白桦HD-Zip基因家族生物信息学及应答盐胁迫分析
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摘要
HD-Zip转录因子蛋白家族是植物特有的一类转录因子蛋白,在植物生长发育和抵抗逆境胁迫等过程中发挥着重要作用。利用白桦全基因组数据库,获得白桦35条HD-Zip蛋白序列,参考拟南芥中该家族的分类方法,将这些成员分成HD-ZipⅠ-Ⅳ四个亚家族,并对这些成员的蛋白保守结构域、氨基酸组成、染色体分布、和理化性质等进行了预测和分析。从高盐处理的白桦幼苗根组织的转录组数据,鉴定了7个差异表达的基因。本研究为进一步研究白桦HD-Zip家族基因调控白桦耐盐性的功能提供了理论支持。
Homeodomain-leucine zipper( HD-Zip) proteins are ubiquitous in plants and participate in various aspects of plant growth and developmental processes as well as environmental responses. Using birch genome database,we acquired 35 putative HD-Zip genes. These genes were classified into four subfamilies,Ⅰ to Ⅳ,based on phylogenetic analysis. The additional conserved domains,protein structures,chromosome distribution and physiological functions of these members were further predicted and analyzed. To gain more insights into the roles of birch HD-Zip genes in salinity tolerance,we identified seven genes which were highly induced by salt stress using transcriptomic data. This study provides a solid foundation for uncovering the biological roles of HDZip genes in salt response from Betula platyphylla.
Homeodomain-leucine zipper( HD-Zip) proteins are ubiquitous in plants and participate in various aspects of plant growth and developmental processes as well as environmental responses. Using birch genome database,we acquired 35 putative HD-Zip genes. These genes were classified into four subfamilies,Ⅰ to Ⅳ,based on phylogenetic analysis. The additional conserved domains,protein structures,chromosome distribution and physiological functions of these members were further predicted and analyzed. To gain more insights into the roles of birch HD-Zip genes in salinity tolerance,we identified seven genes which were highly induced by salt stress using transcriptomic data. This study provides a solid foundation for uncovering the biological roles of HDZip genes in salt response from Betula platyphylla.
引文
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2.Nakashima K,Ito Y,Yamaguchi-Shinozaki K.Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses[J].Plant Physiology,2009,149(1):88-95.
3.Golldack D,Lüking I,Yang O.Plant tolerance to drought and salinity:stress regulating transcription factors and their functional significance in the cellular transcriptional network[J].Plant Cell Reports,2011,30(8):1383-1391.
4.Wang H Y,Wang H L,Shao H B,et al.Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology[J].Frontiers in Plant Science,2016,7:67.
5.Todaka D,Shinozaki K,Yamaguchi-Shinozaki K.Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants[J].Frontiers in Plant Science,2015,6:84.
6.Viola I L,Gonzalez D H.Chapter 6-structure and evolution of plant homeobox genes[J].Plant Transcription Factors:Evolutionary,Structural and Functional Aspects,2016:101-112.
7.Ariel F D,Manavella P A,Dezar C A,et al.The true story of the HD-Zip family[J].Trends in Plant Science,2007,12(9):419-426.
8.Elhiti M,Stasolla C.Structure and function of homodomainleucine zipper(HD-Zip)proteins[J].Plant Signaling&Behavior,2009,4(2):86-88.
9.Arce A L,Raineri J,Capella M,et al.Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors;a potential source of functional diversity[J].BMC Plant Biology,2011,11:42.
10.Henriksson E,Olsson A S B,Johannesson H,et al.Homeodomain leucine zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships[J].Plant Physiology,2005,139(1):509-518.
11.Aoyama T,Dong C H,WU Wu Y,et al.Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco[J].The Plant Cell,1995,7(11):1773-1785.
12.Kim Y K,Son O,Kim M R,et al.ATHB23,an Arabidopsis classⅠhomeodomain-leucine zipper gene,is expressed in the adaxial region of young leaves[J].Plant Cell Reports,2007,26(8):1179-1185.
13.Harris J C,Sornaraj P,Taylor M,et al.Molecular interactions of theγ-clade homeodomain-leucine zipper classⅠtranscription factors during the wheat response to water deficit[J].Plant Molecular Biology,2016,90(4-5):435-452.
