苏云金芽胞杆菌菌株YBT-1520基因组中TA系统的研究
摘要
苏云金芽胞杆菌(Bacillus thuringiensis)菌株YBT-1520的全基因组测序结果表明它含有1条染色体和11个质粒。毒素抗毒素系统(TA系统)最初是在大肠杆菌的低拷贝大质粒上发现的,此后的研究多集中于G~-细菌的大质粒上,对G~+的质粒尤其是小质粒的研究非常少。本研究从NCBI数据库中收集了562条毒素或者抗毒素蛋白质的序列,通过穷举比对在YBT-1520基因组上发现了多种TA系统。
1.质粒pBMB8240上潜在TA系统kyAB的研究
本研究在YBT-1520菌株中发现了新质粒pBMB8240上有两个邻近的开放读码框,分别命名为KyA和KyB蛋白,通过序列分析,发现KyA和KyB分别与已知抗毒素、毒素蛋白有序列一致性。
KyA和kyB基因的克隆实验表明kyA基因很容易克隆;而多次努力克隆到的kyB基因区域都发生了基因突变。KyAB系统装载到不稳定的载体pBMB0631上去之后发现重组质粒的稳定性大大升高。
以上结果表明kyAB系统是一个潜在的TA系统,并且能够增强不稳定质粒的稳定性。这是第一个克隆到大肠杆菌中的来自苏云金芽胞杆菌的质粒TA系统。
2.质粒pBMB7635上潜在TA系统kyCD的研究
本研究发现YBT-1520中的质粒pBMB7635与本实验室以前克隆的质粒pBMB9741有很高的相似性,对pBMB7635重新测序,并将质粒pBMB9741重新命名为pBMB7635。
质粒pBMB7635上有两个邻近的开放读码框,与已经鉴定的TA系统有较高相似性,将这两个分别编码94和133个氨基酸大小的蛋白质分别命名为KyC和KyD蛋白。
KyC、kyD和kyCD系统及临近区域的克隆实验表明kyC基因很容易克隆;而多次努力克隆kyD基因和kyCD系统及临近区域只得到少量转化子,而且这些转化子中kyD区域都发生了基因突变,表明kyCD很可能是TA系统,且不能在大肠杆菌中克隆。
3.质粒pBMB2062的克隆和分析
克隆并分析了菌株YBT-1520中的多拷贝小质粒pBMB2062,序列分析表明,pBMB2062含有2个ORFs(大于75个氨基酸),缺失实验证明ORF1(289aa)对于质粒在芽胞杆菌中的复制和稳定是必需的,ORF2则不是。研究随机选取了7个不同血清型菌株的小质粒进行了克隆和测序,发现这些小质粒的序列高度保守。斑点杂交实验表明该质粒在目前鉴定的84个Bt血清型菌株中的分布为41%。
4.YBT-1520染色体上mazEF系统的克隆和分析
在YBT-1520染色体上找到一对mazEF系统,本实验对mazEF系统进行了敲除突变,改变MazEF的表达水平来探索MazEF的表达与PCD之间的的相互作用,从而进一步研究mazEF的功能。研究发现,敲除了mazEF系统的菌株在45℃培养4天之后,菌体量逐渐减少,取样镜检发现菌体大部分死亡。从另外一个角度证明了染色体上的mazEF系统在PCD中起作用。
本实验通过基因组间上TA系统的比较分析,为进一步研究质粒在不同菌株(包括其它芽胞杆菌群菌株)的分布、进化等提供一定的遗传信息和理论依据,对多拷贝小质粒的稳定机制以及苏云金芽胞杆菌中隐蔽型质粒的功能提出了新的认识。
Bacillus thuringiensis strain YBT-1520,which is highly toxic to lepidopteran pests, was isolated by our lab.In this thesis,we reported the sequence determination and initial analysis of the genome of this strain.The results revealed that this genome consisted of one chromosome and nine plasmids.TA systems have been extensively studied on low-copy-number plasmids in Gram-negative bacteria as addiction systems because of their ability to maintain the plasmids during cell division and a few TA systems have been described on small plasmids in Gram-positive bacteria.
We identified 562 TA loci belonging to the seven known TA gene families and present the results from an exhaustive search for TA loci in the completely sequenced Bacillus genomes.The putative TA loci from YBT-1520 genomes were studied and the putative TA loci from other 6 completely sequenced Bacillus genomes were found by bioinformatics analyse.
1.The study on the putative kyAB TA system from plasmid pBMB8240
Based on the shotgun sequence analysis of the strain YBT-1520 plasmid pBMB8240 was found to be a novel cryptic plasmid.In pBMB8240,two contiguous orfs(this gene pair was tentatively named kyAB for strain kurstaki YBT-1520) were noticed.The putative protein KyA and KyB displays sequence similarities with other antitoxin and toxin protein,respectively.
Attempts to clone the kyA in E.coli DH5αwere easy and successful.In kyB cloning case,all recombinants harbored mutations in the kyB gene,suggesting the toxic activity of KyB protein in E.coli.
Based on sequence homology with other toxin-antitoxin system genes and the lethal activity of KyB in Escherichia coli,the segregational stability kyAB cassette was identified to be the first functional putative TA segregational stability system from B. thuringiensis.
2.The study on the putative kyCD TA system from plasmid pBMB7635
A database sequence search revealed that the B.thuringiensis H1.1 plasmid pGI1 (8254 bp) had DNA sequences and organizations similar to plasmid pBMB9741 except for a fragment of 1.6 kb located upstream from the rep-gene.We designed a pair of contiguous primers to verify the DNA sequence upstream from the rep-gene.Here we named the 'new' plasmid as pBMB7635(7635 bp).
Two orfs(orf94 and orf133) present in pBMB7635 but absent in pBMB9741. ORF94 shares 100%amino acid identity with the TasA putative antitoxin protein of pGI1, while its neighbor ORF133 shares 98%amino acid identity with the TasB putative toxin protein of pGI1.The orf94/orf133 system is denoted kyCD system.
Attempts to clone the kyC in E.coli DH5αwere easy and successful,while continuing efforts to clone kyD gene and kyCD system in E.coli DH5αhave not yet been successful,suggesting the toxic activity of KyD protein,suggesting the KyD protein failed to inhibit the lethal activity of the cognate toxin and kyCD system appeared to be functional but unregulated in E.coli.
3.Plasmid pBMB2062 from YBT-1520 strain was cloned and characterized
A multicopy plasmid pBMB2062 from Bacillus thuringiensis subsp,kurstaki YBT-1520 strain was cloned and characterized by dot-blot analysis with the ORF1 fragment as a probe,and it was found to be present in 41%B.thuringiensis strains.The sequences of 7 pBMB2062-like plasmids from randomly selected B.thuringiensis strains (positive signal in the dot-blot analysis) were highly conserved.Two orfs,orf1 and orf2, were present in this plasmid.Orf1 was found to be necessary for plasmid replication, whereas Orf2 did not play a role in replication or stability.Based on its sequence homology,ORF2 was putative solitary antitoxin belonged to MetJ/Arc/CopG family.
4.The mazEF system from YBT-1520 chromosome was cloned and characterized
Based on the sequences homology with other mazEF toxin-antitoxin systems,a novel mazEF system was identified on the YBT-1520 chromosome.To investigate the role of mazEF system in Bacillus thuringiensis,the mazEF system on B.thuringiensis strain BMB171 was knocked out.The conclusion was that the mazEF system was involved in the PCD of the B.thuringiensis strain BMB171.
