Wang L F, Rong W, He C Z. Two Xanthomonas Extracellular Polygalacturonases,PghAxc and PghBxc, Are Regulated by Type III Secretion Regulators HrpX and HrpGand Are Required for Virulence. Mol Plant Microbe Interact,2008,21:555-563.
[22] Rajeshwari R, Jha G, Sonti R V. Role of an in planta-expressed xylanase ofXanthomonas oryzae pv. oryzae in promoting virulence on rice. Mol Plant MicrobeInteract,2005,18:830-837.
[23] Mueller M, Lindner B, Kusumoto S, et al. Aggregates Are the Biologically Active Unitsof Endotoxin. J Biol Chem,2004,279:26307-26313.
[24] Minardi P. Altered Expression of Erwinia amylovora hrp Genes in Tobacco LeavesPretreated with Bacterial Protein-Lipopolysaccharides. J Phytopathol,1995,143:199-205.
[25] Newman M A, Roepenack E, Daniels M, et al. Lipopolysaccharides and plant responsesto phytopathogenic bacteria. Mol Plant Pathol,2000,1:25-31.
[26] Klement Z, Bozsó Z, Ott P G, et al. Symptomless Resistant Response Instead of theHypersensitive Reaction in Tobacco Leaves after Infiltration of Heterologous Pathovarsof Pseudomonas syringae. J Phytopathol,1999,147:467-475.
[27] Dow J M, Osbourn A E, Wilson T J, et al. A locus determining pathogenicity ofXanthomonas campestris is involved in lipopolysaccharide biosynthesis. Mol PlantMicrobe Interact,1995,8:768-777.
[28] Goel A K, Rajagopal L, Sonti R V. Pigment and virulence deficiencies associated withmutations in the aroE gene of Xanthomonas oryzae pv. oryzae. Appl Environ Microbiol,2001,67:245-250.
[29] Rajagopal L, Sundari C S, Balasubramanian D, et al. The bacterial pigmentxanthomonadin offers protection against photodamage. Febs Lett,1997,415:125-128.
[30] Poplawsky A R, Urban S C, Chun W. Biological role of xanthomonadin pigments inXanthomonas campestris pv. campestris. Appl Environ Microbiol,2000,66:5123-5127.
[31] Josenhans C, Suerbaum S. The role of motility as a virulence factor in bacteria. Int J MedMicrobiol,2002,291:605-614.
[32] Chesnokova O, Coutinho J B, Khan I H, et al. Characterization of flagella genes ofAgrobacterium tumefaciens, and the effect of a bald strain on virulence. Mol Microbiol,1997,23:579-590.
[33] Yao J, Allen C. Chemotaxis Is Required for Virulence and Competitive Fitness of theBacterial Wilt Pathogen Ralstonia solanacearum. J Bacteriol,2006,188:3697-3708.
[34] Shen Y, Chern M, Silva F G, et al. Isolation of a Xanthomonas oryzae pv. oryzaeflagellar operon region and molecular characterization of flhF. Mol Plant MicrobeInteract,2001,14:204-213.
[35] Yang T C, Leu Y W, Chang-Chien H C, et al. Flagellar Biogenesis of Xanthomonascampestris Requires the Alternative Sigma Factors RpoN2and FliA and Is TemporallyRegulated by FlhA, FlhB, and FlgM. J Bacteriol,2009,191:2266-2275.
[36] Costerton J W, Stewart P S, Greenberg E P. Bacterial Biofilms: A Common Cause ofPersistent Infections. Science,1999,284:1318-1322.
[37] Crossman L, Dow J M. Biofilm formation and dispersal in Xanthomonas campestris.Microbes Infect,2004,6(6):623-629.
[38] Dow J M, Crossman L, Findlay K, et al. Biofilm dispersal in Xanthomonas campestris iscontrolled by cell-cell signaling and is required for full virulence to plants. PNAS,2003,100(19):10995-11000.
[39] Hammer B K, Bassler B L. Quorum sensing controls biofilm formation in Vibriocholerae. Mol Microbiol,2003,50:101-104.
[40] Williamson N R, Fineran P C, Ogawa W, et al. Integrated regulation involving quorumsensing, a two-component system, a GGDEF/EAL domain protein and apost-transcriptional regulator controls swarming and RhlA-dependent surfactantbiosynthesis in Serratia. Environ microbial,2008,10:1202-1217.
[41] Waters C M, Bassler B L. Quorum sensing: Cell to cell communication in bacteria. AnnuRev Cell Dev Biol,2005,21:319-346.
[42] Bassler B L. How bacteria talk to each other: regulation of gene expression by quorumsensing. Curr Opin Microbiol,1999,2(6):582-587.
[43] Miller M B, Bassler B L. Quorum sensing in bacteria. Annu Rev Microbiol,2001,55:165-199.
[44] Chen X, Schauder S, Potier N, et al. Structural identification of a bacterialquorum-sensing signal containing boron. Nature,2002,415:545-549.
[45] Miller S T, Xavier K B, Campagna S R, et al. Salmonella typhimurium Recognizes aChemically Distinct Form of the Bacterial Quorum-Sensing Signal AI-2. Mol Cell,2004,15:677-687.
[46] Zhang L H, Dong Y H. Quorum sensing and signal interference: diverse implications.Mol Microbiol,2004,53:1563-1571.
[47] Atkinson S, Chang C Y, Sockett R E, et al. Quorum sensing in Yersinia enterocoliticacontrols swimming and swarming motility. J Bacteriol,2006,188:1451-1461.
[48] Wang L H, He Y W, Gao Y, et al. A bacterial cell-cell communication signal withcross-kingdom structural analogues. Mol Microbiol,2004,51:903-912.
[49] Chun W, Cui J, Poplawsky A. Purification, characterization and biological role of apheromone produced by Xanthomonas campestris pv. campestris. Physiol Mol PlantPathol,1997,51:1-14.
[50] Barber C E, Tang J L, Feng J X, et al. A novel regulatory system required forpathogenicity of Xanthomonas campestris is mediated by a small diffusible signalmolecule. Mol Microbiol,1997,24:555-566.
[51] Slater H, A. Alvarez-Morales, C. E. Barber, et al. A two-component system involving anHD-GYP domain protein links cell-cell signalling to pathogenicity gene expression inXanthomonas campestris. Mol Microbiol,2000,38:986-1003.
[52] Ryan R P, Fouhy Y, Lucey J F, et al. Cell-cell signaling in Xanthomonas campestrisinvolves an HD-GYP domain protein that functions in cyclic di-GMP turnover. PNAS,2006,103(17):6712-6717.
[53] Poplawsky A R, Chun W. pigB determines a diffusible factor needed for extracellularpolysaccharide slime and xanthomonadin production in Xanthomonas campestris pv.campestris. J Bacteriol,1997,179:439-444.
[54] Chatterjee S, Sonti R V. rpfF mutants of Xanthomonas oryzae pv. oryzae are deficient forvirulence and growth under low iron conditions. Mol Plant Microbe Interact,2002,15:463-471.
[55] Tang J L, J. X. Feng, Q. Q. Li, et al. Cloning and characterization of the rpfC gene ofXanthomonas oryzae pv. oryzae: involvement in exopolysaccharide production andvirulence to rice. Mol Plant Microbe Interact,1996,9:664-666.
[56] Dangl J L, Jones J D G. Plant pathogens and integrated defence responses to infection.Nature,2001,411(6839):826-833.
[57] He S Y, K. Nomura, T. S. Whittam. Type III protein secretion mechanism in mammalianand plant pathogens. Biochimica et Biophysica Acta,2004,1694:181-206.
[58] Heesemann J, Algermissen B, Laufs R. Genetically manipulated virulence ofYersinia-enterocolitica. Infect Immun,1984,46(1):105-110.
[59] Lindgren P B, Peet R C, Panopoulos N J. Gene-cluster of Psendomonas-syringae pvphaseolicola controls pathogenicity of bean-plants and hypersensitivity on nonhostplants. J Bacteriol,1986,168(2):512-522.
[60] Alfano J R, Collmer A. Type III secretion system effector proteins: Double agents inbacterial disease and plant defense. Annu Rev Phytopathol,2004,42:385-414.
[61] Alfano J R, Collmer A. Bacterial Pathogens in Plants: Life up against the Wall. PlantCell,1996,8:1683-1698.
[62] Dobrindt U, Hochhut B, Hentschel U, et al. Genomic islands in pathogenic andenvironmental microorganisms. Nat Rev Microbiol,2004,2(5):414-424.
[63] Brown I R, Mansfield J W, Taira S, et al. Immunocytochemical localization of HrpA andHrpZ supports a role for the Hrp pilus in the transfer of effector proteins fromPseudomonas syringae pv. tomato across the host plant cell wall. Mol Plant MicrobeInteract,2001,14:394-404.
[64] Ghosh P. Process of protein transport by the type III secretion system. Microbiol MolBiol R,2004,68(4):771-775.
[65] Buttner D, Bonas U. Getting across-bacterial type III effector proteins on their way tothe plant cell. Embo J,2002,21(20):5313-5322.
[66] Bogdanove A J, Beer S V, Bonas U, et al. Unified nomenclature for broadly conservedhrp genes of phytopathogenic bacteria. Mol Microbiol,1996,20(3):681-683.
[67] Tampakaki A P, Fadouloglou V E, Gazi A D, et al. Conserved features of type IIIsecretion. Cell Microbiol,2004,6(9):805-816.
[68] Greenberg J T, Yao N. The role and regulation of programmed cell death inplant-pathogen interactions. Cell Microbiol,2004,6(3):201-211.
[69] Bestwick C S, Bennett M H, Mansfield J W. Hrp mutant of Pseudomonas-syringae pvphaseolicola induces cell-wall alterations but not membrane damage leading to thehypersensitive reaction in lettuce. Plant Physiol,1995,108(2):503-516.
[70] Lamb C, Dixon R A. The oxidative burst in plant disease resistance. Annu Rev PlantPhys,1997,48:251-275.
[71] Wendehenne D, Durner J, Klessig D F. Nitric oxide: a new player in plant signalling anddefence responses. Curr Opin Plant Biol,2004,7(4):449-455.
[72] Dixon R A, Harrison M J. Activation, structure, and organization of genes involved inmicrobial defense in plants. Adv Genet,1990,28:165-234.
[73] Durrant W E, Dong X. Systemic acquired resistance. Annu Rev Phytopathol,2004,42:185-209.
[74] Abramovitch R B, Martin G B. Strategies used by bacterial pathogens to suppress plantdefenses. Current Opinion in Plant Biology,2004,7(4):356-364.
[75] de Torres M, Mansfield J W, Grabov N, et al. Pseudomonas syringae effector AvrPtoBsuppresses basal defence in Arabidopsis. Plant J,2006,47(3):368-382.
[76] Jackson R W, Athanassopoulos E, Tsiamis G, et al. Identification of a pathogenicityisland, which contains genes for virulence and avirulence, on a large native plasmid inthe bean pathogen Pseudomonas syringae pathovar phaseolicola. Proc Natl Acad SciUSA,1999,96(19):10875-10880.
[77] Reuber T L, Ausubel F M. Isolation of arabidopsis genes that differentiate betweenresistance responses mediated by the RPS2and RPM1disease resistance genes. PlantCell,1996,8(2):241-249.
[78] Ritter C, Dangl J L. Interference between two specific pathogen recognition eventsmediated by distinct plant disease resistance genes. Plant Cell,1996,8(2):251-257.
[79] Tsiamis G, Mansfield J W, Hockenhull R, et al. Cultivar-specific avirulence andvirulence functions assigned to avrPphF in Pseudomonas syringae pv. phaseolicola, thecause of bean halo-blight disease. Embo J,2000,19(13):3204-3214.
[80] Petnicki-Ocwieja T, Schneider D J, Tam V C, et al. Genomewide identification ofproteins secreted by the Hrp type III protein secretion system of Pseudomonas syringaepv. tomato DC3000. Proc Natl Acad Sci USA,2002,99:7652-7657.
[81] Sugio A, Yang B, White F F. Characterization of the hrpF pathogenicity peninsula ofXanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact,2005,18:546-554.
[82] Xiao Y, Heu S, Yi J, et al. Identification of a putative alternate sigma factor andcharacterization of a multicomponent regulatory cascade controlling the expression ofPseudomonas syringae pv. syringae Pss61hrp and hrmA genes. J Bacteriol,1994,176:1025-1036.
[83] Wei Z M, Beer S V. hrpL activates Erwinia amylovora hrp gene transcription and is amember of the ECF subfamily of sigma factors. J Bacteriol,1995,177:6201-6210.
[84] Wengelnik K, VandenAckerveken G, Bonas U. HrpG, a key hrp regulatory protein ofXanthomonas campestris pv vesicatoria is homologous to two-component responseregulators. Mol Plant Microbe In,1996,9(8):704-712.
[85] Wengelnik K, Bonas U. HrpXv, an AraC-type regulator, activates expression of five ofthe six loci in the hrp cluster of Xanthomonas campestris pv vesicatoria. J Bacteriol,1996,178(12):3462-3469.
[86] Furutani A, Nakayama T, Ochiai H, et al. Identification of novel HrpXo regulonspreceded by two cis-acting elements, a plant-inducible promoter box and a-10box-likesequence, from the genome database of Xanthomonas oryzae pv. oryzae. FEMSMicrobiol Lett,2006,259(1):133-141.
[87] Koebnik R, Kruger A, Thieme F, et al. Specific binding of the Xanthomonas campestrispv. vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoterboxes. J Bacteriol,2006,188(21):7652-7660.
[88] Fenselau S, Balbo I, Bonas U. Determinants of pathogenicity in Xanthomonas campestrispv. campestris pv. vesicatoria are related to proteins involved in secretion in bacterialpathogens of animals. Mol Plant Microbe In,1992,5(5):390-396.
[89] Fenselau S, Bonas U. Sequence and expression analysis of the hrpB pathogenicityoperon of Xanthomonas campestris pv vesicatoria which encodes eight proteins withsimilarity to components of the Hrp, Ysc, Spa, and Fli secretion systems. Mol PlantMicrobe In,1995,8(6):845-854.
[90] Huguet E, Hahn K, Wengelnik K, et al. hpaA mutants of Xanthomonas campestris pv.vesicatoria are affected in pathogenicity but retain the ability to induce host-specifichypersensitive reaction. Mol Microbiol,1998,29(6):1379-1390.
[91] Gürlebeck D, Thieme F, Bonas U. Type III effector proteins from the plant pathogenXanthomonas and their role in the interaction with the host plant. J Plant Physiol,2006,163(3):233-255.
[92] Leach J E, White F F. Bacterial avirulence genes. Annu Rev Phytopathol,1996,34:153-179.
[93] Yang B, White F F. Diverse members of the AvrBs3/PthA family of type III effectors aremajor virulence determinants in bacterial blight disease of rice. Mol Plant Microbe In,2004,17(11):1192-1200.
[94] Gurlebeck D, Szurek B, Bonas U. Dimerization of the bacterial effector protein AvrBs3in the plant cell cytoplasm prior to nuclear import. Plant J,2005,42(2):175-187.
[95] Marois E, Van den Ackerveken G, Bonas U. The Xanthomonas type III effector proteinAvrBs3modulates plant gene expression and induces cell hypertrophy in the susceptiblehost. Mol Plant Microbe In,2002,15(7):637-646.
[96] Schornack S, Meyer A, Romer P, et al. Gene-for-gene-mediated recognition ofnuclear-targeted AvrBs3-like bacterial effector proteins. J Plant Physiol,2006,163(3):256-272.
