高粱LEA基因家族的鉴定及表达分析
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摘要
有研究表明,干旱、低温和盐等环境胁迫能够诱导LEA基因的表达。为了探索LEA基因家族在高粱响应外界刺激过程中起到的作用,本研究通过生物信息学的方法对LEA基因家族在高粱全基因组水平进行鉴定和分析,于高粱全基因组中共鉴定出35个基因家族成员,不均匀地分布于高粱8条染色体上,结合系统进化树和保守结构域分析结果,将高粱LEA基因家族成员分为7组。亲水性分析和结构无序性预测表明高粱LEA蛋白绝大多数为亲水性且结构无序。基因结构分析显示了各分组基因结构上的保守性。高粱LEA基因的启动子分析发现了一些与激素和非生物胁迫响应相关的顺式作用元件。对激素和干旱胁迫下高粱LEA基因的表达分析发现外界胁迫能够诱导部分高粱LEA基因的表达。
A large number of studies have indicated that environmental stresses such as drought,low temperature and salt can induce the expression of LEA gene. In order to explore their roles in response to external stimuli in sorghum,LEA gene family was identified and analyzed by bioinformatics at the sorghum genome level. A total of 35 LEA gene family members were found in the sorghum genome,which were unevenly distributed on 8 chromosomes of sorghum. According to the results of phylogenetic tree and conserved domain analysis,the sorghum LEA gene family members were divided into 7 groups. Hydrophilic analysis and structural disorder prediction indicated that most of the sorghum LEA proteins were hydrophilic and structurally disordered. Gene structure analysis revealed structural conservation of each grouped gene. Promoter analysis found some cis-acting elements associated with hormonal and abiotic stress. The expression analysis of LEA gene under hormone and drought stress showed that external stress could induce the expression of some LEA genes.
A large number of studies have indicated that environmental stresses such as drought,low temperature and salt can induce the expression of LEA gene. In order to explore their roles in response to external stimuli in sorghum,LEA gene family was identified and analyzed by bioinformatics at the sorghum genome level. A total of 35 LEA gene family members were found in the sorghum genome,which were unevenly distributed on 8 chromosomes of sorghum. According to the results of phylogenetic tree and conserved domain analysis,the sorghum LEA gene family members were divided into 7 groups. Hydrophilic analysis and structural disorder prediction indicated that most of the sorghum LEA proteins were hydrophilic and structurally disordered. Gene structure analysis revealed structural conservation of each grouped gene. Promoter analysis found some cis-acting elements associated with hormonal and abiotic stress. The expression analysis of LEA gene under hormone and drought stress showed that external stress could induce the expression of some LEA genes.
引文
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[27]Liu Y,Wang L,Xing X,et al.ZmLEA3,a multifunc-tional group 3 LEA protein from maize(Zea mays L.),is involved in biotic and abiotic stresses[J].Plant Cell Physiol,2013,54(6):944-959.
[28]Houde M,Dallaire S,N′Dong D,et al.Overexpres-sion of the acidic dehydrin WCOR410 improves freezing tolerance in transgenic strawberry leaves[J].Plant Bio-technol J,2004,2(5):381-387.
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[30]Hara M,Terashima S,Fukaya T,et al.Enhancement of cold tolerance and inhibition of lipid peroxidation by citrus dehydrin in transgenic tobacco[J].Planta,2003,217(2):290-298.
[31]Wang M,Li P,Li C,et al.SiLEA14,a novel atypical LEA protein,confers abiotic stress resistance in foxtail millet[J].BMC Plant Biol,2014,14(1):290.
[32]Liang J,Zhou M,Zhou X,et al.JcLEA,a novel LEA-like protein from Jatropha curcas,confers a high level of tolerance to dehydration and salinity in Arabidopsis thali-ana[J].Plos One,2013,8(12):e83056.
[33]Goyal K,Walton L J,Tunnacliffe A.LEA proteins prevent protein aggregation due to water stress[J].Bio-chem J,2005,388(1):151-157.
[34]Grelet J,Benamar A,Teyssier E,et al.Identification in pea seed mitochondria of a late-embryogenesis abun-dant protein able to protect enzymes from drying[J].Plant Physiol,2005,137(1):157-167.
[35]Reyes J L,Gil J V,Garay Arroyo A,et al.Hydrophil-ins from distant organisms can protect enzymatic activi-ties from water limitation effects in vitro[J].Plant Cell Environ,2010,28(6):709-718.