1.质粒pBMB8240上潜在TA系统kyAB的研究
本研究在YBT-1520菌株中发现了新质粒pBMB8240上有两个邻近的开放读码框,分别命名为KyA和KyB蛋白,通过序列分析,发现KyA和KyB分别与已知抗毒素、毒素蛋白有序列一致性。
KyA和kyB基因的克隆实验表明kyA基因很容易克隆;而多次努力克隆到的kyB基因区域都发生了基因突变。KyAB系统装载到不稳定的载体pBMB0631上去之后发现重组质粒的稳定性大大升高。
以上结果表明kyAB系统是一个潜在的TA系统,并且能够增强不稳定质粒的稳定性。这是第一个克隆到大肠杆菌中的来自苏云金芽胞杆菌的质粒TA系统。
2.质粒pBMB7635上潜在TA系统kyCD的研究
本研究发现YBT-1520中的质粒pBMB7635与本实验室以前克隆的质粒pBMB9741有很高的相似性,对pBMB7635重新测序,并将质粒pBMB9741重新命名为pBMB7635。
质粒pBMB7635上有两个邻近的开放读码框,与已经鉴定的TA系统有较高相似性,将这两个分别编码94和133个氨基酸大小的蛋白质分别命名为KyC和KyD蛋白。
KyC、kyD和kyCD系统及临近区域的克隆实验表明kyC基因很容易克隆;而多次努力克隆kyD基因和kyCD系统及临近区域只得到少量转化子,而且这些转化子中kyD区域都发生了基因突变,表明kyCD很可能是TA系统,且不能在大肠杆菌中克隆。
3.质粒pBMB2062的克隆和分析
克隆并分析了菌株YBT-1520中的多拷贝小质粒pBMB2062,序列分析表明,pBMB2062含有2个ORFs(大于75个氨基酸),缺失实验证明ORF1(289aa)对于质粒在芽胞杆菌中的复制和稳定是必需的,ORF2则不是。研究随机选取了7个不同血清型菌株的小质粒进行了克隆和测序,发现这些小质粒的序列高度保守。斑点杂交实验表明该质粒在目前鉴定的84个Bt血清型菌株中的分布为41%。
4.YBT-1520染色体上mazEF系统的克隆和分析
在YBT-1520染色体上找到一对mazEF系统,本实验对mazEF系统进行了敲除突变,改变MazEF的表达水平来探索MazEF的表达与PCD之间的的相互作用,从而进一步研究mazEF的功能。研究发现,敲除了mazEF系统的菌株在45℃培养4天之后,菌体量逐渐减少,取样镜检发现菌体大部分死亡。从另外一个角度证明了染色体上的mazEF系统在PCD中起作用。
本实验通过基因组间上TA系统的比较分析,为进一步研究质粒在不同菌株(包括其它芽胞杆菌群菌株)的分布、进化等提供一定的遗传信息和理论依据,对多拷贝小质粒的稳定机制以及苏云金芽胞杆菌中隐蔽型质粒的功能提出了新的认识。
Bacillus thuringiensis strain YBT-1520,which is highly toxic to lepidopteran pests, was isolated by our lab.In this thesis,we reported the sequence determination and initial analysis of the genome of this strain.The results revealed that this genome consisted of one chromosome and nine plasmids.TA systems have been extensively studied on low-copy-number plasmids in Gram-negative bacteria as addiction systems because of their ability to maintain the plasmids during cell division and a few TA systems have been described on small plasmids in Gram-positive bacteria.
We identified 562 TA loci belonging to the seven known TA gene families and present the results from an exhaustive search for TA loci in the completely sequenced Bacillus genomes.The putative TA loci from YBT-1520 genomes were studied and the putative TA loci from other 6 completely sequenced Bacillus genomes were found by bioinformatics analyse.
1.The study on the putative kyAB TA system from plasmid pBMB8240
Based on the shotgun sequence analysis of the strain YBT-1520 plasmid pBMB8240 was found to be a novel cryptic plasmid.In pBMB8240,two contiguous orfs(this gene pair was tentatively named kyAB for strain kurstaki YBT-1520) were noticed.The putative protein KyA and KyB displays sequence similarities with other antitoxin and toxin protein,respectively.
Attempts to clone the kyA in E.coli DH5αwere easy and successful.In kyB cloning case,all recombinants harbored mutations in the kyB gene,suggesting the toxic activity of KyB protein in E.coli.
Based on sequence homology with other toxin-antitoxin system genes and the lethal activity of KyB in Escherichia coli,the segregational stability kyAB cassette was identified to be the first functional putative TA segregational stability system from B. thuringiensis.
2.The study on the putative kyCD TA system from plasmid pBMB7635
A database sequence search revealed that the B.thuringiensis H1.1 plasmid pGI1 (8254 bp) had DNA sequences and organizations similar to plasmid pBMB9741 except for a fragment of 1.6 kb located upstream from the rep-gene.We designed a pair of contiguous primers to verify the DNA sequence upstream from the rep-gene.Here we named the 'new' plasmid as pBMB7635(7635 bp).
Two orfs(orf94 and orf133) present in pBMB7635 but absent in pBMB9741. ORF94 shares 100%amino acid identity with the TasA putative antitoxin protein of pGI1, while its neighbor ORF133 shares 98%amino acid identity with the TasB putative toxin protein of pGI1.The orf94/orf133 system is denoted kyCD system.
Attempts to clone the kyC in E.coli DH5αwere easy and successful,while continuing efforts to clone kyD gene and kyCD system in E.coli DH5αhave not yet been successful,suggesting the toxic activity of KyD protein,suggesting the KyD protein failed to inhibit the lethal activity of the cognate toxin and kyCD system appeared to be functional but unregulated in E.coli.
3.Plasmid pBMB2062 from YBT-1520 strain was cloned and characterized
A multicopy plasmid pBMB2062 from Bacillus thuringiensis subsp,kurstaki YBT-1520 strain was cloned and characterized by dot-blot analysis with the ORF1 fragment as a probe,and it was found to be present in 41%B.thuringiensis strains.The sequences of 7 pBMB2062-like plasmids from randomly selected B.thuringiensis strains (positive signal in the dot-blot analysis) were highly conserved.Two orfs,orf1 and orf2, were present in this plasmid.Orf1 was found to be necessary for plasmid replication, whereas Orf2 did not play a role in replication or stability.Based on its sequence homology,ORF2 was putative solitary antitoxin belonged to MetJ/Arc/CopG family.
4.The mazEF system from YBT-1520 chromosome was cloned and characterized
Based on the sequences homology with other mazEF toxin-antitoxin systems,a novel mazEF system was identified on the YBT-1520 chromosome.To investigate the role of mazEF system in Bacillus thuringiensis,the mazEF system on B.thuringiensis strain BMB171 was knocked out.The conclusion was that the mazEF system was involved in the PCD of the B.thuringiensis strain BMB171.
引文
1.萨姆布鲁克J,拉塞尔D W.分子克隆实验指南.第三版.(黄培堂等译).北京:科学出版社,2002.
2.孙明,魏芳,刘子铎,喻子牛.质粒pBMB2062的克隆及遗传稳定载体的构建.遗传学报,2000,27:932-938.
3.Afif H,Allali N,Couturier M,Van Melderen L.The ratio between CcdA and CcdB modulates the transcriptional repression of the ccd poison-antidote system.Mol Microbiol,2001,41:73-82.