[97] Szurek B, Rossier O, Hause G, et al. Type III-dependent translocation of theXanthomonas AvrBs3protein into the plant cell. Mol Microbiol,2002,46(1):13-23.
[98] Fujikawa T, Ishihara H, Leach J E, et al. Suppression of defense response in plants by theavrBs3/pthA gene family of Xanthomonas spp. Mol Plant Microbe In,2006,19(3):342-349.
[99] Szurek B, Marois E, Bones U, et al. Eukaryotic features of the Xanthomonas type IIIeffector AvrBs3: protein domains involved in transcriptional activation and theinteraction with nuclear import receptors from pepper. Plant J,2001,26(5):523-534.
[100] VandenAckerveken G, Marois E, Bonas U. Recognition of the bacterial avirulenceprotein AvrBs3occurs inside the host plant cell. Cell,1996,87(7):1307-1316.
[101] Hotson A, Chosed R, Shu H J, et al. Xanthomonas type III effector XopD targetsSUMO-conjugated proteins in planta. Mol Microbiol,2003,50(2):377-389.
[102] Lopez-Solanilla E, Bronstein P A, Schneider A R, et al. HopPtoN is a Pseudomonassyringae Hrp (type III secretion system) cysteine protease effector that suppressespathogen-induced necrosis associated with both compatible and incompatible plantinteractions. Mol Microbiol,2004,54(2):353-365.
[103] Mudgett M B, Staskawicz B J. Characterization of the Pseudomonas syringae pv. tomatoAvrRpt2protein: demonstration of secretion and processing during bacterialpathogenesis. Mol Microbiol,1999,32(5):927-941.
[104] Roden J, Eardley L, Hotson A, et al. Characterization of the Xanthomonas AvrXv4effector, a SUMO protease translocated into plant cells. Mol Plant Microbe In,2004,17(6):633-643.
[105] Shao F, Golstein C, Ade J, et al. Cleavage of Arabidopsis PBS1by a bacterial type IIIeffector. Science,2003,301(5637):1230-1233.
[106] Bretz J R, Mock N M, Charity J C, et al. A translocated protein tyrosine phosphatase ofPseudomonas syringae pv. tomato DC3000modulates plant defence response toinfection. Mol Microbiol,2003,49(2):389-400.
[107] Espinosa A, Guo M, Tam V C, et al. The Pseudomonas syringae type III-secreted proteinHopPtoD2possesses protein tyrosine phosphatase activity and suppresses programmedcell death in plants. Mol Microbiol,2003,49(2):377-387.
[108] Janjusevic R, Abramovitch R B, Martin G B, et al. A bacterial inhibitor of hostprogrammed cell death defenses is an E3ubiquitin ligase. Science,2006,311(5758):222-226.
[109] Mascher T, Helmann J D, Unden G. Stimulus Perception in Bacterial Signal-TransducingHistidine Kinases. Microbiol Mol Biol Rev,2006,70(4):910-938.
[110] Parkinson J S, Kofoid E C. Communication modules in bacterial signaling proteins.Annu Rev Genet,1992,26:71-112.
[111] Stock A, Koshland D E, Stock J. Homologies between the salmonella-typhimurium Cheyprotein and proteins involved in the regulation of chemotaxis, membrane-proteinsynthesis, and sporulation. Proceedings of the National Academy of Sciences of theUnited States of America,1985,82(23):7989-7993.
[112] Stock A M, Robinson V L, Goudreau P N. Two-component signal transduction. AnnuRev Biochem,2000,69:183-215.
[113] Stock J, Da Re S. Signal transduction: Response regulators on and off. Curr Biol,2000,10(11):R420-R424.
[114] Galperin M Y. A census of membrane-bound and intracellular signal transductionproteins in bacteria: Bacterial IQ, extroverts and introverts. BMC Microbiol,2005,5.
[115] Perego M, Hoch J A. Protein aspartate phosphatases control the output oftwo-component signal transduction systems. Trends Genet,1996,12(3):97-101.
[116] Perego M. Kinase-phosphatase competition regulates Bacillus subtilis development.Trends Microbiol,1998,6(9):366-370.
[117] Jung K, Altendorf K. Truncation of amino acids12-128causes deregulation of thephosphatase activity of the sensor kinase KdpD of Escherichia coli. J Biol Chem,1998,273(28):17406-17410.
[118] Dutta R, Inouye M. Reverse phosphotransfer from OmpR to EnvZ in akinase(-)/phosphatase(+) mutant of EnvZ (EnvZ center dot N347D), a bifunctional signaltransducer of Escherichia coli. J Biol Chem,1996,271(3):1424-1429.
[119] Tang J L, Liu Y N, Barber C E, et al. Genetic and molecular analysis of a cluster of rpfgenes involved in positive regulation of synthesis of extracellular enzymes andpolysaccharide in Xanthomonas campestris pathovar campestris. Molecular&GeneralGenetics,1991,226(3):409-417.
[120] Fouhy Y, Lucey J F, Ryan R P, et al. Cell-cell signaling, cyclic di-GMP turnover andregulation of virulence in Xanthomonas campestris. Research in Microbiol,2006,157(10):899-904.
[121] Wengelnik K, Rossier O, Bonas U. Mutations in the regulatory gene hrpG ofXanthomonas campestris pv. vesicatoria result in constitutive expression of all hrp genes.J Bacteriol,1999,181(21):6828-6831.
[122] Noel L, Thieme F, Nennstiel D, et al. cDNA-AFLP analysis unravels a genome-widehrpG-regulon in the plant pathogen Xanthomonas campestris pv. vesicatoria. MolMicrobiol,2001,41(6):1271-1281.
[123] Yamazaki A, Hirata H, Tsuyumu S. HrpG regulates type II secretory proteins inXanthomonas axonopodis pv. citri. Journal of General Plant Pathology,2008,74(2):138-150.
[124] Romling U, Gomelsky M, Galperin M Y. C-di-GMP: the dawning of a novel bacterialsignalling system. Mol Microbiol,2005,57(3):629-639.
[125] Galperin M Y, Nikolskaya A N, Koonin E V. Novel domains of the prokaryotictwo-component signal transduction systems. FEMS Microbiol Lett,2001,203(1):11-21.
[126] Sasakura Y, Kanda K, Yoshimura-Suzuki T, et al. Investigation of the relationshipbetween protein-protein interaction and catalytic activity of a heme-regulatedphosphodiesterase from Escherichia coli (Ec DOS) by protein microarray. Biochemistry,2005,44(28):9598-9605.
[127] Hasegawa K, Masuda S, Ono T. Light induced structural changes of a full-length proteinand its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF).Biochemistry,2006,45(11):3785-3793.
[128] Martinez-Wilson H F, Tamayo R, Tischler A D, et al. The Vibrio cholerae hybrid sensorkinase VieS contributes to motility and biofilm regulation by altering the cyclicdiguanylate level. J Bacteriol,2008,190(19):6439-6447.
[129] Tschowri N, Busse S, Hengge R. The BLUF-EAL protein YcgF acts as a directanti-repressor in a blue-light response of Escherichia coli. Genes&Development,2009,23(4):522-534.
[130] Hickman J W, Tifrea D F, Harwood C S. A chemosensory system that regulates biofilmformation through modulation of cyclic diguanylate levels. Proc Natl Acad Sci USA,2005,102(40):14422-14427.
[131] Kulasekara H D, Ventre I, Kulasekara B R, et al. A novel two-component systemcontrols the expression of Pseudomonas aeruginosa fimbrial cup genes. Mol Microbiol,2005,55(2):368-380.
[132] Ryan R, Fouhy Y, Lucey J, et al. Functional genomics of the role of cyclic di-GMPsignaling in the virulence and environmental adaptation of Xanthomonas campestris.Abstracts of the General Meeting of the American Society for Microbiology,2007,107:393.
[133] Paul R, Weiser S, Amiot N C, et al. Cell cycle-dependent dynamic localization of abacterial response regulator with a novel di-guanylate cyclase output domain. Gene Dev,2004,18(6):715-727.
[134] Fineran P C, Williamson N R, Lilley K S, et al. Virulence and Prodigiosin AntibioticBiosynthesis in Serratia Are Regulated Pleiotropically by the GGDEF/EAL DomainProtein, PigX. J Bacteriol,2007,189(21):7653-7662.
[135] Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro,2009,7(4):263-273.
[136] Ryan R P, Fouhy Y, Lucey J F, et al. Cyclic di-GMP signalling in the virulence andenvironmental adaptation of Xanthomonas campestris. Mol Microbiol,2007,63(2):429-442.
[137] Cotter P A, Stibitz S. c-di-GMP-mediated regulation of virulence and biofilm formation.Curr Opin Microbiol,2007,10(1):17-23.
[138] Amikam D, Galperin M Y. PilZ domain is part of the bacterial c-di-GMP binding protein.Bioinformatics,2006,22(1):3-6.
[139] Weber H, Pesavento C, Possling A, et al. Cyclic-di-GMP-mediated signalling within thesigma(S) network of Escherichia coli. Mol Microbiol,2006,62(4):1014-1034.
[140] Pesavento C, Becker G, Sommerfeldt N, et al. Inverse regulatory coordination of motilityand curli-mediated adhesion in Escherichia coli. Gene Dev,2008,22(17):2434-2446.
[141] Kirillina O, Fetherston J D, Bobrov A G, et al. HmsP, a putative phosphodiesterase, andHmsT, a putative diguanylate cyclase, control Hms-dependent biofilm formation inYersinia pestis. Mol Microbiol,2004,54(1):75-88.
[142] Bobrov A G, Kirillina O, Forman S, et al. Insights into Yersinia pestis biofilmdevelopment: topology and co-interaction of Hms inner membrane proteins involved inexopolysaccharide production. Environ Microbiol,2008,10(6):1419-1432.
[143] Hickman J W, Harwood C S. Identification of FleQ from Pseudomonas aeruginosa as ac-di-GMP-responsive transcription factor. Mol Microbiol,2008,69(2):376-389.
[144] Fong J C N, Yildiz F H. Interplay between cyclic AMP-Cyclic AMP receptor protein andcyclic di-GMP signaling in Vibrio cholerae biofilm formation. J Bacteriol,2008,190(20):6646-6659.
[145] Sommerfeldt N, Possling A, Becker G, et al. Gene expression patterns and differentialinput into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichiacoli. Microbiol-sgm,2009,155:1318-1331.
[146] Bibikov S I, Biran R, Rudd K E, et al. A signal transducer for aerotaxis in Escherichiacoli. J Bacteriol,1997,179(12):4075-4079.
[147] S derb ck E, Reyes-Ramirez F, Eydmann T, et al. The redox-and fixednitrogen-responsive regulatory protein NIFL from Azotobacter vinelandii comprisesdiscrete flavin and nucleotide-binding domains. Mol Microbiol,1998,28(1):179-192.
[148] Hill S, Austin S, Eydmann T, et al. Azotobacter vinelandii NIFL is a flavoprotein thatmodulates transcriptional activation of nitrogen-fixation genes via a redox-sensitiveswitch. Proc Natl Acad Sci USA,1996,93(5):2143-2148.
[149] Macheroux P, Schonbrunn E, Svergun D I, et al. Evidence for a major structural changein Escherichia coli chorismate synthase induced by flavin and substrate binding.Biochem J,1998,335:319-327.
[150] Taylor B L. Role of proton motive force in sensory transduction in bacteria. Annu RevMicrobiol,1983,37:551-573.
[151] Glagolev A N. Reception of the energy level in bacterial taxis. Journal of TheoreticalBiology,1980,82(2):171-185.
[152] Baryshev V A, Glagolev A N, Skulachev V P. Sensing of delta-mebarh+in phototaxis ofhalobacterium halobrium. Nature,1981,292(5821):338-340.
[153] Nambu J R, Lewis J O, Wharton K A, et al. The drosophila single-minded gene encodesa helix-loop-helix protein that acts as a master regulator of CNS midline development.Cell,1991,67(6):1157-1167.
[154] Lagarias D M, Wu S H, Lagarias J C. Atypical phytochrome gene structure in the greenalga Mesotaenium caldariorum. Plant Molecular Biology,1995,29(6):1127-1142.
[155] Borgstahl G E O, Williams D R, Getzoff E D.1.4angstrom structure of photoactiveyellow protein, a cytosolic photoreceptor-unusual fold, active-site, and chromophore.Biochemistry,1995,34(19):6278-6287.
[156] Rebbapragada A, Johnson M S, Harding G P, et al. The Aer protein and the serinechemoreceptor Tsr independently sense intracellular energy levels and transduce oxygen,redox, and energy signals for Escherichia coli behavior. Proc Natl Acad Sci USA,1997,94(20):10541-10546.
[157] Zhulin I B, Taylor B L, Dixon R. PAS domain S-boxes in Archaea, bacteria and sensorsfor oxygen and redox. Trends Biochem Sci,1997,22(9):331-333.
[158] Pellequer J L, Wager-Smith K A, Kay S A, et al. Photoactive yellow protein: A structuralprototype for the three-dimensional fold of the PAS domain superfamily. Proc Natl AcadSci USA,1998,95(11):5884-5890.
[159] Gong W M, Hao B, Mansy S S, et al. Structure of a biological oxygen sensor: A newmechanism for heme-driven signal transduction. Proc Natl Acad Sci USA,1998,95(26):15177-15182.
[160] Fearon I M, Palmer A C V, Balmforth A J, et al. Hypoxia inhibits the recombinantalpha(1C) subunit of the human cardiac L-type Ca2+channel. J Physiol-london,1997,500(3):551-556.
[161] Ponting C P, Aravind L. PAS: a multifunctional domain family comes to light. Curr Biol,1997,7(11):R674-R677.
[162] Huala E, Oeller P W, Liscum E, et al. Arabidopsis NPH1: A protein kinase with aputative redox-sensing domain. Science,1997,278(5346):2120-2123.
[163] Cabral J H M, Lee A, Cohen S L, et al. Crystal structure and functional analysis of theHERG potassium channel N terminus: A eukaryotic PAS domain. Cell,1998,95(5):649-655.
[164] Zhulin I B, Taylor B L. Correlation of PAS domains with electron transport-associatedproteins in completely sequenced microbial genomes. Mol Microbiol,1998,29(6):1522-1523.
[165] Alex L A, Simon M I. Protein histidine kinases and signal-transduction in prokaryotesand eukaryotes. Trends Genet,1994,10(4):133-138.
[166] Schuster S C, Noegel A A, Oehme F, et al. The hybrid histidine kinase DokA is part ofthe osmotic response system of Dictyostelium. Embo J,1996,15(15):3880-3889.
[167] Kakimoto T. CKI1, a histidine kinase homolog implicated in cytokinin signaltransduction. Science,1996,274(5289):982-985.
[168] Gamble R L, Coonfield M L, Schaller G E. Histidine kinase activity of the ETR1ethylene receptor from Arabidopsis. Proc Natl Acad Sci USA,1998,95(13):7825-7829.
[169] Taylor B L, Zhulin I B. PAS domains: Internal sensors of oxygen, redox potential, andlight. Microbiol Mol Biol R,1999,63(2):479-507.
[170] Soderling S H, Bayuga S J, Beavo J A. Cloning and characterization of a cAMP-specificcyclic nucleotide phosphodiesterase. Proceedings of the National Academy of Sciencesof the United States of America,1998,95(15):8991-8996.
[171] McLaughlin M E, Sandberg M A, Berson E L, et al. Recessive mutations in the geneencoding the beta-subunit of Rod phosphodiesterase in patients with retinitis-pigmentosa.Nat Genet,1993,4(2):130-134.