14.Zhao Y,Ma Q,Jin X L,et al.A novel maize homeodomainleucine zipper(HD-Zip)Ⅰgene,Zmhdz10,positively regulates drought and salt tolerance in both rice and Arabidopsis[J].Plant and Cell Physiology,2014,55(6):1142-1156.
15.Ciarbelli A R,Ciolfi A,Salvucci S,et al.The Arabidopsis homeodomain-leucine ZipperⅡgene family:diversity and redundancy[J].Plant Molecular Biology,2008,68:465.
16.Franklin K A,Praekelt U,Stoddart W M,et al.Phytochromes B,D and E act redundantly to control multiple physiological responses in Arabidopsis[J].Plant Physiology,2003,131(3):1340-1346.
17.Carabelli M,Turchi L,Ruzza V,et al.Homeodomain-Leucine zipperⅡfamily of transcription factors to the limelight:central regulators of plant development[J].Plant Signaling&Behavior,2013,8(9):e25447.
18.Park M Y,Kim S A,Lee S J,et al.ATHB17 is a positive regulator of abscisic acid response during early seedling growth[J].Molecules and Cells,2013,35(2):125-133.
19.Mukherjee K,Bürglin T R.MEKHLA,a novel domain with similarity to PAS domains,is fused to plant homeodomainleucine zipperⅢproteins[J].Plant Physiology,2006,140(4):1142-1150.
20.Prigge M J,Otsuga D,Alonso J M,et al.ClassⅢhomeodomain-leucine zipper gene family members have overlapping,antagonistic,and distinct roles in Arabidopsis development[J].The Plant Cell,2005,17(1):61-76.
21.Zhu Y Y,Song D L,Sun J Y,et al.Ptr HB7,a classⅢHD-Zip gene,plays a critical role in regulation of vascular cambium differentiation in Populus[J].Molecular Plant,2013,6(4):1331-1343.
22.Robischon M,Du J,Miura E,et al.The Populus classⅢHD ZIP,popREVOLUTA,influences cambium initiation and patterning of woody stems[J].Plant Physiology,2011,155(3):1214-1225.
23.Chew W,Hrmova M,Lopato S.Role of homeodomain leucine zipper(HD-Zip)Ⅳtranscription factors in plant development and plant protection from deleterious environmental factors[J].International Journal of Molecular Sciences,2013,14(4):8122-8147.
24.Ingram G C,Boisnard-Lorig C,Dumas C,et al.Expression patterns of genes encoding HD-ZipⅣhomeo domain proteins define specific domains in maize embryos and meristems[J].The Plant Journal,2000,22(5):401-414.
25.Ito M,Sentoku N,Nishimura A,et al.Position dependent expression of GL2-type homeobox gene,Roc1:significance for protoderm differentiation and radial pattern formation in early rice embryogenesis[J].The Plant Journal,2002,29(4):497-507.
26.Nakamura M,Katsumata H,Abe M,et al.Characterization of the classⅣhomeodomain-leucine zipper gene family in Arabidopsis[J].Plant Physiology,2006,141(4):1363-1375.
27.Ciarbelli A R,Ciolfi A,Salvucci S,et al.The Arabidopsis Homeodomain-leucine ZipperⅡgene family:diversity and redundancy[J].Plant Molecular Biology,2008,68(4-5):465-478.
28.Agalou A,Purwantomo S,verns E,et al.A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members[J].Plant Molecular Biology,2008,66(1-2):87-103.
29.Chen J H,Song Y P,Zhang H,et al.Genome-wide analysis of gene expression in response to drought stress in Populus simonii[J].Plant Molecular Biology Reporter,2013,31(4):946-962.
30.Hu R B,Chi X Y,Chai G H,et al.Genome-wide identification,evolutionary expansion,and expression profile of homeodomain-leucine zipper gene family in poplar(Populus trichocarpa)[J].PLo S One,2012,7(2):e31149.
31.Yue H,Shu D T,Wang M,et al.Genome-wide identification and expression analysis of the HD-Zip gene family in wheat(Triticum aestivum L.)[J].Genes,2018,9(2):70.
32.Zhang J,Zhu Q H,Moncuquet P,et al.Genome-wide identification and characterization of the homeodomain-leucine zipperⅠfamily of genes in cotton(Gossypium spp.)[J].Plant Gene,2016,7:50-61.
33.Belamkar V,Weeks N T,Bharti A K,et al.Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean(Glycine max)during dehydration and salt stress[J].BMC Genomics,2014,15:950.