4.Ahmad S I,Kirk S H,Eisenstark A.Thymine metabolism and thymineless death in prokaryotes and eukaryotes.Annu Rev Microbiol,1998,52:591-625.
5.Aizenman E,Engelberg-Kulka H,Glaser G.An Escherichia coli chromosomal 'addiction module' regulated by guanosine 3',5'-bispyrophosphate:a model for programmed bacterial cell death.Proc Natl Acad Sci USA,1996,93:6059-6063.
6.Allen G C Jr,Kornberg A.Fine balance in the regulation of DnaB helicase by DnaC protein in replication in Escherichia coli.J Biol Chem,1991,266,22096-22101.
7.Ameisen J C.The origin of programmed cell death.Science,1996 272:1278-1279.
8.Amitai S,Yassin Y,Engelberg-Kulka H.MazF-mediated cell death in Escherichia coli:A point of no return.J Bacteriol,2004,186:8295-8300.
9.Anantharaman V and Aravind L.New connections in the prokaryotic toxin-antitoxin network:relationship with the eukaryotic nonsense-mediated RNA decay system.Genome Biol,2003,4:R81.
10.Arcus V L.Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.J Biol Chem,2004,279:16471-16478.
11.Arcus V L.The PIN-domain toxin-antitoxin array in mycobacteria.Trends Microbiol,2005,13:360-365
12.Bahassi E M,O'Dea M H,Allali N,Messens J,Gellert M,Couturier M.Interactions of CcdB with DNA gyrase.Inactivation of GyrA,poisoning of the gyrase-DNA complex,and the antidote action of CcdA.J Biol Chem,1999,274:10936-10944.
13.Bech F W.Sequence of the relB transcription unit from Escherichia coli and identification of the relB gene.EMBO J,1985,4:1059-1066.
14. Bernard P and Couturier M. The 41 carboxyterminal residues of the miniF plasmid CcdA protein are sufficient to antagonize the killer activity of the CcdB protein. Mol Gen Genet, 1991, 226:297-304.
15. Bernard P and Couturier M. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J Mol Biol, 1992, 226:735-745.
16. Bernard P, Kezdy K E, Van Melderen L, Steyaert J, Wyns L, Pato M L. The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase. J Mol Biol, 1993,234:534-541.
17. Black D S, Kelly A J, Mardis M J, Moyed H S. Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol, 1991, 173: 5732-5739.
18. Bloomfield G A, Whittle G, McDonagh M B, Katz M E, Cheetham B F. Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events, a killer system, and a new genetic element. Microbiology, 1997, 143: 553-562.
19. Buts B, Lah J, Dao-Thi M H, Wyns L, Loris R. Toxin-antitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci, 2006, 30: 673-679.
20. Camacho A G. In vitro and in vivo stability of the ε2ζ2 protein complex of the broad host-range Streptococcus pyogenes pSM 19035 addiction system. Biol Chem, 2002, 383: 1701-1713.
21. Chatterji D and Kumar O A. Revisiting the stringent response, ppGpp and starvation signaling. Curr Opin Microbiol, 2001, 4: 160-165.
22. Cherny I and Gazit E. The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target. J Biol Chem, 2004, 279: 8252-8261.
23. Christensen S K, Maenhaut-Michel G, Mine N, Gottesman S, Gerdes K. Overproduction of the lon protease triggers inhibition of translation in Escherichia coli: Involvement of the yefM-yoeB toxin-antitoxin system. Mol Microbiol, 2004, 51: 1705-1717.
24. Christensen S K, Mikkelsen M, Pedersen K, Gerdes K. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc Natl Acad Sci USA, 2001, 98: 14328-14333.
25. Christensen S K, Pedersen K, Hensen F G, Gerdes K. Toxin-antitoxin loci as stress-response elements: ChpAK/MazF and ChpBK cleave translated mRNAs and are counteracted by tmRNA. J Mol Biol, 2003, 332: 809-819.
26. Christensen S K and Gerdes K. Delayed-relaxed response explained by hyperactivation of RelE. Mol Microbiol, 2004, 53: 587-597.
27. Christensen S K and Gerdes K. RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol Microbiol, 2003, 48: 1389-1400.
28. Clissold P M and Ponting C P. PIN domains in nonsense mediated mRNA decay and RNAi. Curr Biol, 2000, 10: 888-890.
29. Cohen S S, Barner H D. Studies on the unbalanced growth in Escherichia coli. Proc Natl Acad Sci USA, 1954,40: 885-893.
30. Cole S T. Massive gene decay in the leprosy bacillus. Nature, 2001, 409: 1007-1011.
31. Cooper T F and Heinemann J A. Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc NatlAcad Sci USA, 2000, 97: 12643-12648.
32. Critchlow S E. The interaction of the F plasmid killer protein, CcdB, with DNA gyrase: induction of DNA cleavage and blocking of transcription. J Mol Biol, 1997, 273: 826-839.
33. Dao-Thi M H. Intricate interactions within the ccd plasmid addiction system. J Biol Chem, 2002, 277: 3733-3742.
34. Dao-Thi M H. Molecular basis of gyrase poisoning by the addiction toxin CcdB. J Mol Biol, 2005, 348: 1091-1102.
35. Debrabant A, Lee N, Bertholtet S, Duncan R, Nakhasi H L. Programmed cell death in trypanosomatid and other unicellular organisms. Int J Parasitol, 2003, 33: 257-267.
36. Engelberg-Kulka H, Reches M, Narasimhan S, Schoulaker-Schwarz R, Klemes Y. RexB bacteriophage k is an anti cell death gene. Proc Nail Acad Sci USA, 1998, 95: 15481-15486.
37. Engelberg-Kulka H, Reches M, Sat B, Amitai S, Hazan R Bacterial programmed cell death as a target for antibiotics. Trends Microbiol, 2004, 12: 66-71.
38. Engelberg-Kulka, H. Bacterial programmed cell death and antibiotics. ASM News, 2002, 67: 617-625.
39. Engelberg-Kulka, Hazan R, Amitai S. mazEF: A chromosomal toxin-antitoxin module that triggers programmed cell death in bacteria. J Cell Science, 2005, 118: 4327-4332.
40. Fico S and Mahillon J. TasA-tasB, a new putative toxin-antitoxin (TA) system from Bacillus thuringiensis pGI1 plasmid is a widely distributed composite mazE-doc TA system. BMC Genomics., 2006, 7: 259.
41. Fuqua C, Greenberg E P. Cell-to-cell communication in Escherichia coli and Salmonella typhimurium: They may be talking, but who's listening? Proc Natl Acad Sci USA, 1998, 95: 6571-6572.
42. Gazit E and Sauer R T. The Doc toxin and Phd antidote proteins of the bacteriophage P1 plasmid addiction system form a heterotrimeric complex. J Biol Chem, 1999,274: 16813-16818.
43. Gerdes K, Christensen S K, Lobner-Olesen. A Prokaryotic toxin-antitoxin stress response loci. Nature Rev Microbiol, 2005, 3: 371-382.
44. Gerdes, K. Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J, 1986, 5: 2023-2029.
45. Gerdes K. Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J Bacteriol, 2000, 182: 561-572.
46. Gerdes K, Moller-Jensen J, Ebersbach G, Kruse T and Nordstrom K. Bacterial mitotic machineries. Cell, 2004, 116: 359-366.