[172] Yan C, Zhao A Z, Bentley J K, et al. Molecular cloning and characterization of acalmodulin-dependent phosphodiesterase enriched in olfactory sensory neurons. ProcNatl Acad Sci USA,1995,92(21):9677-9681.
[173] de Philip P, Batut J, Boistard P. Rhizobium meliloti Fix L is an oxygen sensor andregulates R. meliloti nifA and fixK genes differently in Escherichia coli. J Bacteriol,1990,172(8):4255-4262.
[174] David M, Daveran M L, Batut J, et al. Cascade regulation of nif gene expression inRhizobium-meliloti. Cell,1988,54(5):671-683.
[175] Baur B, Fischer K, Winter K, et al. cDNA sequence of a protein kinase from theinducible crassulacean acid metabolism plant mesembry anthemum crystallinum L,encoding a Snf-1homolog. Plant Physiol,1994,106(3):1225-1226.
[176] Gillesgonzalez M A, Gonzalez G, Perutz M F, et al. Heme based sensors, exemplified bythe kinase FixL, are a new class of heme protein with distinctive ligand binding andautoxidation. Biochemistry-us,1994,33(26):8067-8073.
[177] Gillesgonzalez M A, Gonzalez G, Perutz M F. Kinase activity of oxygen sensor FixLdepends on the spin state of its heme iron. Biochemistry-us,1995,34(1):232-236.
[178] Monson E K, Weinstein M, Ditta G S, et al. The FixL protein of rhizobium-meliloti canbe separated into a heme-binding oxygen-sensing domain and a functional C-terminalknase domain. Proc Nati Acad Sci USA,1992,89(10):4280-4284.
[179] Taylor B L, Zhulin I B. In search of higher energy: metabolism-dependent behaviour inbacteria. Mol Microbiol,1998,28(4):683-690.
[180] Liu J D, Parkinson J S. Genetic evidence for intercation between the Chew and Tsrproteins during chemoreceptor signaling by Escherichia coli. J Bacteriol,1991,173(16):4941-4951.
[181] Barak R, Eisenbach M. Regulation of interaction between signaling protein CheY andflagellar motor during bacterial chemotaxis, in Current Topics in Cellular Regulation,1996,34:137-158.
[182] Welch M, Oosawa K, Aizawa S I, et al. Phosphorylation dependent binding of a signalmolecule to the flagellar switch of bacteria. Proceedings of the National Academy ofSciences of the United States of America,1993,90(19):8787-8791.
[183] Burbulys D, Trach K A, Hoch J A. Initiation of sporulation in Bacillus subtilis iscontrolled by a multicomponent phosphorelay. Cell,1991,64(3):545-552.
[184] Sprenger W W, Hoff W D, Armitage J P, et al. The enbacterium ectothiorhodospirahalophila is negatively phototactic, with a wavelength dependence that fits theabsorption spectrum of the photoactive yellow protein. J Bacteriol,1993,175(10):3096-3104.
[185] Kagawa T, Kimura M, Wada M. Blue Light-Induced Phototropism of InflorescenceStems and Petioles is Mediated by Phototropin Family Members phot1and phot2. PlantCell Physiol,2009,50(10):1774-1785.
[186] Bhoo S H, Davis S J, Walker J, et al. Bacteriophytochromes are photochromic histidinekinases using a biliverdin chromophore. Nature,2001,414(6865):776-779.
[187] Andel F, Lagarias J C, Mathies R A. Resonance Raman analysis of chromophorestructure in the lumi-R photoproduct of phytochrome. Biochemistry-us,1996,35(50):15997-16008.
[188] Matysik J, Hildebrandt P, Schlamann W, et al. Fourier-transform resonanceraman-spectroscopy of intermediates of the phytochrome photocycle. Biochemistry-us,1995,34(33):10497-10507.
[189] Rudiger W, Thummler F, Cmiel E, et al. Chromophore structure of the physiologicallyactive form (PFR) of phytochrome. Proc Nati Acad Sci USA,1983,80(20):6244-6248.
[190] Lamparter T, Michael N, Mittmann F, et al. Phytochrome from Agrobacteriumtumefaciens has unusual spectral properties and reveals an N-terminal chromophoreattachment site. Proc Nati Acad Sci USA,2002,99(18):11628-11633.
[191] Alexandre M T A, van Grondelle R, Hellingwerf K J, et al. Perturbation of theground-state electronic structure of FMN by the conserved cysteine in phototropin LOV2domains. Phys Chem Chem Phys,2008,10(44):6693-6702.
[192] Christie J M. Phototropin blue-light receptors. Annual Review of Plant Biology,2007,58:21-45.
[193] Konig K, Teschke M, Sigusch B, et al. Red light kills bacteria via photodynamic action.Cell Mol Biol,2000,46(7):1297-1303.
[194] Pattison D, Davies M. Actions of ultraviolet light on cellular structures, in Cancer: CellStructures, Carcinogens and Genomic Instability. Birkh user Basel,2006:131-157.
[195] Avila-Perez M, Hellingwerf K J, Kort R. Blue light activates the sigma(B)-dependentstress response of Bacillus subtilis via YtvA. J Bacteriol,2006,188(17):6411-6414.
[196] Gaidenko T A, Kim T J, Weigel A L, et al. The blue-light receptor YtvA acts in theenvironmental stress signaling pathway of Bacillus subtilis. J Bacteriol,2006,188(17):6387-6395.
[197] Buttani V, Losi A, Eggert T, et al. Conformational analysis of the blue-light sensingprotein YtvA reveals a competitive interface for LOV-LOV dimerization andinterdomain interactions. Photochem Photobiol Sci,2007,6(1):41-49.
[198] M glich A, Moffat K. Structural Basis for Light-dependent Signaling in the DimericLOV Domain of the Photosensor YtvA. J Mol Biol,2007,373(1):112-126.
[199] Olmedo M, Ruger-Herreros C, Corrochano L M. Regulation by blue light of the fluffygene encoding a major regulator of conidiation in Neurospora crassa. Genetics,2010,184(3):651-8.
[200] Moriwaki A, Katsube H, Ueno M, et al. Cloning and characterization of the BLR2, thehomologue of the blue-light regulator of Neurospora crassa WC-2, in thephytopathogenic fungus Bipolaris oryzae. Curr Microbiol,2008,56(2):115-121.
[201] He Q Y, Liu Y. Molecular mechanism of light responses in Neurospora: fromlight-induced transcription to photoadaptation. Gene Dev,2005,19(23):2888-2899.
[202] Cheng P, He Q, Yang Y, et al. Functional conservation of light, oxygen, or voltagedomains in light sensing. Proc Nati Acad Sci USA,2003,100(10):5938-5943.
[203] Ballario P, Talora C, Galli D, et al. Roles in dimerization and blue light photoresponse ofthe PAS and LOV domains of Neurospora crassa white collar proteins. Mol Microbiol,1998,29(3):719-729.
[204] Baca M, Borgstahl G E O, Boissinot M, et al. Complete Chemical Structure ofPhotoactive Yellow Protein: Novel Thioester-Linked4-Hydroxycinnamyl Chromophoreand Photocycle Chemistry. Biochemistry-us,1994,33(48):14369-14377.
[205] Kort R, Hoff W D, VanWest M, et al. The xanthopsins: A new family of eubacterialblue-light photoreceptors. Embo J,1996,15(13):3209-3218.
[206] Getzoff E D, Gutwin K N, Genick U K. Anticipatory active-site motions andchromophore distortion prime photoreceptor PYP for light activation. Nat Struct MolBiol,2003,10(8):663-668.
[207] Kyndt J A, Fitch J C, Meyer T E, et al. The photoactivated PYP domain ofRhodospirillum centenum Ppr accelerates the recovery of the bacteriophytochromedomain after white light illumination. Biochemistry-us,2007,46(28):8256-8262.
[208] Harper S M, Neil L C, Gardner K H. Structural basis of a phototropin light switch.Science,2003,301(5639):1541-1544.
[209] Doi M, Shigenaga A, Emi T, et al. A transgene encoding a blue-light receptor, phot1,restores blue-light responses in the Arabidopsis phot1phot2double mutant. J Exp Bot,2004,55(396):517-523.
[210] Kaiserli E, Sullivan S, Jones M A, et al. Domain Swapping to Assess the MechanisticBasis of Arabidopsis Phototropin1Receptor Kinase Activation and Endocytosis by BlueLight. Plant Cell,2009,21(10):3226-3244.
[211] Christie J M, Salomon M, Nozue K, et al. LOV (light, oxygen, or voltage) domains ofthe blue-light photoreceptor phototropin (nph1): Binding sites for the chromophore flavinmononucleotide. Proc Nati Acad Sci USA,1999,96(15):8779-8783.
[212] Christie J, Jones M, Sullivan S, et al. Structure-function analysis of phototropinblue-light receptors. Comp Biochem Physiol Mol Integrat Physiol,2007,146(4):499-507.
[213] Cao Z, Livoti E, Losi A, et al. A Blue Light-inducible Phosphodiesterase Activity in theCyanobacterium Synechococcus elongatus. Photochem Photobiol,2010,86(3):606-611.
[214] Swartz T E, Tseng T, Frederickson M A, et al. Blue-Light-Activated Histidine Kinases:Two-Component Sensors in Bacteria. Science,2007,317(5841):1090-1093.
[215] Cheng P, Yang Y, Gardner K H, et al. PAS Domain-Mediated WC-1/WC-2Interaction IsEssential for Maintaining the Steady-State Level of WC-1and the Function of BothProteins in Circadian Clock and Light Responses of Neurospora. Mol Cell Biol,2002,22(2):517-524.
[216] Brody M S, Stewart V, Price C W. Bypass suppression analysis maps the signallingpathway within a multidomain protein: the RsbP energy stress phosphatase2C fromBacillus subtilis. Mol Microbiol,2009,72(5):1221-1234.
[217] Warmke J, Drysdale R, Ganetzky B. A distinct potassium channel polypeptide encodedby the Drosophila eag locus. Science,1991,252(5012):1560-1562.
[218] Wang Z, Wilson G F, Griffith L C. Calcium/Calmodulin-dependent Protein Kinase IIPhosphorylates and Regulates the Drosophila Eag Potassium Channel. J Biol Chem,2002,277(27):24022-24029.
[219] Warmke J W, Ganetzky B. A family of potassium channel genes related to eag indrosophila and mammals. Proc Natl Acad Sci USA,1994,91(8):3438-3442.
[220] Wang Q, Chen Q, A. T J. Genetics, molecular mechanisms and management of long QTsyndrome. Ann Med,1998,30:58–65.
[221] Vincent G M. The molecular genetics of the long QT syndrome:genes causing faintingand sudden death. Annu Rev Med,1998,49:263–274.
[222] Klenk H P, Clayton R A, Tomb J F, et al. The complete genome sequence of thehyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature,1997,390(6658):364-&.
[223] Karimova G, Bellalou J, Ullmann A. Phosphorylation-dependent binding of BvgA to theupstream region of the cyaA gene of Bordetella pertussis. Mol Microbiol,1996,20(3):489-496.
[224] Laszlo D J, L. T B. Aerotaxis in Salmonella typhimurium: role of electron transport. JBacteriol,1981,145:990–1001.
[225] Taylor B L, Miller J B, Warrick H M, et al. Electron acceptor taxis and blue light effecton bacteria chemotaxis. J Bacteriol,1979,140(2):567-573.
[226] Bespalov V A, Zhulin I B, Taylor B L. Behavioral responses of Escherichia coli tochanges in redox potential. Proc Natl Acad Sci USA1996,93:10084–10089.
[227] Iuchi S, C. L E. arcA (dye), a global regulatory gene in Escherichia coli mediatingrepression of enzymes in aerobic pathways. Proc Natl Acad Sci USA,1988,85:1888–1892.
[228] Iuchi S, Lin E C. Adaptation of Escherichia coli to redox environments by geneexpression. Mol Microbiol,1993,9:9–15.
[229] Zhang W S, Brooun A, McCandless J, et al. Signal transduction in the ArchaeonHalobacterium salinarium is processed through three subfamilies of13soluble andmembrane-bound transducer proteins. Proc Natl Acad Sci USA,1996,93(10):4649-4654.
[230] Brooun A, Bell J, Freitas T, et al. An archaeal aerotaxis transducer combines subunit Icore structures of eukaryotic cytochrome c oxidase and eubacterial methyl acceptingchemotaxis proteins. J Bacteriol,1998,180:1642–1646.
[231] Dolla A, Fu R, Brumlik M J, et al. Nucleotide sequence of dcrA, a Desulfovibrio vulgarisHildenborough chemoreceptor gene, and its expression in Escherichia coli. J Bacteriol,1992,174:1726–1733.
[232] Fu R, Wall J D, Voordouw G. DcrA, a c-type heme-containing methyl-accepting proteinfrom Desulfovibrio vulgaris Hildenborough, senses the oxygen concentration or redoxpotential of the environment. J Bacteriol,1994,176:344–350.
[233] Gomelsky M, Kaplan S. Molecular genetic analysis suggesting interactions betweenAppA and PpsR in regulation of photosynthesis geneexpression in Rhodobactersphaeroides2.4.1.. J Bacteriol,1997,179:128–134.
[234] Zeilstra-Ryalls J, Gomelsky M, Eraso J M, et al. Control of photosystem formation inRhodobacter sphaeroides. J Bacteriol,1998,180:2801–2809.
[235] Coschigano P W, Young L Y. Identification and sequence analysis of two regulatorygenes involved in anaerobic toluene metabolism by strain T1. Appl Environ Microbiol,1997,63:652–660.
[236] Golby P, Davies S, Kelly D J, et al. Identification and characterization of atwo-component sensor-kinase and response-regulator system (DcuS-DcuR) controllinggene expression in response to C4-dicarboxylates in Escherichia coli. J Bacteriol,1999,181:1238–1248.
[237] Zientz E, Bongaerts J, Unden G. Fumarate regulation of gene expression in Escherichiacoli by the DcuSR (dcuSR genes) two-component regulatory system. J Bacteriol,1998,180:5421–5425.
[238] Bott M. Anaerobic citrate metabolism and its regulation in enterobacteria. ArchMicrobiol,1997,167:78–88.
[239] Bott M, Meyer M, Dimroth P. Regulation of anaerobic citrate metabolism in Klebsiellapneumoniae. Mol Microbiol,1995,18:533–546.
[240] Dixon R. The oxygen-responsive NIFL-NIFA complex: a novel two-componentregulatory system controlling nitrogenase synthesis in gamma-proteobacteria. ArchMicrobiol,1998,169:371–380.
[241] Gropp F, Betlach M C. The bat gene of Halobacterium halobium encodes a trans-actingoxygen inducibility factor. Proc Natl Acad Sci USA,1994,91:5475–5479.
[242] Blanco G, Drummond M, Woodley P, et al. Sequence and molecular analysis of the nifLgene of Azotobacter vinelandii. Mol Microbiol,1993,9:869–879
[243] Macheroux P, S. Hill, S. Austin, et al. Electron donation to the flavoprotein NifL, aredox-sensing transcriptional regulator. Biochem J,1998,332:413–419.
[244] Schmitz R A. NifL of Klebsiella pneumoniae carries an N-terminally bound FADcofactor, which is not directly required for the inhibitory function of NifL. FemsMicrobiol Lett,1997,157:313–318.
[245] Gilles-Gonzalez M A, Ditta G S, Helinski D R. A haemo-protein with kinase activityencoded by the oxygen sensor of Rhizobium meliloti. Nature,1991,350:170–172.
[246] Kaminski P A, Elmerich C. Involvement of fixLJ in the regulation of nitrogen fixation inAzorhizobium caulinodans. Mol Microbiol,1991,5:665–673.
