大豆bHLH转录因子家族成员的进化及功能分化研究
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摘要
碱性螺旋-环-螺旋蛋白(basic Helix-Loop-Hleix,bHLH)转录因子家族是动植物中最大的转录因子家族之一,主要由碱性氨基酸区域和螺旋-环-螺旋区域组成,在动植物生长发育和胁迫应答反应中发挥着重要作用.本研究通过对大豆全基因组生物信息学分析和分子生物学研究手段,深入研究了大豆bHLH基因家族的进化机制,同时探讨了该基因家族在大豆中的功能分化.结果表明,大豆中含有340个非冗余的bHLH基因家族成员,通过对这些成员的Pfam蛋白结构域、Motif组成和系统进化关系的分析,将这些成员分为15组共24个亚家族,在大豆20条染色体上呈现不均匀分布.bHLH理化性质差异较大,编码的大豆氨基酸数量为91～815aa,相对分子量为10 273.88～91 300.38,理论等电点为4.56～10.40;碱性氨基酸区含有His5-Glu9-Arg13保守序列,与靶基因结合有关,HLH区含有Arg23和Arg55,与形成二聚体有关,同时含有5种保守元件.多数成员在大豆根以及花发育的5个时期中具有组织表达特异性,不同基因表达量差异较大.
The basic Helix-Loop-Hleix( bHLH) gene family,one of the largest plant transcript factor families,played an important role in the growth and development in plants and animals. The evolutionary mechanism of the soybean bHLH gene family was analyzed,further the function differentiation through bioinformatics and molecular biology methods was discussed. The results showed that the soybean contains 340 members of bHLH genes,which can be divided into 24 subgroups through the domain structures,motif compositions and phylogenetic relationships,and distributed in 20 chromosomes unevenly. The chemical characteristic of bHLH genes were significantly different with the length of amino acid was 91 ～ 815,the relative molecular weight was 10 273.88 ～ 91 300.38,and the theoretical equivalence point varies from 4. 56 to 10. 40. The alkaline amino acid region contains the conservative sequence of His5-Glu9-Arg13,which is associated with the target gene. The bHLH region contains Arg23 and Arg55 and contains five conservative elements,which is related to the formation of dimer. Most of the members showed specific tissue expression and different gene expression levels in root and the development of flower in soybean.
The basic Helix-Loop-Hleix( bHLH) gene family,one of the largest plant transcript factor families,played an important role in the growth and development in plants and animals. The evolutionary mechanism of the soybean bHLH gene family was analyzed,further the function differentiation through bioinformatics and molecular biology methods was discussed. The results showed that the soybean contains 340 members of bHLH genes,which can be divided into 24 subgroups through the domain structures,motif compositions and phylogenetic relationships,and distributed in 20 chromosomes unevenly. The chemical characteristic of bHLH genes were significantly different with the length of amino acid was 91 ～ 815,the relative molecular weight was 10 273.88 ～ 91 300.38,and the theoretical equivalence point varies from 4. 56 to 10. 40. The alkaline amino acid region contains the conservative sequence of His5-Glu9-Arg13,which is associated with the target gene. The bHLH region contains Arg23 and Arg55 and contains five conservative elements,which is related to the formation of dimer. Most of the members showed specific tissue expression and different gene expression levels in root and the development of flower in soybean.
引文
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[34] HE X,ZHANG J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicategene evolution[J]. Genetics,2005,169(2):1157-1164.
[35] PAPP B,PAL C,HURST L D. Dosage sensitivity and the evolution of gene families in yeast[J]. Nature,2003,424(6945):194-197.
[36] WANG L,CAO C,MA Q,et al. RNA-seq analyses of multiple meristems of soybean:Novel and alternative transcripts,ev-olutionary and functional implications[J]. BMC Plant Biology,2014,14(1):169-187.
[2] BEATTY P H,GOOD A G. Future prospects for cereals that fix nitrogen[J]. Science,2011,333(6041):416-417.
[3] MASSARI M E,MURRE C. Helix-loop-helix proteins:regulators of transcription in eucaryotic organisms[J]. Molecular andCellular Biology,2000,20(2):429-440.
[4] RAMSAY N A,GLOVER B J. MYB-bHLH-WD40 protein complex and the evolution of cellular diversity[J]. Trends in PlantScience,2005,10(2):63-70.
[5] YANG F,WANG Q,SCHMITZ G,et al. The b HLH protein ROX acts in concert with RAX1 and LAS to modulate axillarymeristem formation in Arabidopsis[J]. Plant Journal,2012,71(1):61-70.
[6] HEIM M A,JAKOBY M,WERBER M,et al. The basic helix-loop-helix transcription factor family in plants:a ge-nome-wide study of protein structure and functional diversity[J]. Molecular Biology and Evolution,2003,20(5):735-747.
[7] IKEDA M,FUJIWARA S,MITSUDA N,et al. A triantagonistic basic helix-loop-helix system regulates cell elongation in Ar-abidopsis[J]. Plant Cell,2012,24(11):4483-4497.
[8] HAO Y,OH E,CHOI G,et al. Interactions between HLH and b HLH factors modulate light-regulated plant development[J].Molecular Plant,2012,5(3):688-697.
[9] CASTILLON A,SHEN H,HUQ E. Phytochrome interacting factors:Central players in phytochrome-mediated light signalingnetworks[J]. Trends in Plant Science,2007,12(11):514-521.
[10] RYBEL B D,MOLLER B,YOSHIDA S,et al. A b HLH complex controls embryonic vascular tissue establishment and inde-terminate growth in Arabidopsis[J]. Developmental Cell,2013,24(4):426-437.
[11] ZHAO D. Control of anther cell differentiation:a teamwork of receptor-like kinases[J]. Sexual Plant Reprodroduction,2009,22(4):221-228.