47. Gerdes K, Rasmussen P B, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci USA, 1986,83:3116-3120.
48. Godoy V G, Jarosz D F, Walker F L, Simmons L A, Walker G. Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression. EMBO J, 2006, 25: 868-879.
49. Gogos A. Crystal structure of YdcE from Bacillus subtilis. Proteins, 2003, 53: 320-322.
50. Gonzalez-Pastor J E, Hobbs E C, Losick R. Cannibalism by sporulating bacteria. Science, 2003, 301:510-513.
51. Gotfredsen M, Gerdes, K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Mol Microbiol, 1998,29: 1065-1076.
52. Gozuacik D, Kimchi A. Autophagy as a cell death and tumor suppressor mechanism. Oncogene, 2004, 23: 2891-2906.
53. Grady R, Hayes F. Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of Enterococcus faecium. Mol Microbiol, 2003, 47: 1419-1432.
54. Greenfield T J. The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism. Mol Microbiol, 2000, 37: 652-660.
55. Gronlund H, Gerdes K. Toxin-antitoxin systems homologous with relBE of Escherichia coli plasmid P307 are ubiquitous in prokaryotes. J Mol Biol, 1999, 285: 1401-1415.
56. Gross M, Marianovsky I, Glaser G. MazG-A regulator of programmed cell death in Escherichia coli. Mol Microbiol. 2006, 59: 590-601.
57. Hargreaves D. Structural and functional analysis of the kid toxin protein from E. coli plasmid R1. Structure, 2002, 10: 1425-1433.
58. Hayes F. Toxins-antitoxins: Plasmid maintenance, programmed cell death, and cell cycle arrest. Science, 2003, 301: 1496-1499.
59. Hayes C S and Sauer R T. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol Cell, 2003, 12:903-911.
60. Hazan R, Sat B, Engelberg-Kulka H. Escherichia coli mazEF-mediated cell death is triggered by various stressful conditions. J Bacteriol, 2004, 186: 3663-3669.
61. Hazan R and Engelberg-Kulka H. Escherichia coli mazEF mediated cell death as a defense mechanismthat inhibits the spread of phage P1. Mol Genet Genomics, 2004, 272: 227-234.
62. Hazan R, Sat B, Reches M, Engelberg-Kulka H. Postsegregational killing mediated by the P1 phage 'addiction module' phd-doc requires the Escherichia coli programmed cell death system mazEF. J Bacteriol, 2001, 183: 2046-2050.
63. Hiraga S, Jaffe A, Ogura T, Mori H, Takahashi H. F plasmid ccd mechanism in Escherichia coli. J Bacteriol, 1986, 166: 100-104.
64. Ivanova N, Pavlov M Y, Felden B, Ehrenberg M. Ribosome rescue by tmRNA requires truncated mRNAs. J Mol Biol, 2004, 338: 33-41.
65. Jensen R B and Gerdes K. Programmed cell death in bacteria: proteic plasmid stabilization systems. Mol Microbiol, 1995, 17: 205-210.
66. Jensen R B, Grohmann E, Schwab H, Diaz-Orejas R, Gerdes K. Comparison of ccd of F, parDE of RP4, and parD of Rl using a novel conditional replication control system of plasmid R1. Mol Microbiol, 1995, 17: 211-220.
67. Jiang Y, Pogliano J, Helinski D R, Konieczny I. ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase. Mol Microbiol, 2002, 44: 971-979.
68. Kaiser D, Losick R. How and why bacteria talk to each other. Cell, 1993, 73: 873-885.
69. Kamada K and Hanaoka F. Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin. Mol Cell, 2005, 19: 497-509.
70. Kamada K, Hanaoka F and Burley S K. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell, 2003, 11: 875-884.
71. Karzai A W, Roch E D, Sauer R T. The SsrA-Smp system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol, 2000, 7: 449-455.
72. Keren I. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol, 2004, 186: 8172-8180.
73. Kerr J F R, Wyllie A H, Curie A R. Apoptosis: A basic biological phenomenon with wide-ranging implication in tissue kinetics. Br J Cancer, 1972, 26: 239-257.
74. Kolodkin-Gal I, Engelberg-Kulka H. Induction of Escherichia coli chromosomal mazEF by stressful conditions causes an irreversible loss of viability. J Bacteriol, 2006, 188:3420-3423.
75. Korch S B, Henderson T A, Hill T M. Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p) ppGpp synthesis. Mol Microbiol, 2003, 50: 1199-1213.
76. Kuroda A. Inorganic polyphosphate kinase is required to stimulate protein degradation and for adaptation to amino acid starvation in Escherichia coli. Proc Natl Acad Sci USA, 1999,96: 14264-14269.
77. Kuroda A. Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science, 2001, 293: 705-708.
78. Lah, J. Recognition of the intrinsically flexible addiction antidote MazE by a dromedary single domain antibody fragment. Structure, thermodynamics of binding, stability and influence on interactions with DNA. J Biol Chem, 2003, 278: 14101-14111.
79. Lah J. Energetics of structural transitions of the addiction antitoxin MazE. Is a programmed bacterial cell death dependent on the intrinsically flexible nature of the antitoxins. J Biol Chem, 2005, 280: 17397-17407.
80. Laurie A D. The role of the alarmone (p) ppGpp in aN competition for core RNA polymerase. J Biol Chem, 2003, 278: 1494-1503.
81. Lehnherr H and Yarmolinsky M B. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci USA, 1995, 92: 3274-3277.
82. Lemos J A C, Brown T A Jr, Abranches J, Burne R A. Characteristics of Streptococcus mutans strains lacking MazEF and RelBE toxin-antitoxin modules. FEMS Microbiol Lett, 2005, 253: 250-257.
83. Lewis K. Persister cells and the riddle of biofilm survival. Biochemistry, 2005, 70: 267-274.
84. Loris R. Crystal structure of CcdB, a topoisomerase poison from E. coli. J Mol Biol, 1999, 285: 1667-1676.
85. Loris R. Crystal structure of the intrinsically flexible addiction antidote MazE. J Biol Chem, 2003, 278: 28252-28257.
86. Magnuson R and Yarmolinsky M B. Corepression of the P1 addiction operon by Phd and Doc. J Bacteriol, 1998, 180: 6342-6351.
87. Maki S. Partner switching mechanisms in inactivation and rejuvenation of Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA (CcdA). J Mol Biol, 1996, 256: 473-482.
88. Marianovsky I. The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J Biol Chem, 2001, 276: 5975-5984.
89. Masuda Y and Ohtsubo E. Mapping and disruption of the chpB locus in Escherichia coli. J Bacteriol, 1994, 176: 5861-5863.
90. Masuda Y, Miyakawa K, Nishimura Y, Ohtsubo E. chpA and chpB, Escherichia coli chromosomal homologs of the pern locus responsible for stable maintenance of plasmid R100. J Bacteriol, 1993, 175: 6850-6856.
91. Meinhart A, Alonso J C, Strater N, Saenger W. Crystal structure of the plasmid maintenance system ε/ζ: functional mechanism of toxin ζ and inactivation by ε2 ζ2 complex formation. Proc Natl Acad Sci USA, 2003, 100: 1661-1666.
92. Mittenhuber G. Occurence of mazEF-like antitoxin/toxin systems in bacteria. J Mol Microbiol Biotechnol, 1999, 1: 295-302.