[247] Anthamatten D, Hennecke H. The regulatory status of the fixL-and fixJ-like genes inBradyrhizobium japonicum maybe different from that in Rhizobium meliloti. Mol GenGenet,1991,225:38–48.
[248] Dhooghe I, Michiels J, Vlassak K, et al. Structural and functional analysis of the fixljgenes of Rhizabium leguminosarum biovar phasoli cnpaf512. Mol General Genetics,1995,249(1):117-126.
[249] Patschkowski T, Schluter A, Priefer U B. Rhizobium leguminosarum pv viciae contains asecond fnr/fixK-like gene and an unusual fixL homologue. Mol Microbiol,1996,21(2):267-280.
[250] Fischer H M. Genetic regulation of nitrogen fixation in Rhizabia. Microbiol reviews,1994,58(3):352-386.
[251] Fischer H M. Environmental regulation of rhizobial symbiotic nitrogen fixation genes.Trends Microbiol,1996,4(8):317-320.
[252] Gong W, Hao B, Chan M K. New Mechanistic Insights from Structural Studies of theOxygen-Sensing Domain of Bradyrhizobium japonicum FixL. Biochemistry-us,2000,39(14):3955-3962.
[253] Genick U K, Soltis S M, Kuhn P, et al. Structure at0.85angstrom resolution of an earlyprotein photocycle intermediate. Nature,1998,392(6672):206-209.
[254] Delgado-Nixon V M, Gonzalez G, Gilles-Gonzalez M-A. Dos, a Heme-Binding PASProtein from Escherichia coli, Is a Direct Oxygen Sensor. Biochemistry-us,2000,39(10):2685-2691.
[255] Kurokawa H, Lee D S, Watanabe M, et al. A redox-controlled molecular switch revealedby the crystal structure of a bacterial heme PAS sensor. J Biol Chem,2004,279(19):20186-20193.
[256] Liebl U, Bouzhir-Sima L, Kiger L, et al. Ligand Binding Dynamics to the Heme Domainof the Oxygen Sensor Dos from Escherichia coli. Biochemistry-us,2003,42(21):6527-6535.
[257] Park H J, Suquet C, Satterlee J D, et al. Insights into signal transduction involving PASdomain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichiacoli dos heme domain (EcDosH). Biochemistry-us,2004,43(10):2738-2746.
[258] Tuckerman J R, Gonzalez G, Sousa E H S, et al. An Oxygen-Sensing DiguanylateCyclase and Phosphodiesterase Couple for c-di-GMP Control. Biochemistry-us,2009,48(41):9764-9774.
[259] Cohen-Bazire G, Sistrom W R, Stanier R Y. Kinetic studies of pigment synthesis bynon-sulphur purple bacteria. J Cell Comp Physiol,1957,49:25–68.
[260] Bauer C E, Bird T H. Regulatory circuits controlling photo-synthesis gene expression.Cell,1996,85:5–8.
[261] Drews G. Adaptation of the bacterial photosynthetic apparatus to different lightintensities. Trends Biochem Sci,1986,6:255–257.
[262] Gomelsky M, Kaplan S. Genetic evidence that ppsr from Rhodobacteria sphaeroides2.4.1functions as a repressor of puc and bchf expression. J Bacteriol,1995,177(6):1634-1637.
[263] Ponnampalam S N, Buggy J J, Bauer C E. Characterization of an aerobic repressor thatcoordinately regulates bacteriochlorophyll, carotenoid, and light harvesting-II expressionin Rhodobacter capsulatus. J Bacteriol,1995,177(11):2990-2997.
[264] Penfold R J, Pemberton J M. A gene from the photosynthetic gene cluster ofRhodobacter sphaeroides induces trans-suppression of bacterilchlorophyll andcarotenoid levels in R. sphaeroides and R. capsulatus. Curr Microbiol,1991,23(5):259-263.
[265] Ponnampalam S N, Bauer C E. DNA binding characteristics of CrtJ-Aredox-responding repressor of bacteriochlorophyll, carotenoid, and light harvesting-IIgene expression in Rhodobacter capsulatus. J Biol Chem,1997,272(29):18391-18396.
[266] Zhulin I B, Rowsell E H, Johnson M S, et al. Glycerol elicits energy taxis of Escherichiacoli and Salmonella typhimurium. J Bacteriol,1997,179(10):3196-3201.
[267] Hamblin M J, Shaw J G, Kelly D J. Sequnce analysis and interposon mutagenesis of asensor kinase (Dcts) and response regulator (Dctr) controlling synthesis of the highaffinity C4-dicarboxylate transport system in Rhodobacter capsulatus. Mol Gen Genet,1993,237(1-2):215-224.
[268] Huang Z J, Edery I, Rosbash M. PAS in a dimerization domain common to drosophilaperiod and several transcription factors. Nature,1993,364(6434):259-262.
[269] Pongratz I, Antonsson C, Whitelaw M L, et al. Role of the PAS Domain in Regulation ofDimerization and DNA Binding Specificity of the Dioxin Receptor. Mol Cell Biol,1998,18(7):4079-4088.
[270] Gekakis N, Staknis D, Nguyen H B, et al. Role of the CLOCK protein in the mammaliancircadian mechanism. Science,1998,280(5369):1564-1569.
[271] Schibler U. Circadian rhythms-New cogwheels in the clockworks. Nature,1998,393(6686):620-621.
[272] Rowlands J C, Gustafsson J A. Aryl hydrocarbon receptor-mediated signal transduction.Crit Rev Toxicol,1997,27(2):109-134.
[273] Edgerton M D, Jones A M. Subunit interactions in the carboxy terminal domain ofphytochrome. Biochemistry-us,1993,32(32):8239-8245.
[274] Li X D, Xu J, Li M. The human Delta1261mutation of the HERG potassium channelresults in a truncated protein that contains a subunit interaction domain and decreases thechannel expression. J Biol Chem,1997,272(2):705-708.
[275] da Silva A C R, Ferro J A, Reinach F C, et al. Comparison of the genomes of twoXanthomonas pathogens with differing host specificities. Nature,2002,417(6887):459-463.
[276] Qian W, Jia Y T, Ren S X, et al. Comparative and functional genomic analyses of thepathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res,2005,15(6):757-767.
[277] Qian W, Han Z-J, Tao J, et al. Genome-Scale Mutagenesis and PhenotypicCharacterization of Two-Component Signal Transduction Systems in Xanthomonascampestris pv. campestris ATCC33913. Mol Plant Microbe In,2008,21(8):1128-1138.
[278] Vorholter F-J, Schneiker S, Goesmann A, et al. The genome of Xanthomonas campestrispv. campestris B100and its use for the reconstruction of metabolic pathways involved inxanthan biosynthesis. J Biotechnol,2008,134(1-2):33-45.
[279] Sch fer A, Tauch A, J ger W, et al. Small mobilizable multi-purpose cloning vectorsderived from the Escherichia coli plasmids pK18and pK19: selection of defineddeletions in the chromosome of Corynebacterium glutamicum. Gene,1994,145(1):69-73.
[280] Figurski D H, Helinski D R. Replication of an origin-containing derivative of plasmidRK2dependent on a plasmid function provided in trans. Proc Nati Acad Sci USA,1979,76(4):1648-1652.
[281] Huynh T V, Dahlbeck D, Staskawicz B J. Bacterial-blight of soybean-Regulation of apathogen gene determining host cultivar specificity. Science,1989,245(4924):1374-1377.
[282] Davis A R, Kostek B, Mason B B, et al. Expression of hepatitis B surface antigen with arecombinant adenovirus. Proc Nati Acad Sci USA,1985,82(22):7560-7564.
[283] GRANT S N, JESSEE J, BLOOM F, et al. Differential plasmid rescue from transgenicmouse DNAs into Escherichia coli methylation-restriction mutants. Proc Nati Acad SciUSA,1990,87:4645-4649.
[284] Simon R, Priefer U, Puhler A. A Broad Host Range Mobilization System for In VivoGenetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria. Nat Biotech,1983,1(9):784-791.
[285] Nishiguchi, Nishiguchi M, Yoshida, et al. A receptor-like protein kinase with alectin-like domain from lombardy poplar: gene expression in response to wounding andcharacterization of phosphorylation activity. Mol Genet Genomics,2002,267(4):506-514.
[286] Keen N T, Boyd C, Henrissat B. Cloning and characterization of a xylanase gene fromcorn strains of Erwinia chrysanthemi. Mol Plant Microbe Interact,1996,9:651-657.
[287] DiLuzio W R, Turner L, Mayer M, et al. Escherichia coli swim on the right-hand side.Nature,2005,435(7046):1271-1274.
[288] Lim B, Beyhan S, Meir J, et al. Cyclic-diGMP signal transduction systems in Vibriocholerae: modulation of rugosity and biofilm formation. Mol Microbiol,2006,60:331-348.
[289] Letunic I, Doerks T, Bork P. SMART6: recent updates and new developments. NucleicAcids Res,2009,37(suppl1):D229-D232.
[290] Finn R D, Mistry J, Tate J, et al. The Pfam protein families database. Nucleic Acids Res,2010,38(suppl1):D211-D222.
[291] Chan W M. The UniProt Knowledgebase (UniProtKB): a freely accessible,comprehensive and expertly curated protein sequence database. Genetics Research,2010,92(1):78-79.
[292] Christie J M, Corchnoy S B, Swartz T E, et al. Steric interactions stabilize the signalingstate of the LOV2domain of phototropin1. Biochemistry-us,2007,46(32):9310-9319.
[293] Key J, Hefti M, Purcell E B, et al. Structure of the redox sensor domain of Azotobactervinelandii NifL at atomic resolution: Signaling, dimerization, and mechanism.Biochemistry-us,2007,46(12):3614-3623.
[294] Cole C, Barber J D, Barton G J. The Jpred3secondary structure prediction server.Nucleic Acids Res,2008,36(suppl2):W197-W201.
[295] Jones D T. Protein secondary structure prediction based on position-specific scoringmatrices. J Mol Biol,1999,292(2):195-202.
[296] Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated proteinstructure and function prediction. Nature Protocols,2010,5:725-738.
[297] M glich A, Ayers R A, Moffat K. Structure and Signaling Mechanism ofPer-ARNT-Sim Domains. Structure,2009,17(10):1282-1294.
[298] Jaiswal R K, Manjeera G, Gopal B. Role of a PAS sensor domain in the Mycobacteriumtuberculosis transcription regulator Rv1364c. Biochem Bioph Res Co,2010,398(3):342-349.
[299] Jeanmougin F, Thompson J D, Gouy M, et al. Multiple sequence alignment with ClustalX. Trends Biochem Sci,1998,23(10):403-405.
[300] Larkin M A, Blackshields G, Brown N P, et al. Clustal W and Clustal X version2.0.Bioinformatics,2007,23(21):2947-2948.
[301] Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evolutionary Genetics Analysis(MEGA) software version4.0. Mol Biol Evol,2007(24):1596-1599.
[302] Saitou N, Nei M. The neighbor-joining method: A new method for reconstructingphylogenetic trees. Mol Biol Evol,1987(4):406-425.
[303] Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins, inEvolving Genes and Proteins. Bryson V, Vogel H J, eds. Academic Press: New York,1965,97-166.
[304] Li W, Godzik A. VISSA: a program to visualize structural features from structuresequence alignment. Bioinformatics,2006,22(7):887-888.
[305] Kawabata T. MATRAS: a program for protein3D structure comparison. Nucleic AcidsRes,2003,31(3367-3379).
[306] Rajagopal S, Moffat K. Crystal structure of a photoactive yellow protein from a sensorhistidine kinase: Conformational variability and signal transduction. Proc Nati Acad SciUSA,2003,100(4):1649-1654.
[307] Ulrich L E, Koonin E V, Zhulin I B. One-component systems dominate signaltransduction in prokaryotes. Trends Microbiol,2005,13(2):52-56.
[308] Ulrich L E, Zhulin I B. MiST: a microbial signal transduction database. Nucleic AcidsRes,2007,35:D386-D390.
[309] Ho Y-S J, Burden L M, Hurley J H. Structure of the GAF domain, a ubiquitous signalingmotif and a new class of cyclic GMP receptor. The EMBO Journal,2000,19(20):5288-5299.
[310] Su Y-s, Lagarias J C. Light-Independent Phytochrome Signaling Mediated by DominantGAF Domain Tyrosine Mutants of Arabidopsis Phytochromes in Transgenic Plants.Plant Cell,2007,19(7):2124-2139.
[311] Chang A L, Tuckerman J R, Gonzalez G, et al. Phosphodiesterase A1, a Regulator ofCellulose Synthesis in Acetobacter xylinum, Is a Heme-Based Sensor. Biochemistry-us,2001,40(12):3420-3426.
[312] Hefti M H, Francoijs K J, de Vries S C, et al. The PAS fold-A redefinition of the PASdomain based upon structural prediction. Eur J Biochem,2004,271(6):1198-1208.
[313] Christie J M, Swartz T E, Bogomolni R A, et al. Phototropin LOV domains exhibitdistinct roles in regulating photoreceptor function. The Plant Journal,2002,32(2):205-219.
[2] Chan J W, Goodwin P H. The molecular genetics of virulence of Xanthomonascampestris. Biotechnol Adv,1999,17:489-508.
[3] Vauterin L, Hoste B, Kersters K, et al. Reclassification of Xanthomonas. Int J SystBacteriol,1995,45(472-489).
[4] Schaad N W, Postnikova E, Lacy G H, et al. Reclassification of Xanthomonas campestrispv. citri (ex Hasse1915) Dye1978forms A, B/C/D, and E as X. smithii subsp. citri (exHasse) sp. nov. nom. rev. comb. nov, X. fuscans subsp. aurantifolii (ex Gabriel1989) sp.nov. nom. rev. comb. nov, and X. alfalfae subsp. citrumelo (ex Riker and Jones) Gabrielet al,1989sp. nov. nom. rev. comb. nov; X. campestris pv malvacearum (ex smith1901)Dye1978as X. smithii subsp. smithii nov. comb. nov. nom. nov; X. campestris pv.alfalfae (ex Riker and Jones,1935) dye1978as X. alfalfae subsp. alfalfae (ex Riker et al.,1935) sp. nov. nom. rev; and "var. fuscans" of X. campestris pv. phaseoli (ex Smith,1987) Dye1978as X. fuscans subsp. fuscans sp. nov. Syst Appl Microbiol,2005,28(494-518).
[5] Goncalves E R, Rosato Y B. Phylogenetic analysis of Xanthomonas species based upon16S-23S rDNA intergenic spacer sequences. Int J Syst Evol Microbiol2002,52:355-361.
[6] Alvarez A M. Black rot of crucifers Mechanisms of Resistance to Plant Diseases, ed.Slusarenko A J, Fraser R S S, and van Loon L C. Dordrecht: Kluwer AcademicPublications.2000,21-52.
[7] Gordon C A, Hodges N A, Marriott C. Antibiotic interaction and diffusion throughalginate and exopolysaccharide of cystic fibrosis-derived Pseudomonas aeruginosa. JAntimicrob Chemother,1988,22:667-674.
[8] Costerton J W, Cheng K J, Geesey G G, et al. Bacterial Biofilms in Nature and Disease.Anna Rev Micmbiol,1987,41:435-464.
[9] Katzen F, Ferreiro D U, Oddo C G, et al. Xanthomonas campestris pv. campestris gummutants: effects on xanthan biosynthesis and plant virulence. J Bacteriol,1998,180:1607-1617.
