雷蒙德氏棉和亚洲棉Alfin-like PHD finger家族的生物信息学分析
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摘要
Alfin-like PHD finger是植物中特有的一类转录调控因子,在调控植物生长发育、非生物胁迫响应及抗病反应等过程中起重要作用。为全面了解Alfin-like PHD finger基因家族在雷蒙德氏棉和亚洲棉基因组中的数目、分布情况及家族各成员间的关系,进而研究和揭示Alfin-like PHD finger在棉花抵抗逆境胁迫中的作用。运用生物信息学的方法在雷蒙德氏棉(D5)和亚洲棉(A2)全基因组中分别鉴定出12个和10个Alfin-like PHD finger基因家族成员,并对家族成员的基因结构、染色体定位、保守结构域及进化关系等方面进行分析。结果表明,雷蒙德氏棉和亚洲棉中Alfin-like PHD finger转录因子具有高度保守的DUF3594结构域和PHD结构域,两个二倍体棉花中该家族基因成员之间为一对一关系;雷蒙德氏棉中的12个成员基因分布在5条染色体上,亚洲棉中的10个成员基因也分布在5条染色体上;亚细胞定位预测发现,该家族的基因分别定位于细胞核、叶绿体基质、过氧化物酶体和细胞质基质;根据结构域差异和系统发育分析结果,将Alfin-like PHD finger转录因子家族分为3个进化分支。上述结果为分离鉴定棉花中新的逆境胁迫响应基因提供参考。
Alfin-like PHD finger protein encodes a small specific type of plant transcription regulators that are involved in plant growth and development, abiotic stress response and disease resistance. This study was to fully understand the number and distribution and the relationships of Alfin-like PHD finger family among Gossypium arboretum(A2) and Gossypium raimondii(D5). Moreover, the influence of the gene on abiotic stress response were revealed. 12 and 10 Alfin-like PHD finger proteins were identified from the diploid cotton Gossypium arboretum(A2) and Gossypium raimondii(D5) genome database. The gene structure, chromosome location, conserved domains and evolutionary relationships were analyzed. The result showed the putative proteins of these genes contained highly conserved PHD motif and DUF3594 domain. The members of Gossypium arboretum and Gossypium raimondii were one to one relationships. In addition, 12 gene members of D5 cotton were distributed on 5 chromosomes, and 10 members of A2 cotton were also located on 5 chromosomes. It wasfound that the genes of the family were localized in the nucleus, chloroplast stroma, peroxisome and cytoplasmic matrix respectively. These proteins could be classified into 3 subgroups according to their structure and phylogenic relationship. These results might provide references for the isolation and identification of the abiotic stress responsive genes in cotton.
Alfin-like PHD finger protein encodes a small specific type of plant transcription regulators that are involved in plant growth and development, abiotic stress response and disease resistance. This study was to fully understand the number and distribution and the relationships of Alfin-like PHD finger family among Gossypium arboretum(A2) and Gossypium raimondii(D5). Moreover, the influence of the gene on abiotic stress response were revealed. 12 and 10 Alfin-like PHD finger proteins were identified from the diploid cotton Gossypium arboretum(A2) and Gossypium raimondii(D5) genome database. The gene structure, chromosome location, conserved domains and evolutionary relationships were analyzed. The result showed the putative proteins of these genes contained highly conserved PHD motif and DUF3594 domain. The members of Gossypium arboretum and Gossypium raimondii were one to one relationships. In addition, 12 gene members of D5 cotton were distributed on 5 chromosomes, and 10 members of A2 cotton were also located on 5 chromosomes. It wasfound that the genes of the family were localized in the nucleus, chloroplast stroma, peroxisome and cytoplasmic matrix respectively. These proteins could be classified into 3 subgroups according to their structure and phylogenic relationship. These results might provide references for the isolation and identification of the abiotic stress responsive genes in cotton.