93. Munoz-Gomez A J. Insights into the specificity of RNA cleavage by the Escherichia coli MazF toxin. FEBS Lett, 2004, 567: 316-320.
94. Murray K D and Bremer H. Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli. J Mol Biol, 1996, 259: 41-57.
95. Naito T, Kusano K and Kobayashi I. Selfish behavior of restriction-modification systems. Science, 1995, 267:897-899.
96. Nystrom, T. Conditional senescence in bacteria: death of the immortals. Mol Microbiol, 2003,48: 17-23.
97. Nystrom T. Role of guanosine tetraphosphate in gene expression and the survival of glucose or seryl-transfer RNA starved cells of Escherichia coli K12. Mol Gen Genet, 1994, 245: 355-362.
98. Nystrom T. Stationary-phase physiology. Annu Rev Microbiol, 2004, 58: 161-181.
99. Oberer M. Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system. J Biol Chem, 1999, 380: 1413-1420.
100. Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier P E, Parinello H, Claverie J M, Raoult D. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol, 2005, 3: e248.
101. Ogura T and Hiraga S. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc Natl Acad Sci USA, 1983, 80: 4784-4788.
102. Pandey D P and Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res, 2005, 33: 966-976.
103. Parsek M R and Greenberg E P. Quorum sensing signals in development of Pseudomonas aeruginosa biofilms. Methods Enzymol, 1999, 310: 43-55.
104. Paul B J. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell, 2004, 118:311-322.
105. Pedersen K, Christensen S K, Gerdes K. Rapid induction and reversal of bacteriostatic conditions by controlled expression of toxins and antitoxins. Mol Microbiol, 2002, 45: 501-510.
106. Pedersen K. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell, 2003, 112: 131-140.
107. Pellgrini O, Mathy N, Gogos A, Shapiro L, Condon C. The Bacillus subtilis ydcDE operon encodes an endoribonuclease of MazF/PemK family and its inhibitor. Mol Microbiol, 2005, 56: 1139-1148.
108. Perederina A. Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell, 2004, 118: 297-309.
109. Pomerantsev A P. Genetic organization of the Francisella plasmid pFNL10. Plasmid, 2001, 46: 210-222.
110. Pullinger G D and Lax A J. A Salmonella dublin virulence plasmid locus that affects bacterial growth under nutrientlimited conditions. Mol Microbiol, 1992, 6: 1631-1643.
111. Roberts R C, Spangler C, Helinski D R. Characteristics and significance of DNA binding activity of plasmid stabilization protein ParD from the broad host-range plasmid RK2.J Biol Chem, 1993, 268: 27109-27117.
112. Rowe-Magnus D A. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res, 2003, 13: 428-442.
113. Ruiz-Echevarria M J, Gimenez-Gallego G, Sabariegos-Jareno R, Diaz-Orejas R. Kid, a small protein of the parD stability system of plasmid R1, is an inhibitor of DNA replication acting at the initiation of DNA synthesis. J Mol Biol, 1995, 247: 568-577.
114. Sat B, Hazan R, Fisher T, Khaner H, Glaser G. Programmed cell death in Escherichia coli: Some antibiotics can trigger the MazEF lethality. J Bacteriol, 2001, 183: 2041-2045.
115. Sat B, Reches M, Engelberg-Kulka H. The Escherichia coli chromosomal 'suicide module' mazEF is involved in thymine-less death. J Bacteriol, 2003, 185: 1803-1807.
116. Sayeed S, Reaves L, Radnedge L, Austin S. The stability region of the large virulence plasmid of Shigella flexneri encodes an efficient postsegregational killing system. J Bacteriol, 2000, 182: 2416-2421.
117. Shapiro J A. Thinking about bacterial populations as multi-cellular organisms. Annu Rev Microbiol, 1998, 52: 81-104.
118. Sia E A, Roberts R C, Easter C, Helinski D R, Figurski D H. Different relative importances of the par operons and the effect of conjugal transfer on the maintenance of intact promiscuous plasmid RK2. J Bacteriol, 1995, 177: 2789-2797.
119. Smith J A and Magnuson R D. Modular organization of the Phd repressor/antitoxin protein. J Bacteriol, 2004, 186: 2692-2698.
120. Sobecky P A, Easter C L, Bear P D, Helinski D R. Characterization of the stable maintenance properties of the par region of broad-host-range plasmid RK2. J Bacteriol, 1996, 178: 2086-2093.
121. Suzuki M. Single protein production in living cells facilitated by an mRNA interferase. Mol Cell, 2005, 18: 253-261.
122. Takagi H. Crystal structure of an archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects. Nat Struct Mol Biol, 2005,12:327-331.
123. Tarn J E and Kline B C. Control of the ccd operon in plasmid F. J Bacteriol, 1989, 171:2353-2360.
124. Tian Q B. Specific protein-DNA and protein-protein interaction in the hig gene system, a plasmid-borne proteic killer gene system of plasmid Rtsl. Plasmid, 2001,45:63-74.
125. Tian Q B, Ohnishi M, Tabuchi A, Terawaki Y. A new plasmid-encoded proteic killer gene system: cloning, sequencing, and analyzing hig locus of plasmid Rtsl. Biochem Biophys Res Commun, 1996, 220: 280-284.
126. Tsuchimoto S, Ohtsubo H, Ohtsubo E. Two genes, pemK and pemI, responsible for stable maintenance of resistance plasmid R100. J Bacteriol, 1988, 170: 1461-1466.
127. Van Melderen L. Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria. Mol Microbiol, 1994, 11: 1151-1157.
128. Van Melderen L. ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions. J Biol Chem, 1996, 271: 27730-27738.
129. Vaughn J L, Feher V, Naylor S, Strauch M A, Cavanagh J. Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator abrB. Nature Struct Biol, 2000, 7: 1139-1146.
130. Waters C M and Bassler B L. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol, 2005, 21: 319-346.
131. Withey J H and Friedman D I. A salvage pathway for protein structures: tmRNA and trans-translation. Annu Rev Microbiol, 2003, 57: 101-123.
132. Yarmolinsky M B. Programmed cell death in bacterial population. Science, 1995, 267: 836-837.
133. Zhang J and Inouye M. MazG, a nucleoside triphosphate pyrophosphohydrolase, interacts with Era, an essential GTPase in Escherichia coli. J Bacteriol, 2002, 184: 5323-5329.
134. Zhang Y, Zhang J, Hara H, Kato I, Inouye M. Insight into mRNA cleavage mechanism by MazF, an mRNA interferase. J Biol Chem, 2004, 280: 3143-3150.
135. Zhang Y, Zhang J, Hoeflich K P, Ikura M, Quing G. MazF cleaves cellular mRNA specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell, 2003, 12:913-923.
136. Zhang J, Zhang Y, Zhu L, Suzuki M, Inouye M. Interference of mRNA function by sequence-specific endoribonuclease PemK. J Biol Chem, 2004, 279: 20678-20684.
137. Zhang X Z, Yan X, Cui Z L, Hong Q, Li S P. MazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis. Nucleic Acids Research, 2006, 34, e71.
138. Zhang Y X. Characterization of a novel toxin-antitoxin module, VapBC, encoded by Leptospira interrogans chromosome. Cell Res, 2004, 14: 208-216.
2.孙明,魏芳,刘子铎,喻子牛.质粒pBMB2062的克隆及遗传稳定载体的构建.遗传学报,2000,27:932-938.