[10] Morris E R, Rees D A, Young G, et al. Order-disorder transition for a bacterialpolysaccharide in solution: a role for polysaccharide conformation in recognitionbetween Xanthomonas pathogen and its plant host. J Mol Biol,1977,110:1-16.
[11] Newman M A, Conrads-Strauch J, Scofield G, et al. Defense-related gene induction inBrassica campestris in response to defined mutants of Xanthomonas campestris withaltered pathogenicity. Mol Plant Microbe Interact,1994,7:553-563.
[12] Vojnov A A, Slater H, Newman M A, et al. Regulation of the synthesis of cyclic glucanin Xanthomonas campestris by a diffusible signal molecule. Arch Microbiol,2001,176:415-420.
[13] Yun M H, Torres P S, El-Oirdi M, et al. Xanthan induces plant susceptibility bysuppressing callose deposition. Plant Physiol,2006,141:178-187.
[14] Xu G W, Gonzalez C F. Evaluation of TN4431-induced protease mutants ofXanthomonas campestris pv. oryzae for growth in plants and pathogenicity.Phytopathology,198979:1210-1215.
[15] Dow J M, Clarke B R, Milligan D E, et al. Extracellular proteases from Xanthomonascampestris pv. campestris, the black rot pathogen. Appl Environ Microbiol,1990,56(10):2994-2998.
[16] Roberts D P, Denny T P, Schell M A. Cloning of the egl gene of Pseudomonassolanacearum and analysis of its role in phytopathogenicity. J Bacteriol,1988,170:1445-1451.
[17] Walker D S, Reeves P, Salmond G P C. The major secreted cellulase, CelV of Erwiniacarotovora subsp. carotovora is an important soft rot virulence factor. Mol PlantMicrobe Interact,1994,7:425-431.
[18] Gough C L, Dow J M, Keen J, et al. Nucleotide sequence of the engXCA gene encodingthe major endoglucanase of Xanthomonas campestris pv. campestris. Gene,1990,89:53-59.
[19] Schr ter K, Flaschel E, Pühler A, et al. Xanthomonas campestris pv. campestris secretesthe endoglucanases ENGXCA and ENGXCB: construction of anendoglucanase-deficient mutant for industrial xanthan production. Appl MicrobiolBiotechnol,2001,55:727-733.
[20] Hsiao Y M, Zheng M H, Hu R M, et al. Regulation of the pehA gene encoding the majorpolygalacturonase of Xanthomonas campestris by Clp and RpfF. Microbiology,2008154:705-713.
[21] Wang L F, Rong W, He C Z. Two Xanthomonas Extracellular Polygalacturonases,PghAxc and PghBxc, Are Regulated by Type III Secretion Regulators HrpX and HrpGand Are Required for Virulence. Mol Plant Microbe Interact,2008,21:555-563.
[22] Rajeshwari R, Jha G, Sonti R V. Role of an in planta-expressed xylanase ofXanthomonas oryzae pv. oryzae in promoting virulence on rice. Mol Plant MicrobeInteract,2005,18:830-837.
[23] Mueller M, Lindner B, Kusumoto S, et al. Aggregates Are the Biologically Active Unitsof Endotoxin. J Biol Chem,2004,279:26307-26313.
[24] Minardi P. Altered Expression of Erwinia amylovora hrp Genes in Tobacco LeavesPretreated with Bacterial Protein-Lipopolysaccharides. J Phytopathol,1995,143:199-205.
[25] Newman M A, Roepenack E, Daniels M, et al. Lipopolysaccharides and plant responsesto phytopathogenic bacteria. Mol Plant Pathol,2000,1:25-31.
[26] Klement Z, Bozsó Z, Ott P G, et al. Symptomless Resistant Response Instead of theHypersensitive Reaction in Tobacco Leaves after Infiltration of Heterologous Pathovarsof Pseudomonas syringae. J Phytopathol,1999,147:467-475.
[27] Dow J M, Osbourn A E, Wilson T J, et al. A locus determining pathogenicity ofXanthomonas campestris is involved in lipopolysaccharide biosynthesis. Mol PlantMicrobe Interact,1995,8:768-777.
[28] Goel A K, Rajagopal L, Sonti R V. Pigment and virulence deficiencies associated withmutations in the aroE gene of Xanthomonas oryzae pv. oryzae. Appl Environ Microbiol,2001,67:245-250.
[29] Rajagopal L, Sundari C S, Balasubramanian D, et al. The bacterial pigmentxanthomonadin offers protection against photodamage. Febs Lett,1997,415:125-128.
[30] Poplawsky A R, Urban S C, Chun W. Biological role of xanthomonadin pigments inXanthomonas campestris pv. campestris. Appl Environ Microbiol,2000,66:5123-5127.
[31] Josenhans C, Suerbaum S. The role of motility as a virulence factor in bacteria. Int J MedMicrobiol,2002,291:605-614.
[32] Chesnokova O, Coutinho J B, Khan I H, et al. Characterization of flagella genes ofAgrobacterium tumefaciens, and the effect of a bald strain on virulence. Mol Microbiol,1997,23:579-590.
[33] Yao J, Allen C. Chemotaxis Is Required for Virulence and Competitive Fitness of theBacterial Wilt Pathogen Ralstonia solanacearum. J Bacteriol,2006,188:3697-3708.
[34] Shen Y, Chern M, Silva F G, et al. Isolation of a Xanthomonas oryzae pv. oryzaeflagellar operon region and molecular characterization of flhF. Mol Plant MicrobeInteract,2001,14:204-213.
[35] Yang T C, Leu Y W, Chang-Chien H C, et al. Flagellar Biogenesis of Xanthomonascampestris Requires the Alternative Sigma Factors RpoN2and FliA and Is TemporallyRegulated by FlhA, FlhB, and FlgM. J Bacteriol,2009,191:2266-2275.
[36] Costerton J W, Stewart P S, Greenberg E P. Bacterial Biofilms: A Common Cause ofPersistent Infections. Science,1999,284:1318-1322.
[37] Crossman L, Dow J M. Biofilm formation and dispersal in Xanthomonas campestris.Microbes Infect,2004,6(6):623-629.
[38] Dow J M, Crossman L, Findlay K, et al. Biofilm dispersal in Xanthomonas campestris iscontrolled by cell-cell signaling and is required for full virulence to plants. PNAS,2003,100(19):10995-11000.
[39] Hammer B K, Bassler B L. Quorum sensing controls biofilm formation in Vibriocholerae. Mol Microbiol,2003,50:101-104.
[40] Williamson N R, Fineran P C, Ogawa W, et al. Integrated regulation involving quorumsensing, a two-component system, a GGDEF/EAL domain protein and apost-transcriptional regulator controls swarming and RhlA-dependent surfactantbiosynthesis in Serratia. Environ microbial,2008,10:1202-1217.
[41] Waters C M, Bassler B L. Quorum sensing: Cell to cell communication in bacteria. AnnuRev Cell Dev Biol,2005,21:319-346.
[42] Bassler B L. How bacteria talk to each other: regulation of gene expression by quorumsensing. Curr Opin Microbiol,1999,2(6):582-587.
[43] Miller M B, Bassler B L. Quorum sensing in bacteria. Annu Rev Microbiol,2001,55:165-199.
[44] Chen X, Schauder S, Potier N, et al. Structural identification of a bacterialquorum-sensing signal containing boron. Nature,2002,415:545-549.
[45] Miller S T, Xavier K B, Campagna S R, et al. Salmonella typhimurium Recognizes aChemically Distinct Form of the Bacterial Quorum-Sensing Signal AI-2. Mol Cell,2004,15:677-687.
[46] Zhang L H, Dong Y H. Quorum sensing and signal interference: diverse implications.Mol Microbiol,2004,53:1563-1571.
[47] Atkinson S, Chang C Y, Sockett R E, et al. Quorum sensing in Yersinia enterocoliticacontrols swimming and swarming motility. J Bacteriol,2006,188:1451-1461.
[48] Wang L H, He Y W, Gao Y, et al. A bacterial cell-cell communication signal withcross-kingdom structural analogues. Mol Microbiol,2004,51:903-912.
[49] Chun W, Cui J, Poplawsky A. Purification, characterization and biological role of apheromone produced by Xanthomonas campestris pv. campestris. Physiol Mol PlantPathol,1997,51:1-14.
[50] Barber C E, Tang J L, Feng J X, et al. A novel regulatory system required forpathogenicity of Xanthomonas campestris is mediated by a small diffusible signalmolecule. Mol Microbiol,1997,24:555-566.
[51] Slater H, A. Alvarez-Morales, C. E. Barber, et al. A two-component system involving anHD-GYP domain protein links cell-cell signalling to pathogenicity gene expression inXanthomonas campestris. Mol Microbiol,2000,38:986-1003.
[52] Ryan R P, Fouhy Y, Lucey J F, et al. Cell-cell signaling in Xanthomonas campestrisinvolves an HD-GYP domain protein that functions in cyclic di-GMP turnover. PNAS,2006,103(17):6712-6717.
[53] Poplawsky A R, Chun W. pigB determines a diffusible factor needed for extracellularpolysaccharide slime and xanthomonadin production in Xanthomonas campestris pv.campestris. J Bacteriol,1997,179:439-444.
[54] Chatterjee S, Sonti R V. rpfF mutants of Xanthomonas oryzae pv. oryzae are deficient forvirulence and growth under low iron conditions. Mol Plant Microbe Interact,2002,15:463-471.
[55] Tang J L, J. X. Feng, Q. Q. Li, et al. Cloning and characterization of the rpfC gene ofXanthomonas oryzae pv. oryzae: involvement in exopolysaccharide production andvirulence to rice. Mol Plant Microbe Interact,1996,9:664-666.
[56] Dangl J L, Jones J D G. Plant pathogens and integrated defence responses to infection.Nature,2001,411(6839):826-833.
[57] He S Y, K. Nomura, T. S. Whittam. Type III protein secretion mechanism in mammalianand plant pathogens. Biochimica et Biophysica Acta,2004,1694:181-206.
[58] Heesemann J, Algermissen B, Laufs R. Genetically manipulated virulence ofYersinia-enterocolitica. Infect Immun,1984,46(1):105-110.
[59] Lindgren P B, Peet R C, Panopoulos N J. Gene-cluster of Psendomonas-syringae pvphaseolicola controls pathogenicity of bean-plants and hypersensitivity on nonhostplants. J Bacteriol,1986,168(2):512-522.
[60] Alfano J R, Collmer A. Type III secretion system effector proteins: Double agents inbacterial disease and plant defense. Annu Rev Phytopathol,2004,42:385-414.
[61] Alfano J R, Collmer A. Bacterial Pathogens in Plants: Life up against the Wall. PlantCell,1996,8:1683-1698.
[62] Dobrindt U, Hochhut B, Hentschel U, et al. Genomic islands in pathogenic andenvironmental microorganisms. Nat Rev Microbiol,2004,2(5):414-424.
[63] Brown I R, Mansfield J W, Taira S, et al. Immunocytochemical localization of HrpA andHrpZ supports a role for the Hrp pilus in the transfer of effector proteins fromPseudomonas syringae pv. tomato across the host plant cell wall. Mol Plant MicrobeInteract,2001,14:394-404.
[64] Ghosh P. Process of protein transport by the type III secretion system. Microbiol MolBiol R,2004,68(4):771-775.
[65] Buttner D, Bonas U. Getting across-bacterial type III effector proteins on their way tothe plant cell. Embo J,2002,21(20):5313-5322.
[66] Bogdanove A J, Beer S V, Bonas U, et al. Unified nomenclature for broadly conservedhrp genes of phytopathogenic bacteria. Mol Microbiol,1996,20(3):681-683.
[67] Tampakaki A P, Fadouloglou V E, Gazi A D, et al. Conserved features of type IIIsecretion. Cell Microbiol,2004,6(9):805-816.
[68] Greenberg J T, Yao N. The role and regulation of programmed cell death inplant-pathogen interactions. Cell Microbiol,2004,6(3):201-211.
[69] Bestwick C S, Bennett M H, Mansfield J W. Hrp mutant of Pseudomonas-syringae pvphaseolicola induces cell-wall alterations but not membrane damage leading to thehypersensitive reaction in lettuce. Plant Physiol,1995,108(2):503-516.
[70] Lamb C, Dixon R A. The oxidative burst in plant disease resistance. Annu Rev PlantPhys,1997,48:251-275.
[71] Wendehenne D, Durner J, Klessig D F. Nitric oxide: a new player in plant signalling anddefence responses. Curr Opin Plant Biol,2004,7(4):449-455.
[72] Dixon R A, Harrison M J. Activation, structure, and organization of genes involved inmicrobial defense in plants. Adv Genet,1990,28:165-234.
[73] Durrant W E, Dong X. Systemic acquired resistance. Annu Rev Phytopathol,2004,42:185-209.
[74] Abramovitch R B, Martin G B. Strategies used by bacterial pathogens to suppress plantdefenses. Current Opinion in Plant Biology,2004,7(4):356-364.
[75] de Torres M, Mansfield J W, Grabov N, et al. Pseudomonas syringae effector AvrPtoBsuppresses basal defence in Arabidopsis. Plant J,2006,47(3):368-382.
[76] Jackson R W, Athanassopoulos E, Tsiamis G, et al. Identification of a pathogenicityisland, which contains genes for virulence and avirulence, on a large native plasmid inthe bean pathogen Pseudomonas syringae pathovar phaseolicola. Proc Natl Acad SciUSA,1999,96(19):10875-10880.
[77] Reuber T L, Ausubel F M. Isolation of arabidopsis genes that differentiate betweenresistance responses mediated by the RPS2and RPM1disease resistance genes. PlantCell,1996,8(2):241-249.
[78] Ritter C, Dangl J L. Interference between two specific pathogen recognition eventsmediated by distinct plant disease resistance genes. Plant Cell,1996,8(2):251-257.
[79] Tsiamis G, Mansfield J W, Hockenhull R, et al. Cultivar-specific avirulence andvirulence functions assigned to avrPphF in Pseudomonas syringae pv. phaseolicola, thecause of bean halo-blight disease. Embo J,2000,19(13):3204-3214.
[80] Petnicki-Ocwieja T, Schneider D J, Tam V C, et al. Genomewide identification ofproteins secreted by the Hrp type III protein secretion system of Pseudomonas syringaepv. tomato DC3000. Proc Natl Acad Sci USA,2002,99:7652-7657.
[81] Sugio A, Yang B, White F F. Characterization of the hrpF pathogenicity peninsula ofXanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact,2005,18:546-554.
[82] Xiao Y, Heu S, Yi J, et al. Identification of a putative alternate sigma factor andcharacterization of a multicomponent regulatory cascade controlling the expression ofPseudomonas syringae pv. syringae Pss61hrp and hrmA genes. J Bacteriol,1994,176:1025-1036.
[83] Wei Z M, Beer S V. hrpL activates Erwinia amylovora hrp gene transcription and is amember of the ECF subfamily of sigma factors. J Bacteriol,1995,177:6201-6210.
[84] Wengelnik K, VandenAckerveken G, Bonas U. HrpG, a key hrp regulatory protein ofXanthomonas campestris pv vesicatoria is homologous to two-component responseregulators. Mol Plant Microbe In,1996,9(8):704-712.
[85] Wengelnik K, Bonas U. HrpXv, an AraC-type regulator, activates expression of five ofthe six loci in the hrp cluster of Xanthomonas campestris pv vesicatoria. J Bacteriol,1996,178(12):3462-3469.