[12]李朝霞,高强,刘雅正,等.玉米Zm PTF1基因克隆和过表达分析[J].湖南农业大学学报(自然科学版),2007,33(4):92-96.LI Chaoxia,GAO Qiang,LIU Yazheng,et al. Cloning of Zm PTF1 from zea mays and its overexpression analysis[J]. Jour-nal of Hunan Agricultural University(Natural Sciences),2007,33(4):92-96.
[13] SEO J S,JOO J,KIM M J,et al. Osb HLH148,a basic helix-loop-helix protein,interacts with Os JAZ proteins in a jas-monate signaling pathway leading to drought tolerance in rice[J]. Plant Journal,2011,65(6):907-921.
[14] WALKER T S,BAIS H P,GROTEWOLD E,et al. Root exudation and rhizosphere biology[J]. Plant Physiology,2003,132(1):44-51.
[15] KE D X,FANG Q,CHEN C F,et al. Small GTPase ROP6 interacts with NFR5 and is involved in nodule formation in Lo-tus Japonicus[J].Plant Physiology,2012,159(1):131-143.
[16] PRELL J,WHITE J P,BOURDES A,et al. Legumes regulate Rhizobium bacteroid development and persistence by thesupply of branched-chain amino acids[J]. Proceedings of the National Academy of Sciences of the United States of America,2009,106(30):12477-12482.
[17] SCHMUTZ J,CANNON S B,SCHLUETER J,et al. Genome sequence of the palaeopolyploid soybean[J]. Nature,2010,463(7278):178-183.
[18] PIRES N,DOLAN L. Origin and diversification of basic-helix-loop-helix proteins in plants[J]. Molecular Biology and Evo-lution,2010,27(4):862-874.
[19] LIVAK K J,SCHMITTGEN T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-[Del-ta][Delta] CT method[J]. Methods,2001,25(4):402-8.
[20] ROBINSON K A,LOPES J M. SURVEY AND SUMMARY:Saccharomyces cerevisiae basic helix-loop-helix proteins regu-late diverse biological processes[J]. Nucleic Acids Research,2000,28(7):1499-1505.
[21] KURBIDAEVA A,EZHOVA T,NOVOKRESHCHENOVA M. Arabidopsis thaliana ICE2 gene:phylogeny,structural evolu-tion and functional diversification from ICE1[J]. Plant Science,2014,229:10-22.
[22] GYOJA F. A genome-wide survey of b HLH transcription factors in the Placozoan Trichoplax adhaerens reveals the ancientrepertoire of this gene family in metazoan[J]. Gene,2014,542(1):29-37.
[23] GOLDBERG R B,BEALS T P,SANDERS P M. Anther development:basic principles and practical applications[J]. PlantCell,1993,5(10):1217-1229.
[24] OHNO S.Evolution by gene duplication[M]. New York,NY,USA:Springer Verlag,1971,23(5):541.
[25]薛亚杰、余亚军、侯佳佳,等.被子植物中核糖体失活蛋白基因家族分子进化研究[J].信阳师范学院学报(自然科学版),2018,31(3):389-395.XUE Yajie,YU Yajun,HOU Jiajia,et al. Molecular evolutionary analysis of Ribosome-Inactivating protein gene family inAngiosperm plant[J]. Journal of Xinyang Normal University(Natural Science Edition),2018,31(3):389-395.
[26] LIU H J,TANG Z X,HAN X M,et al. Divergence in enzymatic activities in the soybean gst supergene family provides newinsight into the evolutionary dynamics of whole-genome duplicates[J]. Molecular Biology and Evolution,2015,32(11):2844-2859.
[27] XIAO G H,HE P,ZHAO P,et al. Genome-wide identification of the Gh ARF gene family reveals that Gh ARF2 andGh ARF18 are involved in cotton fibre cell initiation[J]. Journal of Experimental Botany,2018,69(18):4323-4337.
[28] LU Q,SHAO F J,MACMILLAN C,et al. Genomewide analysis of the lateral organ boundaries domain gene family in Euca-lyptus grandis reveals members that differentially impact secondary growth[J]. Plant Biotechnology Journal,2018,16:124-136.
[29] LI X L,TAO S T,WEI S W,et al. The mining and evolutionary investigation of AP2/ERF genes in pear(Pyrus)[J].BMC Plant Biology,2018,18(46):1-14.
[30] CHENG Lin,HAN Yapeng,REN Ren,et al. Genome-wide identification,classification,and expression analysis of aminoacid transporter gene family in glycine max[J]. Frontiers in Plant Science,2016,7(320):515-528.
[31] HAN Yapeng,LI Xiangyong,CHENG Lin,et al. Genome-wide analysis of soybean jmjc domain-containing proteins suggestsevolutionary conservation following whole-genome duplication[J]. Frontiers in Plant Science,2016,7:1800-1814.
[32] ZHANG J. Evolution by gene duplication:An update[J]. Trends in Ecology&Evolution,2003,18(6):292-298.
[33] FORCE A,LYNCH M,PICKETT F B,et al. Preservation of duplicate genes by complementary,degenerative mutations[J]. Genetics,1999,151(4):1531-1545.
[34] HE X,ZHANG J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicategene evolution[J]. Genetics,2005,169(2):1157-1164.
[35] PAPP B,PAL C,HURST L D. Dosage sensitivity and the evolution of gene families in yeast[J]. Nature,2003,424(6945):194-197.
[36] WANG L,CAO C,MA Q,et al. RNA-seq analyses of multiple meristems of soybean:Novel and alternative transcripts,ev-olutionary and functional implications[J]. BMC Plant Biology,2014,14(1):169-187.