3.Afif H,Allali N,Couturier M,Van Melderen L.The ratio between CcdA and CcdB modulates the transcriptional repression of the ccd poison-antidote system.Mol Microbiol,2001,41:73-82.
4.Ahmad S I,Kirk S H,Eisenstark A.Thymine metabolism and thymineless death in prokaryotes and eukaryotes.Annu Rev Microbiol,1998,52:591-625.
5.Aizenman E,Engelberg-Kulka H,Glaser G.An Escherichia coli chromosomal 'addiction module' regulated by guanosine 3',5'-bispyrophosphate:a model for programmed bacterial cell death.Proc Natl Acad Sci USA,1996,93:6059-6063.
6.Allen G C Jr,Kornberg A.Fine balance in the regulation of DnaB helicase by DnaC protein in replication in Escherichia coli.J Biol Chem,1991,266,22096-22101.
7.Ameisen J C.The origin of programmed cell death.Science,1996 272:1278-1279.
8.Amitai S,Yassin Y,Engelberg-Kulka H.MazF-mediated cell death in Escherichia coli:A point of no return.J Bacteriol,2004,186:8295-8300.
9.Anantharaman V and Aravind L.New connections in the prokaryotic toxin-antitoxin network:relationship with the eukaryotic nonsense-mediated RNA decay system.Genome Biol,2003,4:R81.
10.Arcus V L.Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.J Biol Chem,2004,279:16471-16478.
11.Arcus V L.The PIN-domain toxin-antitoxin array in mycobacteria.Trends Microbiol,2005,13:360-365
12.Bahassi E M,O'Dea M H,Allali N,Messens J,Gellert M,Couturier M.Interactions of CcdB with DNA gyrase.Inactivation of GyrA,poisoning of the gyrase-DNA complex,and the antidote action of CcdA.J Biol Chem,1999,274:10936-10944.
13.Bech F W.Sequence of the relB transcription unit from Escherichia coli and identification of the relB gene.EMBO J,1985,4:1059-1066.
14. Bernard P and Couturier M. The 41 carboxyterminal residues of the miniF plasmid CcdA protein are sufficient to antagonize the killer activity of the CcdB protein. Mol Gen Genet, 1991, 226:297-304.
15. Bernard P and Couturier M. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J Mol Biol, 1992, 226:735-745.
16. Bernard P, Kezdy K E, Van Melderen L, Steyaert J, Wyns L, Pato M L. The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase. J Mol Biol, 1993,234:534-541.
17. Black D S, Kelly A J, Mardis M J, Moyed H S. Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol, 1991, 173: 5732-5739.
18. Bloomfield G A, Whittle G, McDonagh M B, Katz M E, Cheetham B F. Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events, a killer system, and a new genetic element. Microbiology, 1997, 143: 553-562.
19. Buts B, Lah J, Dao-Thi M H, Wyns L, Loris R. Toxin-antitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci, 2006, 30: 673-679.
20. Camacho A G. In vitro and in vivo stability of the ε2ζ2 protein complex of the broad host-range Streptococcus pyogenes pSM 19035 addiction system. Biol Chem, 2002, 383: 1701-1713.
21. Chatterji D and Kumar O A. Revisiting the stringent response, ppGpp and starvation signaling. Curr Opin Microbiol, 2001, 4: 160-165.
22. Cherny I and Gazit E. The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target. J Biol Chem, 2004, 279: 8252-8261.
23. Christensen S K, Maenhaut-Michel G, Mine N, Gottesman S, Gerdes K. Overproduction of the lon protease triggers inhibition of translation in Escherichia coli: Involvement of the yefM-yoeB toxin-antitoxin system. Mol Microbiol, 2004, 51: 1705-1717.
24. Christensen S K, Mikkelsen M, Pedersen K, Gerdes K. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc Natl Acad Sci USA, 2001, 98: 14328-14333.
25. Christensen S K, Pedersen K, Hensen F G, Gerdes K. Toxin-antitoxin loci as stress-response elements: ChpAK/MazF and ChpBK cleave translated mRNAs and are counteracted by tmRNA. J Mol Biol, 2003, 332: 809-819.
26. Christensen S K and Gerdes K. Delayed-relaxed response explained by hyperactivation of RelE. Mol Microbiol, 2004, 53: 587-597.
27. Christensen S K and Gerdes K. RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol Microbiol, 2003, 48: 1389-1400.
28. Clissold P M and Ponting C P. PIN domains in nonsense mediated mRNA decay and RNAi. Curr Biol, 2000, 10: 888-890.
29. Cohen S S, Barner H D. Studies on the unbalanced growth in Escherichia coli. Proc Natl Acad Sci USA, 1954,40: 885-893.
30. Cole S T. Massive gene decay in the leprosy bacillus. Nature, 2001, 409: 1007-1011.
31. Cooper T F and Heinemann J A. Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc NatlAcad Sci USA, 2000, 97: 12643-12648.
32. Critchlow S E. The interaction of the F plasmid killer protein, CcdB, with DNA gyrase: induction of DNA cleavage and blocking of transcription. J Mol Biol, 1997, 273: 826-839.
33. Dao-Thi M H. Intricate interactions within the ccd plasmid addiction system. J Biol Chem, 2002, 277: 3733-3742.
34. Dao-Thi M H. Molecular basis of gyrase poisoning by the addiction toxin CcdB. J Mol Biol, 2005, 348: 1091-1102.
35. Debrabant A, Lee N, Bertholtet S, Duncan R, Nakhasi H L. Programmed cell death in trypanosomatid and other unicellular organisms. Int J Parasitol, 2003, 33: 257-267.
36. Engelberg-Kulka H, Reches M, Narasimhan S, Schoulaker-Schwarz R, Klemes Y. RexB bacteriophage k is an anti cell death gene. Proc Nail Acad Sci USA, 1998, 95: 15481-15486.
37. Engelberg-Kulka H, Reches M, Sat B, Amitai S, Hazan R Bacterial programmed cell death as a target for antibiotics. Trends Microbiol, 2004, 12: 66-71.
38. Engelberg-Kulka, H. Bacterial programmed cell death and antibiotics. ASM News, 2002, 67: 617-625.
39. Engelberg-Kulka, Hazan R, Amitai S. mazEF: A chromosomal toxin-antitoxin module that triggers programmed cell death in bacteria. J Cell Science, 2005, 118: 4327-4332.
40. Fico S and Mahillon J. TasA-tasB, a new putative toxin-antitoxin (TA) system from Bacillus thuringiensis pGI1 plasmid is a widely distributed composite mazE-doc TA system. BMC Genomics., 2006, 7: 259.
41. Fuqua C, Greenberg E P. Cell-to-cell communication in Escherichia coli and Salmonella typhimurium: They may be talking, but who's listening? Proc Natl Acad Sci USA, 1998, 95: 6571-6572.
42. Gazit E and Sauer R T. The Doc toxin and Phd antidote proteins of the bacteriophage P1 plasmid addiction system form a heterotrimeric complex. J Biol Chem, 1999,274: 16813-16818.
43. Gerdes K, Christensen S K, Lobner-Olesen. A Prokaryotic toxin-antitoxin stress response loci. Nature Rev Microbiol, 2005, 3: 371-382.