34.Zhao Y,Zhou Y Q,Jiang H Y,et al.Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize[J].PLo SOne,2011,6(12):e28488.
35.Ding Z H,Fu L L,Yan Y,et al.Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava[J].PLo S One,2017,12(3):e0173043.
36.Perotti M F,Ribone P A,Chan R L.Plant transcription factors from the homeodomain-leucine zipper familyⅠ.Role in development and stress responses[J].IUBMB Life,2017,69(5):280-289.
37.Nakashima K,Jan A,Todaka D,et al.Comparative functional analysis of six drought-responsive promoters in transgenic rice[J].Planta,2014,239(1):47-60.
38.Ariel F,Diet A,Verdenaud M,et al.Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-ZipⅠtranscription factor HB1[J].The Plant Cell,2010,22(7):2171-2183.
39.Dezar C A,Gago G M,González D H,et al.Hahb-4,a sunflower homeobox-leucine zipper gene,is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants[J].Transgenic Research,2005,14(4):429-440.
2.Nakashima K,Ito Y,Yamaguchi-Shinozaki K.Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses[J].Plant Physiology,2009,149(1):88-95.
3.Golldack D,Lüking I,Yang O.Plant tolerance to drought and salinity:stress regulating transcription factors and their functional significance in the cellular transcriptional network[J].Plant Cell Reports,2011,30(8):1383-1391.
4.Wang H Y,Wang H L,Shao H B,et al.Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology[J].Frontiers in Plant Science,2016,7:67.
5.Todaka D,Shinozaki K,Yamaguchi-Shinozaki K.Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants[J].Frontiers in Plant Science,2015,6:84.
6.Viola I L,Gonzalez D H.Chapter 6-structure and evolution of plant homeobox genes[J].Plant Transcription Factors:Evolutionary,Structural and Functional Aspects,2016:101-112.
7.Ariel F D,Manavella P A,Dezar C A,et al.The true story of the HD-Zip family[J].Trends in Plant Science,2007,12(9):419-426.
8.Elhiti M,Stasolla C.Structure and function of homodomainleucine zipper(HD-Zip)proteins[J].Plant Signaling&Behavior,2009,4(2):86-88.
9.Arce A L,Raineri J,Capella M,et al.Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors;a potential source of functional diversity[J].BMC Plant Biology,2011,11:42.
10.Henriksson E,Olsson A S B,Johannesson H,et al.Homeodomain leucine zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships[J].Plant Physiology,2005,139(1):509-518.
11.Aoyama T,Dong C H,WU Wu Y,et al.Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco[J].The Plant Cell,1995,7(11):1773-1785.
12.Kim Y K,Son O,Kim M R,et al.ATHB23,an Arabidopsis classⅠhomeodomain-leucine zipper gene,is expressed in the adaxial region of young leaves[J].Plant Cell Reports,2007,26(8):1179-1185.
13.Harris J C,Sornaraj P,Taylor M,et al.Molecular interactions of theγ-clade homeodomain-leucine zipper classⅠtranscription factors during the wheat response to water deficit[J].Plant Molecular Biology,2016,90(4-5):435-452.
14.Zhao Y,Ma Q,Jin X L,et al.A novel maize homeodomainleucine zipper(HD-Zip)Ⅰgene,Zmhdz10,positively regulates drought and salt tolerance in both rice and Arabidopsis[J].Plant and Cell Physiology,2014,55(6):1142-1156.
15.Ciarbelli A R,Ciolfi A,Salvucci S,et al.The Arabidopsis homeodomain-leucine ZipperⅡgene family:diversity and redundancy[J].Plant Molecular Biology,2008,68:465.
16.Franklin K A,Praekelt U,Stoddart W M,et al.Phytochromes B,D and E act redundantly to control multiple physiological responses in Arabidopsis[J].Plant Physiology,2003,131(3):1340-1346.
17.Carabelli M,Turchi L,Ruzza V,et al.Homeodomain-Leucine zipperⅡfamily of transcription factors to the limelight:central regulators of plant development[J].Plant Signaling&Behavior,2013,8(9):e25447.
18.Park M Y,Kim S A,Lee S J,et al.ATHB17 is a positive regulator of abscisic acid response during early seedling growth[J].Molecules and Cells,2013,35(2):125-133.