引文
A asland R.,Gibson T.J.,and Stewart A.F.,1995,The PHD finger:implications for chromatin mediated transcriptional regulation,Trends in Biochemical Sciences,20(2):56-59
Bastola D.R.,Pethe V.V.,and Winicov I.,1998,Alfin1,a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible Ms PRP2 gene,Plant Mol.Biol.,38(6):1123-1135
Bienz M.,2006,The PHD finger,a nuclear protein-interaction domain,Trends in Biochemical Sciences,31(1):35-40
Feng Y.,Liu Q.P.,and Xue Q.Z.,2004,Comparative phylogenetic analysis of rice and Arabidopsis PHD-finger proteins,Yichuan Xuebao(Acta Genetica Sinica),31(11):1284-1293(冯英,刘庆坡,薛庆中,2004,水稻与拟南芥PHD-finger蛋白的系统分析,遗传学报,31(11):1284-1293)
Kaadige M.R.,and Ayer D.E.,2006,The polybasic region that follows the plant homeodomain zinc finger 1 of Pfl is necessary and sufficient for specific phospboinositide binding,Journal of Biological Chemistry,281(39):28831-28836
Lee W.Y.,Lee D.,Chung W.I.,and Kwon C.S.,2009,Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers,Plant J.,58(3):511-524
Liu R.J.,and Wang H.Q.,2007,Cloning and sequencing of an Alfin1-like zinc finger protein gene in Solanum tuberosum,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),27(4):657-661(刘瑞娟,王海庆,2007,马铃薯Alfin1-like锌指蛋白基因克隆与序列分析,西北植物学报,27(4):657-661)
Liu Y.,Liu C.X.,Li Z.X.,Xia M.,Jiang H.Y.,Cheng B.J.,Zhou J.L.,and Zhu S.W.,2011,Overexpression of a plant homedomain(PHD)-finger transcription Factor,Os PHD1,can enhance stress tolerance in rice,Nongye Shengwu Jishu Xuebao(Journal of Agricultural Biotechnology),19(3):462-469(刘雨,刘春霞,李早霞,夏勉,江海洋,程备久,周君莉,朱苏文,2011,植物同源结构域(PHD)-finger家族转录因子Os PHD1的过量表达可提高水稻的耐逆性能,农业生物技术学报,19(3):462-469)
Schindler U.,Beckmann H.,and Cashmore A.R.,1993,HAT3.1,a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region,Plant J.,4(1):137-150
Song Y.,Gao J.,Yang F.X.,Kua C.S.,Liu J.X.,and Cannon C.H.,2013,Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata,Arabidopsis thaliana,and Thellungiella halophila,PLo S One,8(7):e66838
Wei W.,Zhang Y.Q.,Tao J.J.,Chen H.W.,Li Q.T.,Zhang W.K.,Ma B.,Lin Q.,Zhang J.S.,and Chen S.Y.,2015,The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis Plant J.,81:871-883
Wei W.,Huang J.,Hao Y.J.,Hao Y.G.,Zou H.F.,Wang H.W.Zhao J.Y.,Liu X.L.,Zhang W.K.,Ma B.,Zhang J.S.,and Chen S.Y.,2009,Soybean Gm PHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants,PLo S One,4(9):e7209
Winicov I.I.,and Bastola D.R.,1999,Transgenic overexpression of the transcription factor Alfin1 enhances expression of the endogenous Ms PRP2 gene in Alfalfa and improves salinity tolerance of the plants,Plant Physiol.,120(2):473-480
Winicov I.,1993,c DNA encoding putative zinc finger motifs from salt-tolerant alfalfa(Medicago sativa L.)cells,Plant Physiol.,102(2):681-682
Winicov I.,2000,Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa,Planta,210(3):416-422
Wu S.L.,2013,Functional analysis of rice transcription regulatior Alfin-like PHD1,Thesis for M.S.,University of Chinese A-cademy of Sciences,Supervisor:Zhang J.S.,and Chen S.Y.pp.1-2(仵石磊,2013,水稻Alfin1 like PHD1转录调控因子的功能研究,硕士学位论文,中国科学院大学,导师:张劲松,陈受宜,pp.1-2)
Wu S.N.,Wu M.,Dong Q.,Jiang H.Y.,Cai R.H.,and Xiang Y.,2016,Genome-wide identification,classification and ex pression analysis of the PHD-finger protein family in Populus trichocarpa,Gene,575(1):75-89
Xiao H.B.,2012,Effects of RNA interference of a multiple-stress responsive gene,Os Msr16,in rice,Thesis for M.S.,Sichuan Agriculture University,Supervisor:Chen R.J.,and Xia X.J.,pp.41-50(肖宏博,2012,水稻多逆境响应基因Os Msr16的干扰表达研究,硕士学位论文,四川农业大学,导师:陈荣军,夏新界,pp.41-50)
Zhang F.,Yang Z.N.,and Zhang S.,2009,Genome-wide analysis of PHD-finger protein family in Arabidopsis thaliana,Yunnan Zhiwu Yanjiu(Acta Botanica Yunnanica),31(3):227-238(张帆,杨仲南,张森,2009,拟南芥PHD-finger蛋白家族的全基因组分析,云南植物研究,31(3):227-238)
Zhang X.,Li M.J.,Zhang B.,Yin X.M.,Wang M.L.,and Xia X.J.,2016,Possibility study on improving salt tolerance of rice by overexpressing PHD-finger transcription factor gene Os M-sr16,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(7):1820-1827(张新,李明娟,张斌,殷绪明,王曼玲,夏新界,2016,水稻PHD-finger转录因子基因Os Msr16增强耐盐性的可能性研究,基因组学与应用生物学,35(7):1820-1827)