44. Gerdes, K. Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J, 1986, 5: 2023-2029.
45. Gerdes K. Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J Bacteriol, 2000, 182: 561-572.
46. Gerdes K, Moller-Jensen J, Ebersbach G, Kruse T and Nordstrom K. Bacterial mitotic machineries. Cell, 2004, 116: 359-366.
47. Gerdes K, Rasmussen P B, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci USA, 1986,83:3116-3120.
48. Godoy V G, Jarosz D F, Walker F L, Simmons L A, Walker G. Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression. EMBO J, 2006, 25: 868-879.
49. Gogos A. Crystal structure of YdcE from Bacillus subtilis. Proteins, 2003, 53: 320-322.
50. Gonzalez-Pastor J E, Hobbs E C, Losick R. Cannibalism by sporulating bacteria. Science, 2003, 301:510-513.
51. Gotfredsen M, Gerdes, K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Mol Microbiol, 1998,29: 1065-1076.
52. Gozuacik D, Kimchi A. Autophagy as a cell death and tumor suppressor mechanism. Oncogene, 2004, 23: 2891-2906.
53. Grady R, Hayes F. Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of Enterococcus faecium. Mol Microbiol, 2003, 47: 1419-1432.
54. Greenfield T J. The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism. Mol Microbiol, 2000, 37: 652-660.
55. Gronlund H, Gerdes K. Toxin-antitoxin systems homologous with relBE of Escherichia coli plasmid P307 are ubiquitous in prokaryotes. J Mol Biol, 1999, 285: 1401-1415.
56. Gross M, Marianovsky I, Glaser G. MazG-A regulator of programmed cell death in Escherichia coli. Mol Microbiol. 2006, 59: 590-601.
57. Hargreaves D. Structural and functional analysis of the kid toxin protein from E. coli plasmid R1. Structure, 2002, 10: 1425-1433.
58. Hayes F. Toxins-antitoxins: Plasmid maintenance, programmed cell death, and cell cycle arrest. Science, 2003, 301: 1496-1499.
59. Hayes C S and Sauer R T. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol Cell, 2003, 12:903-911.
60. Hazan R, Sat B, Engelberg-Kulka H. Escherichia coli mazEF-mediated cell death is triggered by various stressful conditions. J Bacteriol, 2004, 186: 3663-3669.
61. Hazan R and Engelberg-Kulka H. Escherichia coli mazEF mediated cell death as a defense mechanismthat inhibits the spread of phage P1. Mol Genet Genomics, 2004, 272: 227-234.
62. Hazan R, Sat B, Reches M, Engelberg-Kulka H. Postsegregational killing mediated by the P1 phage 'addiction module' phd-doc requires the Escherichia coli programmed cell death system mazEF. J Bacteriol, 2001, 183: 2046-2050.
63. Hiraga S, Jaffe A, Ogura T, Mori H, Takahashi H. F plasmid ccd mechanism in Escherichia coli. J Bacteriol, 1986, 166: 100-104.
64. Ivanova N, Pavlov M Y, Felden B, Ehrenberg M. Ribosome rescue by tmRNA requires truncated mRNAs. J Mol Biol, 2004, 338: 33-41.
65. Jensen R B and Gerdes K. Programmed cell death in bacteria: proteic plasmid stabilization systems. Mol Microbiol, 1995, 17: 205-210.
66. Jensen R B, Grohmann E, Schwab H, Diaz-Orejas R, Gerdes K. Comparison of ccd of F, parDE of RP4, and parD of Rl using a novel conditional replication control system of plasmid R1. Mol Microbiol, 1995, 17: 211-220.
67. Jiang Y, Pogliano J, Helinski D R, Konieczny I. ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase. Mol Microbiol, 2002, 44: 971-979.
68. Kaiser D, Losick R. How and why bacteria talk to each other. Cell, 1993, 73: 873-885.
69. Kamada K and Hanaoka F. Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin. Mol Cell, 2005, 19: 497-509.
70. Kamada K, Hanaoka F and Burley S K. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell, 2003, 11: 875-884.
71. Karzai A W, Roch E D, Sauer R T. The SsrA-Smp system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol, 2000, 7: 449-455.
72. Keren I. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol, 2004, 186: 8172-8180.
73. Kerr J F R, Wyllie A H, Curie A R. Apoptosis: A basic biological phenomenon with wide-ranging implication in tissue kinetics. Br J Cancer, 1972, 26: 239-257.
74. Kolodkin-Gal I, Engelberg-Kulka H. Induction of Escherichia coli chromosomal mazEF by stressful conditions causes an irreversible loss of viability. J Bacteriol, 2006, 188:3420-3423.
75. Korch S B, Henderson T A, Hill T M. Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p) ppGpp synthesis. Mol Microbiol, 2003, 50: 1199-1213.
76. Kuroda A. Inorganic polyphosphate kinase is required to stimulate protein degradation and for adaptation to amino acid starvation in Escherichia coli. Proc Natl Acad Sci USA, 1999,96: 14264-14269.
77. Kuroda A. Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science, 2001, 293: 705-708.
78. Lah, J. Recognition of the intrinsically flexible addiction antidote MazE by a dromedary single domain antibody fragment. Structure, thermodynamics of binding, stability and influence on interactions with DNA. J Biol Chem, 2003, 278: 14101-14111.
79. Lah J. Energetics of structural transitions of the addiction antitoxin MazE. Is a programmed bacterial cell death dependent on the intrinsically flexible nature of the antitoxins. J Biol Chem, 2005, 280: 17397-17407.
80. Laurie A D. The role of the alarmone (p) ppGpp in aN competition for core RNA polymerase. J Biol Chem, 2003, 278: 1494-1503.
81. Lehnherr H and Yarmolinsky M B. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci USA, 1995, 92: 3274-3277.
82. Lemos J A C, Brown T A Jr, Abranches J, Burne R A. Characteristics of Streptococcus mutans strains lacking MazEF and RelBE toxin-antitoxin modules. FEMS Microbiol Lett, 2005, 253: 250-257.
83. Lewis K. Persister cells and the riddle of biofilm survival. Biochemistry, 2005, 70: 267-274.
84. Loris R. Crystal structure of CcdB, a topoisomerase poison from E. coli. J Mol Biol, 1999, 285: 1667-1676.
85. Loris R. Crystal structure of the intrinsically flexible addiction antidote MazE. J Biol Chem, 2003, 278: 28252-28257.
86. Magnuson R and Yarmolinsky M B. Corepression of the P1 addiction operon by Phd and Doc. J Bacteriol, 1998, 180: 6342-6351.
87. Maki S. Partner switching mechanisms in inactivation and rejuvenation of Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA (CcdA). J Mol Biol, 1996, 256: 473-482.
88. Marianovsky I. The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J Biol Chem, 2001, 276: 5975-5984.
89. Masuda Y and Ohtsubo E. Mapping and disruption of the chpB locus in Escherichia coli. J Bacteriol, 1994, 176: 5861-5863.
90. Masuda Y, Miyakawa K, Nishimura Y, Ohtsubo E. chpA and chpB, Escherichia coli chromosomal homologs of the pern locus responsible for stable maintenance of plasmid R100. J Bacteriol, 1993, 175: 6850-6856.
91. Meinhart A, Alonso J C, Strater N, Saenger W. Crystal structure of the plasmid maintenance system ε/ζ: functional mechanism of toxin ζ and inactivation by ε2 ζ2 complex formation. Proc Natl Acad Sci USA, 2003, 100: 1661-1666.