[86] Furutani A, Nakayama T, Ochiai H, et al. Identification of novel HrpXo regulonspreceded by two cis-acting elements, a plant-inducible promoter box and a-10box-likesequence, from the genome database of Xanthomonas oryzae pv. oryzae. FEMSMicrobiol Lett,2006,259(1):133-141.
[87] Koebnik R, Kruger A, Thieme F, et al. Specific binding of the Xanthomonas campestrispv. vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoterboxes. J Bacteriol,2006,188(21):7652-7660.
[88] Fenselau S, Balbo I, Bonas U. Determinants of pathogenicity in Xanthomonas campestrispv. campestris pv. vesicatoria are related to proteins involved in secretion in bacterialpathogens of animals. Mol Plant Microbe In,1992,5(5):390-396.
[89] Fenselau S, Bonas U. Sequence and expression analysis of the hrpB pathogenicityoperon of Xanthomonas campestris pv vesicatoria which encodes eight proteins withsimilarity to components of the Hrp, Ysc, Spa, and Fli secretion systems. Mol PlantMicrobe In,1995,8(6):845-854.
[90] Huguet E, Hahn K, Wengelnik K, et al. hpaA mutants of Xanthomonas campestris pv.vesicatoria are affected in pathogenicity but retain the ability to induce host-specifichypersensitive reaction. Mol Microbiol,1998,29(6):1379-1390.
[91] Gürlebeck D, Thieme F, Bonas U. Type III effector proteins from the plant pathogenXanthomonas and their role in the interaction with the host plant. J Plant Physiol,2006,163(3):233-255.
[92] Leach J E, White F F. Bacterial avirulence genes. Annu Rev Phytopathol,1996,34:153-179.
[93] Yang B, White F F. Diverse members of the AvrBs3/PthA family of type III effectors aremajor virulence determinants in bacterial blight disease of rice. Mol Plant Microbe In,2004,17(11):1192-1200.
[94] Gurlebeck D, Szurek B, Bonas U. Dimerization of the bacterial effector protein AvrBs3in the plant cell cytoplasm prior to nuclear import. Plant J,2005,42(2):175-187.
[95] Marois E, Van den Ackerveken G, Bonas U. The Xanthomonas type III effector proteinAvrBs3modulates plant gene expression and induces cell hypertrophy in the susceptiblehost. Mol Plant Microbe In,2002,15(7):637-646.
[96] Schornack S, Meyer A, Romer P, et al. Gene-for-gene-mediated recognition ofnuclear-targeted AvrBs3-like bacterial effector proteins. J Plant Physiol,2006,163(3):256-272.
[97] Szurek B, Rossier O, Hause G, et al. Type III-dependent translocation of theXanthomonas AvrBs3protein into the plant cell. Mol Microbiol,2002,46(1):13-23.
[98] Fujikawa T, Ishihara H, Leach J E, et al. Suppression of defense response in plants by theavrBs3/pthA gene family of Xanthomonas spp. Mol Plant Microbe In,2006,19(3):342-349.
[99] Szurek B, Marois E, Bones U, et al. Eukaryotic features of the Xanthomonas type IIIeffector AvrBs3: protein domains involved in transcriptional activation and theinteraction with nuclear import receptors from pepper. Plant J,2001,26(5):523-534.
[100] VandenAckerveken G, Marois E, Bonas U. Recognition of the bacterial avirulenceprotein AvrBs3occurs inside the host plant cell. Cell,1996,87(7):1307-1316.
[101] Hotson A, Chosed R, Shu H J, et al. Xanthomonas type III effector XopD targetsSUMO-conjugated proteins in planta. Mol Microbiol,2003,50(2):377-389.
[102] Lopez-Solanilla E, Bronstein P A, Schneider A R, et al. HopPtoN is a Pseudomonassyringae Hrp (type III secretion system) cysteine protease effector that suppressespathogen-induced necrosis associated with both compatible and incompatible plantinteractions. Mol Microbiol,2004,54(2):353-365.
[103] Mudgett M B, Staskawicz B J. Characterization of the Pseudomonas syringae pv. tomatoAvrRpt2protein: demonstration of secretion and processing during bacterialpathogenesis. Mol Microbiol,1999,32(5):927-941.
[104] Roden J, Eardley L, Hotson A, et al. Characterization of the Xanthomonas AvrXv4effector, a SUMO protease translocated into plant cells. Mol Plant Microbe In,2004,17(6):633-643.
[105] Shao F, Golstein C, Ade J, et al. Cleavage of Arabidopsis PBS1by a bacterial type IIIeffector. Science,2003,301(5637):1230-1233.
[106] Bretz J R, Mock N M, Charity J C, et al. A translocated protein tyrosine phosphatase ofPseudomonas syringae pv. tomato DC3000modulates plant defence response toinfection. Mol Microbiol,2003,49(2):389-400.
[107] Espinosa A, Guo M, Tam V C, et al. The Pseudomonas syringae type III-secreted proteinHopPtoD2possesses protein tyrosine phosphatase activity and suppresses programmedcell death in plants. Mol Microbiol,2003,49(2):377-387.
[108] Janjusevic R, Abramovitch R B, Martin G B, et al. A bacterial inhibitor of hostprogrammed cell death defenses is an E3ubiquitin ligase. Science,2006,311(5758):222-226.
[109] Mascher T, Helmann J D, Unden G. Stimulus Perception in Bacterial Signal-TransducingHistidine Kinases. Microbiol Mol Biol Rev,2006,70(4):910-938.
[110] Parkinson J S, Kofoid E C. Communication modules in bacterial signaling proteins.Annu Rev Genet,1992,26:71-112.
[111] Stock A, Koshland D E, Stock J. Homologies between the salmonella-typhimurium Cheyprotein and proteins involved in the regulation of chemotaxis, membrane-proteinsynthesis, and sporulation. Proceedings of the National Academy of Sciences of theUnited States of America,1985,82(23):7989-7993.
[112] Stock A M, Robinson V L, Goudreau P N. Two-component signal transduction. AnnuRev Biochem,2000,69:183-215.
[113] Stock J, Da Re S. Signal transduction: Response regulators on and off. Curr Biol,2000,10(11):R420-R424.
[114] Galperin M Y. A census of membrane-bound and intracellular signal transductionproteins in bacteria: Bacterial IQ, extroverts and introverts. BMC Microbiol,2005,5.
[115] Perego M, Hoch J A. Protein aspartate phosphatases control the output oftwo-component signal transduction systems. Trends Genet,1996,12(3):97-101.
[116] Perego M. Kinase-phosphatase competition regulates Bacillus subtilis development.Trends Microbiol,1998,6(9):366-370.
[117] Jung K, Altendorf K. Truncation of amino acids12-128causes deregulation of thephosphatase activity of the sensor kinase KdpD of Escherichia coli. J Biol Chem,1998,273(28):17406-17410.
[118] Dutta R, Inouye M. Reverse phosphotransfer from OmpR to EnvZ in akinase(-)/phosphatase(+) mutant of EnvZ (EnvZ center dot N347D), a bifunctional signaltransducer of Escherichia coli. J Biol Chem,1996,271(3):1424-1429.
[119] Tang J L, Liu Y N, Barber C E, et al. Genetic and molecular analysis of a cluster of rpfgenes involved in positive regulation of synthesis of extracellular enzymes andpolysaccharide in Xanthomonas campestris pathovar campestris. Molecular&GeneralGenetics,1991,226(3):409-417.
[120] Fouhy Y, Lucey J F, Ryan R P, et al. Cell-cell signaling, cyclic di-GMP turnover andregulation of virulence in Xanthomonas campestris. Research in Microbiol,2006,157(10):899-904.
[121] Wengelnik K, Rossier O, Bonas U. Mutations in the regulatory gene hrpG ofXanthomonas campestris pv. vesicatoria result in constitutive expression of all hrp genes.J Bacteriol,1999,181(21):6828-6831.
[122] Noel L, Thieme F, Nennstiel D, et al. cDNA-AFLP analysis unravels a genome-widehrpG-regulon in the plant pathogen Xanthomonas campestris pv. vesicatoria. MolMicrobiol,2001,41(6):1271-1281.
[123] Yamazaki A, Hirata H, Tsuyumu S. HrpG regulates type II secretory proteins inXanthomonas axonopodis pv. citri. Journal of General Plant Pathology,2008,74(2):138-150.
[124] Romling U, Gomelsky M, Galperin M Y. C-di-GMP: the dawning of a novel bacterialsignalling system. Mol Microbiol,2005,57(3):629-639.
[125] Galperin M Y, Nikolskaya A N, Koonin E V. Novel domains of the prokaryotictwo-component signal transduction systems. FEMS Microbiol Lett,2001,203(1):11-21.
[126] Sasakura Y, Kanda K, Yoshimura-Suzuki T, et al. Investigation of the relationshipbetween protein-protein interaction and catalytic activity of a heme-regulatedphosphodiesterase from Escherichia coli (Ec DOS) by protein microarray. Biochemistry,2005,44(28):9598-9605.
[127] Hasegawa K, Masuda S, Ono T. Light induced structural changes of a full-length proteinand its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF).Biochemistry,2006,45(11):3785-3793.
[128] Martinez-Wilson H F, Tamayo R, Tischler A D, et al. The Vibrio cholerae hybrid sensorkinase VieS contributes to motility and biofilm regulation by altering the cyclicdiguanylate level. J Bacteriol,2008,190(19):6439-6447.
[129] Tschowri N, Busse S, Hengge R. The BLUF-EAL protein YcgF acts as a directanti-repressor in a blue-light response of Escherichia coli. Genes&Development,2009,23(4):522-534.
[130] Hickman J W, Tifrea D F, Harwood C S. A chemosensory system that regulates biofilmformation through modulation of cyclic diguanylate levels. Proc Natl Acad Sci USA,2005,102(40):14422-14427.
[131] Kulasekara H D, Ventre I, Kulasekara B R, et al. A novel two-component systemcontrols the expression of Pseudomonas aeruginosa fimbrial cup genes. Mol Microbiol,2005,55(2):368-380.
[132] Ryan R, Fouhy Y, Lucey J, et al. Functional genomics of the role of cyclic di-GMPsignaling in the virulence and environmental adaptation of Xanthomonas campestris.Abstracts of the General Meeting of the American Society for Microbiology,2007,107:393.
[133] Paul R, Weiser S, Amiot N C, et al. Cell cycle-dependent dynamic localization of abacterial response regulator with a novel di-guanylate cyclase output domain. Gene Dev,2004,18(6):715-727.
[134] Fineran P C, Williamson N R, Lilley K S, et al. Virulence and Prodigiosin AntibioticBiosynthesis in Serratia Are Regulated Pleiotropically by the GGDEF/EAL DomainProtein, PigX. J Bacteriol,2007,189(21):7653-7662.
[135] Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro,2009,7(4):263-273.
[136] Ryan R P, Fouhy Y, Lucey J F, et al. Cyclic di-GMP signalling in the virulence andenvironmental adaptation of Xanthomonas campestris. Mol Microbiol,2007,63(2):429-442.
[137] Cotter P A, Stibitz S. c-di-GMP-mediated regulation of virulence and biofilm formation.Curr Opin Microbiol,2007,10(1):17-23.
[138] Amikam D, Galperin M Y. PilZ domain is part of the bacterial c-di-GMP binding protein.Bioinformatics,2006,22(1):3-6.
[139] Weber H, Pesavento C, Possling A, et al. Cyclic-di-GMP-mediated signalling within thesigma(S) network of Escherichia coli. Mol Microbiol,2006,62(4):1014-1034.
[140] Pesavento C, Becker G, Sommerfeldt N, et al. Inverse regulatory coordination of motilityand curli-mediated adhesion in Escherichia coli. Gene Dev,2008,22(17):2434-2446.
[141] Kirillina O, Fetherston J D, Bobrov A G, et al. HmsP, a putative phosphodiesterase, andHmsT, a putative diguanylate cyclase, control Hms-dependent biofilm formation inYersinia pestis. Mol Microbiol,2004,54(1):75-88.
[142] Bobrov A G, Kirillina O, Forman S, et al. Insights into Yersinia pestis biofilmdevelopment: topology and co-interaction of Hms inner membrane proteins involved inexopolysaccharide production. Environ Microbiol,2008,10(6):1419-1432.
[143] Hickman J W, Harwood C S. Identification of FleQ from Pseudomonas aeruginosa as ac-di-GMP-responsive transcription factor. Mol Microbiol,2008,69(2):376-389.
[144] Fong J C N, Yildiz F H. Interplay between cyclic AMP-Cyclic AMP receptor protein andcyclic di-GMP signaling in Vibrio cholerae biofilm formation. J Bacteriol,2008,190(20):6646-6659.
[145] Sommerfeldt N, Possling A, Becker G, et al. Gene expression patterns and differentialinput into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichiacoli. Microbiol-sgm,2009,155:1318-1331.
[146] Bibikov S I, Biran R, Rudd K E, et al. A signal transducer for aerotaxis in Escherichiacoli. J Bacteriol,1997,179(12):4075-4079.
[147] S derb ck E, Reyes-Ramirez F, Eydmann T, et al. The redox-and fixednitrogen-responsive regulatory protein NIFL from Azotobacter vinelandii comprisesdiscrete flavin and nucleotide-binding domains. Mol Microbiol,1998,28(1):179-192.
[148] Hill S, Austin S, Eydmann T, et al. Azotobacter vinelandii NIFL is a flavoprotein thatmodulates transcriptional activation of nitrogen-fixation genes via a redox-sensitiveswitch. Proc Natl Acad Sci USA,1996,93(5):2143-2148.
[149] Macheroux P, Schonbrunn E, Svergun D I, et al. Evidence for a major structural changein Escherichia coli chorismate synthase induced by flavin and substrate binding.Biochem J,1998,335:319-327.
[150] Taylor B L. Role of proton motive force in sensory transduction in bacteria. Annu RevMicrobiol,1983,37:551-573.
[151] Glagolev A N. Reception of the energy level in bacterial taxis. Journal of TheoreticalBiology,1980,82(2):171-185.
[152] Baryshev V A, Glagolev A N, Skulachev V P. Sensing of delta-mebarh+in phototaxis ofhalobacterium halobrium. Nature,1981,292(5821):338-340.
[153] Nambu J R, Lewis J O, Wharton K A, et al. The drosophila single-minded gene encodesa helix-loop-helix protein that acts as a master regulator of CNS midline development.Cell,1991,67(6):1157-1167.
[154] Lagarias D M, Wu S H, Lagarias J C. Atypical phytochrome gene structure in the greenalga Mesotaenium caldariorum. Plant Molecular Biology,1995,29(6):1127-1142.
[155] Borgstahl G E O, Williams D R, Getzoff E D.1.4angstrom structure of photoactiveyellow protein, a cytosolic photoreceptor-unusual fold, active-site, and chromophore.Biochemistry,1995,34(19):6278-6287.
[156] Rebbapragada A, Johnson M S, Harding G P, et al. The Aer protein and the serinechemoreceptor Tsr independently sense intracellular energy levels and transduce oxygen,redox, and energy signals for Escherichia coli behavior. Proc Natl Acad Sci USA,1997,94(20):10541-10546.
[157] Zhulin I B, Taylor B L, Dixon R. PAS domain S-boxes in Archaea, bacteria and sensorsfor oxygen and redox. Trends Biochem Sci,1997,22(9):331-333.
[158] Pellequer J L, Wager-Smith K A, Kay S A, et al. Photoactive yellow protein: A structuralprototype for the three-dimensional fold of the PAS domain superfamily. Proc Natl AcadSci USA,1998,95(11):5884-5890.
[159] Gong W M, Hao B, Mansy S S, et al. Structure of a biological oxygen sensor: A newmechanism for heme-driven signal transduction. Proc Natl Acad Sci USA,1998,95(26):15177-15182.