Bastola D.R.,Pethe V.V.,and Winicov I.,1998,Alfin1,a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible Ms PRP2 gene,Plant Mol.Biol.,38(6):1123-1135
Bienz M.,2006,The PHD finger,a nuclear protein-interaction domain,Trends in Biochemical Sciences,31(1):35-40
Feng Y.,Liu Q.P.,and Xue Q.Z.,2004,Comparative phylogenetic analysis of rice and Arabidopsis PHD-finger proteins,Yichuan Xuebao(Acta Genetica Sinica),31(11):1284-1293(冯英,刘庆坡,薛庆中,2004,水稻与拟南芥PHD-finger蛋白的系统分析,遗传学报,31(11):1284-1293)
Kaadige M.R.,and Ayer D.E.,2006,The polybasic region that follows the plant homeodomain zinc finger 1 of Pfl is necessary and sufficient for specific phospboinositide binding,Journal of Biological Chemistry,281(39):28831-28836
Lee W.Y.,Lee D.,Chung W.I.,and Kwon C.S.,2009,Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers,Plant J.,58(3):511-524
Liu R.J.,and Wang H.Q.,2007,Cloning and sequencing of an Alfin1-like zinc finger protein gene in Solanum tuberosum,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),27(4):657-661(刘瑞娟,王海庆,2007,马铃薯Alfin1-like锌指蛋白基因克隆与序列分析,西北植物学报,27(4):657-661)
Liu Y.,Liu C.X.,Li Z.X.,Xia M.,Jiang H.Y.,Cheng B.J.,Zhou J.L.,and Zhu S.W.,2011,Overexpression of a plant homedomain(PHD)-finger transcription Factor,Os PHD1,can enhance stress tolerance in rice,Nongye Shengwu Jishu Xuebao(Journal of Agricultural Biotechnology),19(3):462-469(刘雨,刘春霞,李早霞,夏勉,江海洋,程备久,周君莉,朱苏文,2011,植物同源结构域(PHD)-finger家族转录因子Os PHD1的过量表达可提高水稻的耐逆性能,农业生物技术学报,19(3):462-469)
Schindler U.,Beckmann H.,and Cashmore A.R.,1993,HAT3.1,a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region,Plant J.,4(1):137-150
Song Y.,Gao J.,Yang F.X.,Kua C.S.,Liu J.X.,and Cannon C.H.,2013,Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata,Arabidopsis thaliana,and Thellungiella halophila,PLo S One,8(7):e66838
Wei W.,Zhang Y.Q.,Tao J.J.,Chen H.W.,Li Q.T.,Zhang W.K.,Ma B.,Lin Q.,Zhang J.S.,and Chen S.Y.,2015,The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis Plant J.,81:871-883
Wei W.,Huang J.,Hao Y.J.,Hao Y.G.,Zou H.F.,Wang H.W.Zhao J.Y.,Liu X.L.,Zhang W.K.,Ma B.,Zhang J.S.,and Chen S.Y.,2009,Soybean Gm PHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants,PLo S One,4(9):e7209
Winicov I.I.,and Bastola D.R.,1999,Transgenic overexpression of the transcription factor Alfin1 enhances expression of the endogenous Ms PRP2 gene in Alfalfa and improves salinity tolerance of the plants,Plant Physiol.,120(2):473-480
Winicov I.,1993,c DNA encoding putative zinc finger motifs from salt-tolerant alfalfa(Medicago sativa L.)cells,Plant Physiol.,102(2):681-682
Winicov I.,2000,Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa,Planta,210(3):416-422
Wu S.L.,2013,Functional analysis of rice transcription regulatior Alfin-like PHD1,Thesis for M.S.,University of Chinese A-cademy of Sciences,Supervisor:Zhang J.S.,and Chen S.Y.pp.1-2(仵石磊,2013,水稻Alfin1 like PHD1转录调控因子的功能研究,硕士学位论文,中国科学院大学,导师:张劲松,陈受宜,pp.1-2)
Wu S.N.,Wu M.,Dong Q.,Jiang H.Y.,Cai R.H.,and Xiang Y.,2016,Genome-wide identification,classification and ex pression analysis of the PHD-finger protein family in Populus trichocarpa,Gene,575(1):75-89
Xiao H.B.,2012,Effects of RNA interference of a multiple-stress responsive gene,Os Msr16,in rice,Thesis for M.S.,Sichuan Agriculture University,Supervisor:Chen R.J.,and Xia X.J.,pp.41-50(肖宏博,2012,水稻多逆境响应基因Os Msr16的干扰表达研究,硕士学位论文,四川农业大学,导师:陈荣军,夏新界,pp.41-50)
Zhang F.,Yang Z.N.,and Zhang S.,2009,Genome-wide analysis of PHD-finger protein family in Arabidopsis thaliana,Yunnan Zhiwu Yanjiu(Acta Botanica Yunnanica),31(3):227-238(张帆,杨仲南,张森,2009,拟南芥PHD-finger蛋白家族的全基因组分析,云南植物研究,31(3):227-238)
Zhang X.,Li M.J.,Zhang B.,Yin X.M.,Wang M.L.,and Xia X.J.,2016,Possibility study on improving salt tolerance of rice by overexpressing PHD-finger transcription factor gene Os M-sr16,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(7):1820-1827(张新,李明娟,张斌,殷绪明,王曼玲,夏新界,2016,水稻PHD-finger转录因子基因Os Msr16增强耐盐性的可能性研究,基因组学与应用生物学,35(7):1820-1827)