92. Mittenhuber G. Occurence of mazEF-like antitoxin/toxin systems in bacteria. J Mol Microbiol Biotechnol, 1999, 1: 295-302.
93. Munoz-Gomez A J. Insights into the specificity of RNA cleavage by the Escherichia coli MazF toxin. FEBS Lett, 2004, 567: 316-320.
94. Murray K D and Bremer H. Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli. J Mol Biol, 1996, 259: 41-57.
95. Naito T, Kusano K and Kobayashi I. Selfish behavior of restriction-modification systems. Science, 1995, 267:897-899.
96. Nystrom, T. Conditional senescence in bacteria: death of the immortals. Mol Microbiol, 2003,48: 17-23.
97. Nystrom T. Role of guanosine tetraphosphate in gene expression and the survival of glucose or seryl-transfer RNA starved cells of Escherichia coli K12. Mol Gen Genet, 1994, 245: 355-362.
98. Nystrom T. Stationary-phase physiology. Annu Rev Microbiol, 2004, 58: 161-181.
99. Oberer M. Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system. J Biol Chem, 1999, 380: 1413-1420.
100. Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier P E, Parinello H, Claverie J M, Raoult D. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol, 2005, 3: e248.
101. Ogura T and Hiraga S. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc Natl Acad Sci USA, 1983, 80: 4784-4788.
102. Pandey D P and Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res, 2005, 33: 966-976.
103. Parsek M R and Greenberg E P. Quorum sensing signals in development of Pseudomonas aeruginosa biofilms. Methods Enzymol, 1999, 310: 43-55.
104. Paul B J. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell, 2004, 118:311-322.
105. Pedersen K, Christensen S K, Gerdes K. Rapid induction and reversal of bacteriostatic conditions by controlled expression of toxins and antitoxins. Mol Microbiol, 2002, 45: 501-510.
106. Pedersen K. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell, 2003, 112: 131-140.
107. Pellgrini O, Mathy N, Gogos A, Shapiro L, Condon C. The Bacillus subtilis ydcDE operon encodes an endoribonuclease of MazF/PemK family and its inhibitor. Mol Microbiol, 2005, 56: 1139-1148.
108. Perederina A. Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell, 2004, 118: 297-309.
109. Pomerantsev A P. Genetic organization of the Francisella plasmid pFNL10. Plasmid, 2001, 46: 210-222.
110. Pullinger G D and Lax A J. A Salmonella dublin virulence plasmid locus that affects bacterial growth under nutrientlimited conditions. Mol Microbiol, 1992, 6: 1631-1643.
111. Roberts R C, Spangler C, Helinski D R. Characteristics and significance of DNA binding activity of plasmid stabilization protein ParD from the broad host-range plasmid RK2.J Biol Chem, 1993, 268: 27109-27117.
112. Rowe-Magnus D A. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res, 2003, 13: 428-442.
113. Ruiz-Echevarria M J, Gimenez-Gallego G, Sabariegos-Jareno R, Diaz-Orejas R. Kid, a small protein of the parD stability system of plasmid R1, is an inhibitor of DNA replication acting at the initiation of DNA synthesis. J Mol Biol, 1995, 247: 568-577.
114. Sat B, Hazan R, Fisher T, Khaner H, Glaser G. Programmed cell death in Escherichia coli: Some antibiotics can trigger the MazEF lethality. J Bacteriol, 2001, 183: 2041-2045.
115. Sat B, Reches M, Engelberg-Kulka H. The Escherichia coli chromosomal 'suicide module' mazEF is involved in thymine-less death. J Bacteriol, 2003, 185: 1803-1807.
116. Sayeed S, Reaves L, Radnedge L, Austin S. The stability region of the large virulence plasmid of Shigella flexneri encodes an efficient postsegregational killing system. J Bacteriol, 2000, 182: 2416-2421.
117. Shapiro J A. Thinking about bacterial populations as multi-cellular organisms. Annu Rev Microbiol, 1998, 52: 81-104.
118. Sia E A, Roberts R C, Easter C, Helinski D R, Figurski D H. Different relative importances of the par operons and the effect of conjugal transfer on the maintenance of intact promiscuous plasmid RK2. J Bacteriol, 1995, 177: 2789-2797.
119. Smith J A and Magnuson R D. Modular organization of the Phd repressor/antitoxin protein. J Bacteriol, 2004, 186: 2692-2698.
120. Sobecky P A, Easter C L, Bear P D, Helinski D R. Characterization of the stable maintenance properties of the par region of broad-host-range plasmid RK2. J Bacteriol, 1996, 178: 2086-2093.
121. Suzuki M. Single protein production in living cells facilitated by an mRNA interferase. Mol Cell, 2005, 18: 253-261.
122. Takagi H. Crystal structure of an archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects. Nat Struct Mol Biol, 2005,12:327-331.
123. Tarn J E and Kline B C. Control of the ccd operon in plasmid F. J Bacteriol, 1989, 171:2353-2360.
124. Tian Q B. Specific protein-DNA and protein-protein interaction in the hig gene system, a plasmid-borne proteic killer gene system of plasmid Rtsl. Plasmid, 2001,45:63-74.
125. Tian Q B, Ohnishi M, Tabuchi A, Terawaki Y. A new plasmid-encoded proteic killer gene system: cloning, sequencing, and analyzing hig locus of plasmid Rtsl. Biochem Biophys Res Commun, 1996, 220: 280-284.
126. Tsuchimoto S, Ohtsubo H, Ohtsubo E. Two genes, pemK and pemI, responsible for stable maintenance of resistance plasmid R100. J Bacteriol, 1988, 170: 1461-1466.
127. Van Melderen L. Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria. Mol Microbiol, 1994, 11: 1151-1157.
128. Van Melderen L. ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions. J Biol Chem, 1996, 271: 27730-27738.
129. Vaughn J L, Feher V, Naylor S, Strauch M A, Cavanagh J. Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator abrB. Nature Struct Biol, 2000, 7: 1139-1146.
130. Waters C M and Bassler B L. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol, 2005, 21: 319-346.
131. Withey J H and Friedman D I. A salvage pathway for protein structures: tmRNA and trans-translation. Annu Rev Microbiol, 2003, 57: 101-123.
132. Yarmolinsky M B. Programmed cell death in bacterial population. Science, 1995, 267: 836-837.
133. Zhang J and Inouye M. MazG, a nucleoside triphosphate pyrophosphohydrolase, interacts with Era, an essential GTPase in Escherichia coli. J Bacteriol, 2002, 184: 5323-5329.
134. Zhang Y, Zhang J, Hara H, Kato I, Inouye M. Insight into mRNA cleavage mechanism by MazF, an mRNA interferase. J Biol Chem, 2004, 280: 3143-3150.
135. Zhang Y, Zhang J, Hoeflich K P, Ikura M, Quing G. MazF cleaves cellular mRNA specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell, 2003, 12:913-923.
136. Zhang J, Zhang Y, Zhu L, Suzuki M, Inouye M. Interference of mRNA function by sequence-specific endoribonuclease PemK. J Biol Chem, 2004, 279: 20678-20684.
137. Zhang X Z, Yan X, Cui Z L, Hong Q, Li S P. MazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis. Nucleic Acids Research, 2006, 34, e71.
138. Zhang Y X. Characterization of a novel toxin-antitoxin module, VapBC, encoded by Leptospira interrogans chromosome. Cell Res, 2004, 14: 208-216.