[160] Fearon I M, Palmer A C V, Balmforth A J, et al. Hypoxia inhibits the recombinantalpha(1C) subunit of the human cardiac L-type Ca2+channel. J Physiol-london,1997,500(3):551-556.
[161] Ponting C P, Aravind L. PAS: a multifunctional domain family comes to light. Curr Biol,1997,7(11):R674-R677.
[162] Huala E, Oeller P W, Liscum E, et al. Arabidopsis NPH1: A protein kinase with aputative redox-sensing domain. Science,1997,278(5346):2120-2123.
[163] Cabral J H M, Lee A, Cohen S L, et al. Crystal structure and functional analysis of theHERG potassium channel N terminus: A eukaryotic PAS domain. Cell,1998,95(5):649-655.
[164] Zhulin I B, Taylor B L. Correlation of PAS domains with electron transport-associatedproteins in completely sequenced microbial genomes. Mol Microbiol,1998,29(6):1522-1523.
[165] Alex L A, Simon M I. Protein histidine kinases and signal-transduction in prokaryotesand eukaryotes. Trends Genet,1994,10(4):133-138.
[166] Schuster S C, Noegel A A, Oehme F, et al. The hybrid histidine kinase DokA is part ofthe osmotic response system of Dictyostelium. Embo J,1996,15(15):3880-3889.
[167] Kakimoto T. CKI1, a histidine kinase homolog implicated in cytokinin signaltransduction. Science,1996,274(5289):982-985.
[168] Gamble R L, Coonfield M L, Schaller G E. Histidine kinase activity of the ETR1ethylene receptor from Arabidopsis. Proc Natl Acad Sci USA,1998,95(13):7825-7829.
[169] Taylor B L, Zhulin I B. PAS domains: Internal sensors of oxygen, redox potential, andlight. Microbiol Mol Biol R,1999,63(2):479-507.
[170] Soderling S H, Bayuga S J, Beavo J A. Cloning and characterization of a cAMP-specificcyclic nucleotide phosphodiesterase. Proceedings of the National Academy of Sciencesof the United States of America,1998,95(15):8991-8996.
[171] McLaughlin M E, Sandberg M A, Berson E L, et al. Recessive mutations in the geneencoding the beta-subunit of Rod phosphodiesterase in patients with retinitis-pigmentosa.Nat Genet,1993,4(2):130-134.
[172] Yan C, Zhao A Z, Bentley J K, et al. Molecular cloning and characterization of acalmodulin-dependent phosphodiesterase enriched in olfactory sensory neurons. ProcNatl Acad Sci USA,1995,92(21):9677-9681.
[173] de Philip P, Batut J, Boistard P. Rhizobium meliloti Fix L is an oxygen sensor andregulates R. meliloti nifA and fixK genes differently in Escherichia coli. J Bacteriol,1990,172(8):4255-4262.
[174] David M, Daveran M L, Batut J, et al. Cascade regulation of nif gene expression inRhizobium-meliloti. Cell,1988,54(5):671-683.
[175] Baur B, Fischer K, Winter K, et al. cDNA sequence of a protein kinase from theinducible crassulacean acid metabolism plant mesembry anthemum crystallinum L,encoding a Snf-1homolog. Plant Physiol,1994,106(3):1225-1226.
[176] Gillesgonzalez M A, Gonzalez G, Perutz M F, et al. Heme based sensors, exemplified bythe kinase FixL, are a new class of heme protein with distinctive ligand binding andautoxidation. Biochemistry-us,1994,33(26):8067-8073.
[177] Gillesgonzalez M A, Gonzalez G, Perutz M F. Kinase activity of oxygen sensor FixLdepends on the spin state of its heme iron. Biochemistry-us,1995,34(1):232-236.
[178] Monson E K, Weinstein M, Ditta G S, et al. The FixL protein of rhizobium-meliloti canbe separated into a heme-binding oxygen-sensing domain and a functional C-terminalknase domain. Proc Nati Acad Sci USA,1992,89(10):4280-4284.
[179] Taylor B L, Zhulin I B. In search of higher energy: metabolism-dependent behaviour inbacteria. Mol Microbiol,1998,28(4):683-690.
[180] Liu J D, Parkinson J S. Genetic evidence for intercation between the Chew and Tsrproteins during chemoreceptor signaling by Escherichia coli. J Bacteriol,1991,173(16):4941-4951.
[181] Barak R, Eisenbach M. Regulation of interaction between signaling protein CheY andflagellar motor during bacterial chemotaxis, in Current Topics in Cellular Regulation,1996,34:137-158.
[182] Welch M, Oosawa K, Aizawa S I, et al. Phosphorylation dependent binding of a signalmolecule to the flagellar switch of bacteria. Proceedings of the National Academy ofSciences of the United States of America,1993,90(19):8787-8791.
[183] Burbulys D, Trach K A, Hoch J A. Initiation of sporulation in Bacillus subtilis iscontrolled by a multicomponent phosphorelay. Cell,1991,64(3):545-552.
[184] Sprenger W W, Hoff W D, Armitage J P, et al. The enbacterium ectothiorhodospirahalophila is negatively phototactic, with a wavelength dependence that fits theabsorption spectrum of the photoactive yellow protein. J Bacteriol,1993,175(10):3096-3104.
[185] Kagawa T, Kimura M, Wada M. Blue Light-Induced Phototropism of InflorescenceStems and Petioles is Mediated by Phototropin Family Members phot1and phot2. PlantCell Physiol,2009,50(10):1774-1785.
[186] Bhoo S H, Davis S J, Walker J, et al. Bacteriophytochromes are photochromic histidinekinases using a biliverdin chromophore. Nature,2001,414(6865):776-779.
[187] Andel F, Lagarias J C, Mathies R A. Resonance Raman analysis of chromophorestructure in the lumi-R photoproduct of phytochrome. Biochemistry-us,1996,35(50):15997-16008.
[188] Matysik J, Hildebrandt P, Schlamann W, et al. Fourier-transform resonanceraman-spectroscopy of intermediates of the phytochrome photocycle. Biochemistry-us,1995,34(33):10497-10507.
[189] Rudiger W, Thummler F, Cmiel E, et al. Chromophore structure of the physiologicallyactive form (PFR) of phytochrome. Proc Nati Acad Sci USA,1983,80(20):6244-6248.
[190] Lamparter T, Michael N, Mittmann F, et al. Phytochrome from Agrobacteriumtumefaciens has unusual spectral properties and reveals an N-terminal chromophoreattachment site. Proc Nati Acad Sci USA,2002,99(18):11628-11633.
[191] Alexandre M T A, van Grondelle R, Hellingwerf K J, et al. Perturbation of theground-state electronic structure of FMN by the conserved cysteine in phototropin LOV2domains. Phys Chem Chem Phys,2008,10(44):6693-6702.
[192] Christie J M. Phototropin blue-light receptors. Annual Review of Plant Biology,2007,58:21-45.
[193] Konig K, Teschke M, Sigusch B, et al. Red light kills bacteria via photodynamic action.Cell Mol Biol,2000,46(7):1297-1303.
[194] Pattison D, Davies M. Actions of ultraviolet light on cellular structures, in Cancer: CellStructures, Carcinogens and Genomic Instability. Birkh user Basel,2006:131-157.
[195] Avila-Perez M, Hellingwerf K J, Kort R. Blue light activates the sigma(B)-dependentstress response of Bacillus subtilis via YtvA. J Bacteriol,2006,188(17):6411-6414.
[196] Gaidenko T A, Kim T J, Weigel A L, et al. The blue-light receptor YtvA acts in theenvironmental stress signaling pathway of Bacillus subtilis. J Bacteriol,2006,188(17):6387-6395.
[197] Buttani V, Losi A, Eggert T, et al. Conformational analysis of the blue-light sensingprotein YtvA reveals a competitive interface for LOV-LOV dimerization andinterdomain interactions. Photochem Photobiol Sci,2007,6(1):41-49.
[198] M glich A, Moffat K. Structural Basis for Light-dependent Signaling in the DimericLOV Domain of the Photosensor YtvA. J Mol Biol,2007,373(1):112-126.
[199] Olmedo M, Ruger-Herreros C, Corrochano L M. Regulation by blue light of the fluffygene encoding a major regulator of conidiation in Neurospora crassa. Genetics,2010,184(3):651-8.
[200] Moriwaki A, Katsube H, Ueno M, et al. Cloning and characterization of the BLR2, thehomologue of the blue-light regulator of Neurospora crassa WC-2, in thephytopathogenic fungus Bipolaris oryzae. Curr Microbiol,2008,56(2):115-121.
[201] He Q Y, Liu Y. Molecular mechanism of light responses in Neurospora: fromlight-induced transcription to photoadaptation. Gene Dev,2005,19(23):2888-2899.
[202] Cheng P, He Q, Yang Y, et al. Functional conservation of light, oxygen, or voltagedomains in light sensing. Proc Nati Acad Sci USA,2003,100(10):5938-5943.
[203] Ballario P, Talora C, Galli D, et al. Roles in dimerization and blue light photoresponse ofthe PAS and LOV domains of Neurospora crassa white collar proteins. Mol Microbiol,1998,29(3):719-729.
[204] Baca M, Borgstahl G E O, Boissinot M, et al. Complete Chemical Structure ofPhotoactive Yellow Protein: Novel Thioester-Linked4-Hydroxycinnamyl Chromophoreand Photocycle Chemistry. Biochemistry-us,1994,33(48):14369-14377.
[205] Kort R, Hoff W D, VanWest M, et al. The xanthopsins: A new family of eubacterialblue-light photoreceptors. Embo J,1996,15(13):3209-3218.
[206] Getzoff E D, Gutwin K N, Genick U K. Anticipatory active-site motions andchromophore distortion prime photoreceptor PYP for light activation. Nat Struct MolBiol,2003,10(8):663-668.
[207] Kyndt J A, Fitch J C, Meyer T E, et al. The photoactivated PYP domain ofRhodospirillum centenum Ppr accelerates the recovery of the bacteriophytochromedomain after white light illumination. Biochemistry-us,2007,46(28):8256-8262.
[208] Harper S M, Neil L C, Gardner K H. Structural basis of a phototropin light switch.Science,2003,301(5639):1541-1544.
[209] Doi M, Shigenaga A, Emi T, et al. A transgene encoding a blue-light receptor, phot1,restores blue-light responses in the Arabidopsis phot1phot2double mutant. J Exp Bot,2004,55(396):517-523.
[210] Kaiserli E, Sullivan S, Jones M A, et al. Domain Swapping to Assess the MechanisticBasis of Arabidopsis Phototropin1Receptor Kinase Activation and Endocytosis by BlueLight. Plant Cell,2009,21(10):3226-3244.
[211] Christie J M, Salomon M, Nozue K, et al. LOV (light, oxygen, or voltage) domains ofthe blue-light photoreceptor phototropin (nph1): Binding sites for the chromophore flavinmononucleotide. Proc Nati Acad Sci USA,1999,96(15):8779-8783.
[212] Christie J, Jones M, Sullivan S, et al. Structure-function analysis of phototropinblue-light receptors. Comp Biochem Physiol Mol Integrat Physiol,2007,146(4):499-507.
[213] Cao Z, Livoti E, Losi A, et al. A Blue Light-inducible Phosphodiesterase Activity in theCyanobacterium Synechococcus elongatus. Photochem Photobiol,2010,86(3):606-611.
[214] Swartz T E, Tseng T, Frederickson M A, et al. Blue-Light-Activated Histidine Kinases:Two-Component Sensors in Bacteria. Science,2007,317(5841):1090-1093.
[215] Cheng P, Yang Y, Gardner K H, et al. PAS Domain-Mediated WC-1/WC-2Interaction IsEssential for Maintaining the Steady-State Level of WC-1and the Function of BothProteins in Circadian Clock and Light Responses of Neurospora. Mol Cell Biol,2002,22(2):517-524.
[216] Brody M S, Stewart V, Price C W. Bypass suppression analysis maps the signallingpathway within a multidomain protein: the RsbP energy stress phosphatase2C fromBacillus subtilis. Mol Microbiol,2009,72(5):1221-1234.
[217] Warmke J, Drysdale R, Ganetzky B. A distinct potassium channel polypeptide encodedby the Drosophila eag locus. Science,1991,252(5012):1560-1562.
[218] Wang Z, Wilson G F, Griffith L C. Calcium/Calmodulin-dependent Protein Kinase IIPhosphorylates and Regulates the Drosophila Eag Potassium Channel. J Biol Chem,2002,277(27):24022-24029.
[219] Warmke J W, Ganetzky B. A family of potassium channel genes related to eag indrosophila and mammals. Proc Natl Acad Sci USA,1994,91(8):3438-3442.
[220] Wang Q, Chen Q, A. T J. Genetics, molecular mechanisms and management of long QTsyndrome. Ann Med,1998,30:58–65.
[221] Vincent G M. The molecular genetics of the long QT syndrome:genes causing faintingand sudden death. Annu Rev Med,1998,49:263–274.
[222] Klenk H P, Clayton R A, Tomb J F, et al. The complete genome sequence of thehyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature,1997,390(6658):364-&.
[223] Karimova G, Bellalou J, Ullmann A. Phosphorylation-dependent binding of BvgA to theupstream region of the cyaA gene of Bordetella pertussis. Mol Microbiol,1996,20(3):489-496.
[224] Laszlo D J, L. T B. Aerotaxis in Salmonella typhimurium: role of electron transport. JBacteriol,1981,145:990–1001.
[225] Taylor B L, Miller J B, Warrick H M, et al. Electron acceptor taxis and blue light effecton bacteria chemotaxis. J Bacteriol,1979,140(2):567-573.
[226] Bespalov V A, Zhulin I B, Taylor B L. Behavioral responses of Escherichia coli tochanges in redox potential. Proc Natl Acad Sci USA1996,93:10084–10089.
[227] Iuchi S, C. L E. arcA (dye), a global regulatory gene in Escherichia coli mediatingrepression of enzymes in aerobic pathways. Proc Natl Acad Sci USA,1988,85:1888–1892.
[228] Iuchi S, Lin E C. Adaptation of Escherichia coli to redox environments by geneexpression. Mol Microbiol,1993,9:9–15.
[229] Zhang W S, Brooun A, McCandless J, et al. Signal transduction in the ArchaeonHalobacterium salinarium is processed through three subfamilies of13soluble andmembrane-bound transducer proteins. Proc Natl Acad Sci USA,1996,93(10):4649-4654.
[230] Brooun A, Bell J, Freitas T, et al. An archaeal aerotaxis transducer combines subunit Icore structures of eukaryotic cytochrome c oxidase and eubacterial methyl acceptingchemotaxis proteins. J Bacteriol,1998,180:1642–1646.
[231] Dolla A, Fu R, Brumlik M J, et al. Nucleotide sequence of dcrA, a Desulfovibrio vulgarisHildenborough chemoreceptor gene, and its expression in Escherichia coli. J Bacteriol,1992,174:1726–1733.
[232] Fu R, Wall J D, Voordouw G. DcrA, a c-type heme-containing methyl-accepting proteinfrom Desulfovibrio vulgaris Hildenborough, senses the oxygen concentration or redoxpotential of the environment. J Bacteriol,1994,176:344–350.
[233] Gomelsky M, Kaplan S. Molecular genetic analysis suggesting interactions betweenAppA and PpsR in regulation of photosynthesis geneexpression in Rhodobactersphaeroides2.4.1.. J Bacteriol,1997,179:128–134.