19.Mukherjee K,Bürglin T R.MEKHLA,a novel domain with similarity to PAS domains,is fused to plant homeodomainleucine zipperⅢproteins[J].Plant Physiology,2006,140(4):1142-1150.
20.Prigge M J,Otsuga D,Alonso J M,et al.ClassⅢhomeodomain-leucine zipper gene family members have overlapping,antagonistic,and distinct roles in Arabidopsis development[J].The Plant Cell,2005,17(1):61-76.
21.Zhu Y Y,Song D L,Sun J Y,et al.Ptr HB7,a classⅢHD-Zip gene,plays a critical role in regulation of vascular cambium differentiation in Populus[J].Molecular Plant,2013,6(4):1331-1343.
22.Robischon M,Du J,Miura E,et al.The Populus classⅢHD ZIP,popREVOLUTA,influences cambium initiation and patterning of woody stems[J].Plant Physiology,2011,155(3):1214-1225.
23.Chew W,Hrmova M,Lopato S.Role of homeodomain leucine zipper(HD-Zip)Ⅳtranscription factors in plant development and plant protection from deleterious environmental factors[J].International Journal of Molecular Sciences,2013,14(4):8122-8147.
24.Ingram G C,Boisnard-Lorig C,Dumas C,et al.Expression patterns of genes encoding HD-ZipⅣhomeo domain proteins define specific domains in maize embryos and meristems[J].The Plant Journal,2000,22(5):401-414.
25.Ito M,Sentoku N,Nishimura A,et al.Position dependent expression of GL2-type homeobox gene,Roc1:significance for protoderm differentiation and radial pattern formation in early rice embryogenesis[J].The Plant Journal,2002,29(4):497-507.
26.Nakamura M,Katsumata H,Abe M,et al.Characterization of the classⅣhomeodomain-leucine zipper gene family in Arabidopsis[J].Plant Physiology,2006,141(4):1363-1375.
27.Ciarbelli A R,Ciolfi A,Salvucci S,et al.The Arabidopsis Homeodomain-leucine ZipperⅡgene family:diversity and redundancy[J].Plant Molecular Biology,2008,68(4-5):465-478.
28.Agalou A,Purwantomo S,verns E,et al.A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members[J].Plant Molecular Biology,2008,66(1-2):87-103.
29.Chen J H,Song Y P,Zhang H,et al.Genome-wide analysis of gene expression in response to drought stress in Populus simonii[J].Plant Molecular Biology Reporter,2013,31(4):946-962.
30.Hu R B,Chi X Y,Chai G H,et al.Genome-wide identification,evolutionary expansion,and expression profile of homeodomain-leucine zipper gene family in poplar(Populus trichocarpa)[J].PLo S One,2012,7(2):e31149.
31.Yue H,Shu D T,Wang M,et al.Genome-wide identification and expression analysis of the HD-Zip gene family in wheat(Triticum aestivum L.)[J].Genes,2018,9(2):70.
32.Zhang J,Zhu Q H,Moncuquet P,et al.Genome-wide identification and characterization of the homeodomain-leucine zipperⅠfamily of genes in cotton(Gossypium spp.)[J].Plant Gene,2016,7:50-61.
33.Belamkar V,Weeks N T,Bharti A K,et al.Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean(Glycine max)during dehydration and salt stress[J].BMC Genomics,2014,15:950.
34.Zhao Y,Zhou Y Q,Jiang H Y,et al.Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize[J].PLo SOne,2011,6(12):e28488.
35.Ding Z H,Fu L L,Yan Y,et al.Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava[J].PLo S One,2017,12(3):e0173043.
36.Perotti M F,Ribone P A,Chan R L.Plant transcription factors from the homeodomain-leucine zipper familyⅠ.Role in development and stress responses[J].IUBMB Life,2017,69(5):280-289.
37.Nakashima K,Jan A,Todaka D,et al.Comparative functional analysis of six drought-responsive promoters in transgenic rice[J].Planta,2014,239(1):47-60.
38.Ariel F,Diet A,Verdenaud M,et al.Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-ZipⅠtranscription factor HB1[J].The Plant Cell,2010,22(7):2171-2183.
39.Dezar C A,Gago G M,González D H,et al.Hahb-4,a sunflower homeobox-leucine zipper gene,is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants[J].Transgenic Research,2005,14(4):429-440.