[36]Imai R,Chang L,Ohta A,et al.A LEA-class gene of tomato confers salt and freezing tolerance when ex-pressed in Saccharomyces cerevisiae[J].Gene,1996,170(2):243-248.
[37]Zhang L,Ohta A,Takagi M,et al.Expression of plant group 2 and group 3 LEA genes in Saccharomyces cerevisiae revealed functional divergence among LEA pro-teins[J].J Biochem,2000,127(4):611-616.
[38]Shih M D,Lin S C,Hsieh J S,et al.Gene cloning and characterization of a soybean(Glycine max L.)LEAprotein,GmPM16[J].Plant Mol Biol,2004,56(5):689-703.
[39]Liu Y,Chakrabortee S,Li R,et al.Both plant and ani-mal LEA proteins act as kinetic stabilisers of polygluta-mine-dependent protein aggregation[J].FEBS Lett,2011,585(4):630-634.
[40]Wang X S,Zhu H B,Jin G L,et al.Genome-scale identification and analysis of LEA genes in rice(Oryza sativa L.)[J].Plant Sci,2007,172(2):414-420.
[2]Bray E A.Molecular responses to water deficit[J].Plant Physiol,1993,103(4):1035-1040.
[3]Bateman A,Birney E,Durbin R,et al.The Pfam pro-tein families database[J].Nucleic Acids Res,2000,28(1):263-266.
[4]Hundertmark M,Hincha D K.LEA(Late Embryogen-esis Abundant)proteins and their encoding genes in Arabidopsis thaliana[J].BMC Genom,2008,9(1):118-120.
[5]Yadira O C,JoséL R,Covarrubias A A.Late embryo-genesis abundant proteins:versatile players in the plant adaptation to water limiting environments[J].Plant Sig-nal Behav,2011,6(4):586-589.
[6]Jean-Marie M,Petter G,Pia H.Structural investiga-tion of disordered stress proteins.Comparison of full-length dehydrins with isolated peptides of their con-served segments[J].Plant Physiol,2006,141(2):638-650.
[7]Garay-Arroyo A,Colmenero-Flores J M,Garciarrubio A,et al.Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water defi-cit[J].J Biol Chem,2000,275(8):5668-5674.
[8]Yadira O C,Francisco C,JoséLuis R,et al.Function-al analysis of the group 4 late embryogenesis abundant proteins reveals their relevance in the adaptive response during water deficit in Arabidopsis[J].Plant Physiol,2011,154(4):373-390.
[9]Hand S C,Menze M A,Toner M,et al.LEA proteins during water stress:not just for plants anymore[J].An-nu Rev Physiol,2010,73(73):115-134.
[10]Sun X,Rikkerink E H A,Jones W T,et al.Multifari-ous roles of intrinsic disorder in proteins illustrate its broad impact on plant biology[J].Plant Cell,2013,25(1):38-55.
[11]Tompa P,Bánki P,Bokor M,et al.Protein-water and protein-buffer interactions in the aqueous solution of an intrinsically unstructured plant dehydrin:NMR intensity and DSC aspects[J].Biophys J,2006,91(6):2243-2249.
[12]Adrien C,Ga L P,Martine N,et al.The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress[J].Plant Cell,2014,26(7):3148-3166.
[13]Sohini C,Rashmi T,Matthew W,et al.Intrinsically disordered proteins as molecular shields[J].Mol Bio-syst,2011,8(1):210-219.
[14]Cao J,Li X.Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato(Solanum lycopersicum)[J].Planta,2015,241(3):757-772.
[15]Kentaro S,Nikolai Kirilov C,Sakae T,et al.Identifi-cation of a novel LEA protein involved in freezing toler-ance in wheat[J].Plant Cell Physiol,2014,55(1):136-147.
[16]Li X,Cao J.Late embryogenesis abundant(LEA)gene family in maize:identification,evolution,and expres-sion profiles[J].Plant Mol Biol Rep,2016,34(1):15-28.
[17]Wu C,Hu W,Yan Y,et al.The late embryogenesis abundant protein family in cassava(Manihot esculenta Crantz):genome-wide characterization and expression during abiotic stress[J].Molecules,2018,23(5):1196.
[18]Finn R D,Jody C,Eddy S R.HMMER web server:in-teractive sequence similarity searching[J].Nucleic Ac-ids Res,2011,39(Web Server issue):29-37.
[19]Dosztányi Z,Csizmók V,Tompa P,et al.The pair-wise energy content estimated from amino acid composi-tion discriminates between folded and intrinsically un-structured proteins[J].J Mol Biol,2005,347(4):827-839.