[234] Zeilstra-Ryalls J, Gomelsky M, Eraso J M, et al. Control of photosystem formation inRhodobacter sphaeroides. J Bacteriol,1998,180:2801–2809.
[235] Coschigano P W, Young L Y. Identification and sequence analysis of two regulatorygenes involved in anaerobic toluene metabolism by strain T1. Appl Environ Microbiol,1997,63:652–660.
[236] Golby P, Davies S, Kelly D J, et al. Identification and characterization of atwo-component sensor-kinase and response-regulator system (DcuS-DcuR) controllinggene expression in response to C4-dicarboxylates in Escherichia coli. J Bacteriol,1999,181:1238–1248.
[237] Zientz E, Bongaerts J, Unden G. Fumarate regulation of gene expression in Escherichiacoli by the DcuSR (dcuSR genes) two-component regulatory system. J Bacteriol,1998,180:5421–5425.
[238] Bott M. Anaerobic citrate metabolism and its regulation in enterobacteria. ArchMicrobiol,1997,167:78–88.
[239] Bott M, Meyer M, Dimroth P. Regulation of anaerobic citrate metabolism in Klebsiellapneumoniae. Mol Microbiol,1995,18:533–546.
[240] Dixon R. The oxygen-responsive NIFL-NIFA complex: a novel two-componentregulatory system controlling nitrogenase synthesis in gamma-proteobacteria. ArchMicrobiol,1998,169:371–380.
[241] Gropp F, Betlach M C. The bat gene of Halobacterium halobium encodes a trans-actingoxygen inducibility factor. Proc Natl Acad Sci USA,1994,91:5475–5479.
[242] Blanco G, Drummond M, Woodley P, et al. Sequence and molecular analysis of the nifLgene of Azotobacter vinelandii. Mol Microbiol,1993,9:869–879
[243] Macheroux P, S. Hill, S. Austin, et al. Electron donation to the flavoprotein NifL, aredox-sensing transcriptional regulator. Biochem J,1998,332:413–419.
[244] Schmitz R A. NifL of Klebsiella pneumoniae carries an N-terminally bound FADcofactor, which is not directly required for the inhibitory function of NifL. FemsMicrobiol Lett,1997,157:313–318.
[245] Gilles-Gonzalez M A, Ditta G S, Helinski D R. A haemo-protein with kinase activityencoded by the oxygen sensor of Rhizobium meliloti. Nature,1991,350:170–172.
[246] Kaminski P A, Elmerich C. Involvement of fixLJ in the regulation of nitrogen fixation inAzorhizobium caulinodans. Mol Microbiol,1991,5:665–673.
[247] Anthamatten D, Hennecke H. The regulatory status of the fixL-and fixJ-like genes inBradyrhizobium japonicum maybe different from that in Rhizobium meliloti. Mol GenGenet,1991,225:38–48.
[248] Dhooghe I, Michiels J, Vlassak K, et al. Structural and functional analysis of the fixljgenes of Rhizabium leguminosarum biovar phasoli cnpaf512. Mol General Genetics,1995,249(1):117-126.
[249] Patschkowski T, Schluter A, Priefer U B. Rhizobium leguminosarum pv viciae contains asecond fnr/fixK-like gene and an unusual fixL homologue. Mol Microbiol,1996,21(2):267-280.
[250] Fischer H M. Genetic regulation of nitrogen fixation in Rhizabia. Microbiol reviews,1994,58(3):352-386.
[251] Fischer H M. Environmental regulation of rhizobial symbiotic nitrogen fixation genes.Trends Microbiol,1996,4(8):317-320.
[252] Gong W, Hao B, Chan M K. New Mechanistic Insights from Structural Studies of theOxygen-Sensing Domain of Bradyrhizobium japonicum FixL. Biochemistry-us,2000,39(14):3955-3962.
[253] Genick U K, Soltis S M, Kuhn P, et al. Structure at0.85angstrom resolution of an earlyprotein photocycle intermediate. Nature,1998,392(6672):206-209.
[254] Delgado-Nixon V M, Gonzalez G, Gilles-Gonzalez M-A. Dos, a Heme-Binding PASProtein from Escherichia coli, Is a Direct Oxygen Sensor. Biochemistry-us,2000,39(10):2685-2691.
[255] Kurokawa H, Lee D S, Watanabe M, et al. A redox-controlled molecular switch revealedby the crystal structure of a bacterial heme PAS sensor. J Biol Chem,2004,279(19):20186-20193.
[256] Liebl U, Bouzhir-Sima L, Kiger L, et al. Ligand Binding Dynamics to the Heme Domainof the Oxygen Sensor Dos from Escherichia coli. Biochemistry-us,2003,42(21):6527-6535.
[257] Park H J, Suquet C, Satterlee J D, et al. Insights into signal transduction involving PASdomain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichiacoli dos heme domain (EcDosH). Biochemistry-us,2004,43(10):2738-2746.
[258] Tuckerman J R, Gonzalez G, Sousa E H S, et al. An Oxygen-Sensing DiguanylateCyclase and Phosphodiesterase Couple for c-di-GMP Control. Biochemistry-us,2009,48(41):9764-9774.
[259] Cohen-Bazire G, Sistrom W R, Stanier R Y. Kinetic studies of pigment synthesis bynon-sulphur purple bacteria. J Cell Comp Physiol,1957,49:25–68.
[260] Bauer C E, Bird T H. Regulatory circuits controlling photo-synthesis gene expression.Cell,1996,85:5–8.
[261] Drews G. Adaptation of the bacterial photosynthetic apparatus to different lightintensities. Trends Biochem Sci,1986,6:255–257.
[262] Gomelsky M, Kaplan S. Genetic evidence that ppsr from Rhodobacteria sphaeroides2.4.1functions as a repressor of puc and bchf expression. J Bacteriol,1995,177(6):1634-1637.
[263] Ponnampalam S N, Buggy J J, Bauer C E. Characterization of an aerobic repressor thatcoordinately regulates bacteriochlorophyll, carotenoid, and light harvesting-II expressionin Rhodobacter capsulatus. J Bacteriol,1995,177(11):2990-2997.
[264] Penfold R J, Pemberton J M. A gene from the photosynthetic gene cluster ofRhodobacter sphaeroides induces trans-suppression of bacterilchlorophyll andcarotenoid levels in R. sphaeroides and R. capsulatus. Curr Microbiol,1991,23(5):259-263.
[265] Ponnampalam S N, Bauer C E. DNA binding characteristics of CrtJ-Aredox-responding repressor of bacteriochlorophyll, carotenoid, and light harvesting-IIgene expression in Rhodobacter capsulatus. J Biol Chem,1997,272(29):18391-18396.
[266] Zhulin I B, Rowsell E H, Johnson M S, et al. Glycerol elicits energy taxis of Escherichiacoli and Salmonella typhimurium. J Bacteriol,1997,179(10):3196-3201.
[267] Hamblin M J, Shaw J G, Kelly D J. Sequnce analysis and interposon mutagenesis of asensor kinase (Dcts) and response regulator (Dctr) controlling synthesis of the highaffinity C4-dicarboxylate transport system in Rhodobacter capsulatus. Mol Gen Genet,1993,237(1-2):215-224.
[268] Huang Z J, Edery I, Rosbash M. PAS in a dimerization domain common to drosophilaperiod and several transcription factors. Nature,1993,364(6434):259-262.
[269] Pongratz I, Antonsson C, Whitelaw M L, et al. Role of the PAS Domain in Regulation ofDimerization and DNA Binding Specificity of the Dioxin Receptor. Mol Cell Biol,1998,18(7):4079-4088.
[270] Gekakis N, Staknis D, Nguyen H B, et al. Role of the CLOCK protein in the mammaliancircadian mechanism. Science,1998,280(5369):1564-1569.
[271] Schibler U. Circadian rhythms-New cogwheels in the clockworks. Nature,1998,393(6686):620-621.
[272] Rowlands J C, Gustafsson J A. Aryl hydrocarbon receptor-mediated signal transduction.Crit Rev Toxicol,1997,27(2):109-134.
[273] Edgerton M D, Jones A M. Subunit interactions in the carboxy terminal domain ofphytochrome. Biochemistry-us,1993,32(32):8239-8245.
[274] Li X D, Xu J, Li M. The human Delta1261mutation of the HERG potassium channelresults in a truncated protein that contains a subunit interaction domain and decreases thechannel expression. J Biol Chem,1997,272(2):705-708.
[275] da Silva A C R, Ferro J A, Reinach F C, et al. Comparison of the genomes of twoXanthomonas pathogens with differing host specificities. Nature,2002,417(6887):459-463.
[276] Qian W, Jia Y T, Ren S X, et al. Comparative and functional genomic analyses of thepathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res,2005,15(6):757-767.
[277] Qian W, Han Z-J, Tao J, et al. Genome-Scale Mutagenesis and PhenotypicCharacterization of Two-Component Signal Transduction Systems in Xanthomonascampestris pv. campestris ATCC33913. Mol Plant Microbe In,2008,21(8):1128-1138.
[278] Vorholter F-J, Schneiker S, Goesmann A, et al. The genome of Xanthomonas campestrispv. campestris B100and its use for the reconstruction of metabolic pathways involved inxanthan biosynthesis. J Biotechnol,2008,134(1-2):33-45.
[279] Sch fer A, Tauch A, J ger W, et al. Small mobilizable multi-purpose cloning vectorsderived from the Escherichia coli plasmids pK18and pK19: selection of defineddeletions in the chromosome of Corynebacterium glutamicum. Gene,1994,145(1):69-73.
[280] Figurski D H, Helinski D R. Replication of an origin-containing derivative of plasmidRK2dependent on a plasmid function provided in trans. Proc Nati Acad Sci USA,1979,76(4):1648-1652.
[281] Huynh T V, Dahlbeck D, Staskawicz B J. Bacterial-blight of soybean-Regulation of apathogen gene determining host cultivar specificity. Science,1989,245(4924):1374-1377.
[282] Davis A R, Kostek B, Mason B B, et al. Expression of hepatitis B surface antigen with arecombinant adenovirus. Proc Nati Acad Sci USA,1985,82(22):7560-7564.
[283] GRANT S N, JESSEE J, BLOOM F, et al. Differential plasmid rescue from transgenicmouse DNAs into Escherichia coli methylation-restriction mutants. Proc Nati Acad SciUSA,1990,87:4645-4649.
[284] Simon R, Priefer U, Puhler A. A Broad Host Range Mobilization System for In VivoGenetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria. Nat Biotech,1983,1(9):784-791.
[285] Nishiguchi, Nishiguchi M, Yoshida, et al. A receptor-like protein kinase with alectin-like domain from lombardy poplar: gene expression in response to wounding andcharacterization of phosphorylation activity. Mol Genet Genomics,2002,267(4):506-514.
[286] Keen N T, Boyd C, Henrissat B. Cloning and characterization of a xylanase gene fromcorn strains of Erwinia chrysanthemi. Mol Plant Microbe Interact,1996,9:651-657.
[287] DiLuzio W R, Turner L, Mayer M, et al. Escherichia coli swim on the right-hand side.Nature,2005,435(7046):1271-1274.
[288] Lim B, Beyhan S, Meir J, et al. Cyclic-diGMP signal transduction systems in Vibriocholerae: modulation of rugosity and biofilm formation. Mol Microbiol,2006,60:331-348.
[289] Letunic I, Doerks T, Bork P. SMART6: recent updates and new developments. NucleicAcids Res,2009,37(suppl1):D229-D232.
[290] Finn R D, Mistry J, Tate J, et al. The Pfam protein families database. Nucleic Acids Res,2010,38(suppl1):D211-D222.
[291] Chan W M. The UniProt Knowledgebase (UniProtKB): a freely accessible,comprehensive and expertly curated protein sequence database. Genetics Research,2010,92(1):78-79.
[292] Christie J M, Corchnoy S B, Swartz T E, et al. Steric interactions stabilize the signalingstate of the LOV2domain of phototropin1. Biochemistry-us,2007,46(32):9310-9319.
[293] Key J, Hefti M, Purcell E B, et al. Structure of the redox sensor domain of Azotobactervinelandii NifL at atomic resolution: Signaling, dimerization, and mechanism.Biochemistry-us,2007,46(12):3614-3623.
[294] Cole C, Barber J D, Barton G J. The Jpred3secondary structure prediction server.Nucleic Acids Res,2008,36(suppl2):W197-W201.
[295] Jones D T. Protein secondary structure prediction based on position-specific scoringmatrices. J Mol Biol,1999,292(2):195-202.
[296] Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated proteinstructure and function prediction. Nature Protocols,2010,5:725-738.
[297] M glich A, Ayers R A, Moffat K. Structure and Signaling Mechanism ofPer-ARNT-Sim Domains. Structure,2009,17(10):1282-1294.
[298] Jaiswal R K, Manjeera G, Gopal B. Role of a PAS sensor domain in the Mycobacteriumtuberculosis transcription regulator Rv1364c. Biochem Bioph Res Co,2010,398(3):342-349.
[299] Jeanmougin F, Thompson J D, Gouy M, et al. Multiple sequence alignment with ClustalX. Trends Biochem Sci,1998,23(10):403-405.
[300] Larkin M A, Blackshields G, Brown N P, et al. Clustal W and Clustal X version2.0.Bioinformatics,2007,23(21):2947-2948.
[301] Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evolutionary Genetics Analysis(MEGA) software version4.0. Mol Biol Evol,2007(24):1596-1599.
[302] Saitou N, Nei M. The neighbor-joining method: A new method for reconstructingphylogenetic trees. Mol Biol Evol,1987(4):406-425.
[303] Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins, inEvolving Genes and Proteins. Bryson V, Vogel H J, eds. Academic Press: New York,1965,97-166.
[304] Li W, Godzik A. VISSA: a program to visualize structural features from structuresequence alignment. Bioinformatics,2006,22(7):887-888.
[305] Kawabata T. MATRAS: a program for protein3D structure comparison. Nucleic AcidsRes,2003,31(3367-3379).
[306] Rajagopal S, Moffat K. Crystal structure of a photoactive yellow protein from a sensorhistidine kinase: Conformational variability and signal transduction. Proc Nati Acad SciUSA,2003,100(4):1649-1654.
[307] Ulrich L E, Koonin E V, Zhulin I B. One-component systems dominate signaltransduction in prokaryotes. Trends Microbiol,2005,13(2):52-56.
[308] Ulrich L E, Zhulin I B. MiST: a microbial signal transduction database. Nucleic AcidsRes,2007,35:D386-D390.
[309] Ho Y-S J, Burden L M, Hurley J H. Structure of the GAF domain, a ubiquitous signalingmotif and a new class of cyclic GMP receptor. The EMBO Journal,2000,19(20):5288-5299.
[310] Su Y-s, Lagarias J C. Light-Independent Phytochrome Signaling Mediated by DominantGAF Domain Tyrosine Mutants of Arabidopsis Phytochromes in Transgenic Plants.Plant Cell,2007,19(7):2124-2139.
[311] Chang A L, Tuckerman J R, Gonzalez G, et al. Phosphodiesterase A1, a Regulator ofCellulose Synthesis in Acetobacter xylinum, Is a Heme-Based Sensor. Biochemistry-us,2001,40(12):3420-3426.
[312] Hefti M H, Francoijs K J, de Vries S C, et al. The PAS fold-A redefinition of the PASdomain based upon structural prediction. Eur J Biochem,2004,271(6):1198-1208.
[313] Christie J M, Swartz T E, Bogomolni R A, et al. Phototropin LOV domains exhibitdistinct roles in regulating photoreceptor function. The Plant Journal,2002,32(2):205-219.
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