[20]Gasteiger E,Gattiker A,Hoogland C,et al.ExPASy:the proteomics server for in-depth protein knowledge and analysis[J].Nucleic Acids Res,2003,31(13):3784-3788
[21]Yu C S,Chen Y C,Lu C H,et al.Prediction of pro-tein subcellular localization[J].Proteins,2006,64(3):643-651.
[22]Hu B,Jin J,Guo A Y,et al.GSDS 2.0:an upgraded gene feature visualization server[J].Bioinformatics,2015,31(8):1296-1297.
[23]Magali L,Patrice D,Gert T,et al.PlantCARE,a da-tabase of plant cis-acting regulatory elements and a por-tal to tools for in silico analysis of promoter sequences[J].Nucleic Acids Res,2002,30(1):325-327.
[24]Kosov?K,V?T?M S P,It P?I.Wheat and barley dehydrins under cold,drought,and salinity--what can LEA-II proteins tell us about plant stress response?[J].Front Plant Sci,2014,5(343):343.
[25]Duan J,Cai W,Park S.OsLEA3-2,an abiotic stress induced gene of rice plays a key role in salt and drought tolerance[J].Plos One,2012,7(9):e45117.
[26]Liu Y,Liang J,Sun L,et al.Group 3 LEA protein,ZmLEA3,is involved in protection from low tempera-ture stress[J].Front Plant Sci,2016,7(190):190.
[27]Liu Y,Wang L,Xing X,et al.ZmLEA3,a multifunc-tional group 3 LEA protein from maize(Zea mays L.),is involved in biotic and abiotic stresses[J].Plant Cell Physiol,2013,54(6):944-959.
[28]Houde M,Dallaire S,N′Dong D,et al.Overexpres-sion of the acidic dehydrin WCOR410 improves freezing tolerance in transgenic strawberry leaves[J].Plant Bio-technol J,2004,2(5):381-387.
[29]Sivamani E,Bahieldin A,Wraith J M,et al.Improved biomass productivity and water use efficiency under wa-ter deficit conditions in transgenic wheat constitutively expressing the barley HVA1 gene[J].Plant Sci,2000,155(1):1-9.
[30]Hara M,Terashima S,Fukaya T,et al.Enhancement of cold tolerance and inhibition of lipid peroxidation by citrus dehydrin in transgenic tobacco[J].Planta,2003,217(2):290-298.
[31]Wang M,Li P,Li C,et al.SiLEA14,a novel atypical LEA protein,confers abiotic stress resistance in foxtail millet[J].BMC Plant Biol,2014,14(1):290.
[32]Liang J,Zhou M,Zhou X,et al.JcLEA,a novel LEA-like protein from Jatropha curcas,confers a high level of tolerance to dehydration and salinity in Arabidopsis thali-ana[J].Plos One,2013,8(12):e83056.
[33]Goyal K,Walton L J,Tunnacliffe A.LEA proteins prevent protein aggregation due to water stress[J].Bio-chem J,2005,388(1):151-157.
[34]Grelet J,Benamar A,Teyssier E,et al.Identification in pea seed mitochondria of a late-embryogenesis abun-dant protein able to protect enzymes from drying[J].Plant Physiol,2005,137(1):157-167.
[35]Reyes J L,Gil J V,Garay Arroyo A,et al.Hydrophil-ins from distant organisms can protect enzymatic activi-ties from water limitation effects in vitro[J].Plant Cell Environ,2010,28(6):709-718.
[36]Imai R,Chang L,Ohta A,et al.A LEA-class gene of tomato confers salt and freezing tolerance when ex-pressed in Saccharomyces cerevisiae[J].Gene,1996,170(2):243-248.
[37]Zhang L,Ohta A,Takagi M,et al.Expression of plant group 2 and group 3 LEA genes in Saccharomyces cerevisiae revealed functional divergence among LEA pro-teins[J].J Biochem,2000,127(4):611-616.
[38]Shih M D,Lin S C,Hsieh J S,et al.Gene cloning and characterization of a soybean(Glycine max L.)LEAprotein,GmPM16[J].Plant Mol Biol,2004,56(5):689-703.
[39]Liu Y,Chakrabortee S,Li R,et al.Both plant and ani-mal LEA proteins act as kinetic stabilisers of polygluta-mine-dependent protein aggregation[J].FEBS Lett,2011,585(4):630-634.
[40]Wang X S,Zhu H B,Jin G L,et al.Genome-scale identification and analysis of LEA genes in rice(Oryza sativa L.)[J].Plant Sci,2007,172(2):414-420.