花生FAT基因家族的全基因组分析
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摘要
酰基-ACP硫酯酶(fatty acyl-ACP thioesterase,FAT)是控制植物种子油脂合成的关键酶,根据其氨基酸序列和底物特异性不同可分为FATA和FATB两类。为了更深入了解花生FAT(Ah FAT)的特点与功能,本研究对Ah FAT家族基因进行了全基因组生物信息学分析。在花生基因组中共有20个FAT基因,不均匀分布在2个基因组的12条染色体上。20个Ah FATs可以分为Ah FATA和Ah FATB两个亚家族,Ah FATA亚家族有2个基因,Ah FATB亚家族有18个基因。Ah FATA家族基因具有6或8个外显子,Ah FATB家族基因结构较为复杂,外显子数目5~8个;Ah FATs都不具有跨膜结构域但是都具有保守的Acyl-ACP_TE结构域。对Ah FAT家族基因进行可变剪接分析,发现只有少数发生了可变剪接,且具有组织特异性。对Ah FATs表达模式分析的结果显示,Ah FATAs和Ah FATBs都在种子发育后期表达量较高。
Fatty acyl-ACP thioesterase(FAT) is the key enzyme regulating the synthesis of plant seed oil. According to the amino acid sequence and substrate specificity,FAT is divided into FATA and FATB subfamily. In order to better understand the characteristics of Ah FAT gene family,the bioinformatics analysis was carried out. There were 20 Ah FAT genes in the peanut genome,which heterogeneously distributed on 12 chromosomes in the two genomes. The twenty Ah FAT genes could be divided into Ah FATA and Ah FATB subfamily,which had 2 and 18 members respectively. The Ah FATA subfamily owned 6 or 8 exons,and the Ah FATB subfamily had complex gene structures with 5 ~ 8 exons. None of the Ah FATs had transmembrane domains,but they all owned the conserved Acyl-ACP_TE domain. The alternative splicing analysis of Ah FAT gene family revealed that only a few Ah FATs undergone alternative splicing and they had different splicing types in different tissues. The Ah FATs expression pattern analysis results showed that both Ah FATAs and Ah FATBs expressed at higher levels in the later stage of seed development.
Fatty acyl-ACP thioesterase(FAT) is the key enzyme regulating the synthesis of plant seed oil. According to the amino acid sequence and substrate specificity,FAT is divided into FATA and FATB subfamily. In order to better understand the characteristics of Ah FAT gene family,the bioinformatics analysis was carried out. There were 20 Ah FAT genes in the peanut genome,which heterogeneously distributed on 12 chromosomes in the two genomes. The twenty Ah FAT genes could be divided into Ah FATA and Ah FATB subfamily,which had 2 and 18 members respectively. The Ah FATA subfamily owned 6 or 8 exons,and the Ah FATB subfamily had complex gene structures with 5 ~ 8 exons. None of the Ah FATs had transmembrane domains,but they all owned the conserved Acyl-ACP_TE domain. The alternative splicing analysis of Ah FAT gene family revealed that only a few Ah FATs undergone alternative splicing and they had different splicing types in different tissues. The Ah FATs expression pattern analysis results showed that both Ah FATAs and Ah FATBs expressed at higher levels in the later stage of seed development.
引文
[1]Chen G,Peng Z Y,Shan L,et al.Functional expression analysis of an acyl-ACP thioesterase Fat B1 from Arachis hypogaea L.seeds in Escherichia coli[J].Journal of Food Agriculture&Environment,2012,10(3):332-336.
[2]Chen G,Peng Z Y,Shan L,et al.Cloning of acyl-ACP thioesterase Fat A from Arachis hypogaea L.and its expression in Escherichia coli[J].Journal of Biomedicine&Biotechnology,2012,2012(2):161-177.
[3]Wen Q,Lei Y,Huang J,et al.Molecular cloning and characterization of an acyl-ACP thioesterase gene(Ah Fat B1)from allotetraploid peanut(Arachis hypogaea L.)[J].African Journal of Biotechnology,2012,11(77):14123-14131.
[4]Salas J J,Ohlrogge J B.Characterization of substrate specificity of plant Fat A and Fat B acyl-ACP thioesterases[J].Archives of Biochemistry&Biophysics,2002,403(1):25-34.
[5]Harwood J.Fatty acid biosynthesis[M]//Murphy D J.Plant lipids:biology,utilization and manipulation.Oxford:Blackwell Publishing,2005:27-66.
[6]刘美兰,龙洪旭,谭晓风.油桐Vf FATB1基因的克隆及其功能的初步分析[J].植物生理学报,2016,52(6):895-904.
[7]王威浩,谭晓风.植物脂酰-酰基载体蛋白硫酯酶研究综述[J].经济林研究,2009,27(2):118-124.
[8]Salas J J,Martínez-Force E,Harwood J L,et al.Biochemistry of high stearic sunflower,a new source of saturated fats[J].Progress in Lipid Research,2014,55(7):30-42.
[9]Inaba Y,Nakahigashi K,Ito T,et al.Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium-chain-specific thioesterase and acyl carrier protein[J].Phycological Research,2017,65(1):94-99.
[10]元冬娟,吴湃,江黎明.高等植物的酰基-ACP硫酯酶研究进展[J].中国油料作物学报,2009,31(1):103-108.
[11]Ghosh S K,Bhattacharjee A,Jha J K,et al.Characterization and cloning of a stearoyl/oleoyl specific fatty acyl-acyl carrier protein thioesterase from the seeds of Madhuca longifolia(latifolia)[J].Plant Physiology&Biochemistry,2007,45(12):887-897.
[12]Serrano-Vega M,Garces R F E.Cloning,characterization and structural model of a Fat A-type thioesterase from sunflower seeds(Helianthus annuus L.)[J].Planta,2005,221(6):868-880.
[13]Dong S,Huang J,Li Y,et al.Cloning,characterization,and expression analysis of acyl-acyl carrier protein(ACP)-thioesterase B from seeds of Chinese Spicehush(Lindera communis)[J].Gene,2014,542(1):16-22.
[14]Zhou Z,Zhang D Q,Lu M Z.Cloning and expression analysis of Pt FATB gene encoding the acyl-acyl carrier protein thioesterase in Populus tomentosa Carr.[J].Journal of Genetics and Genomics,2007,34(3):267-273.
[15]Bonaventure G,Bao X,Ohlrogge J,et al.Metabolic responses to the reduction in palmitate caused by disruption of the FATB gene in Arabidopsis[J].Plant Physiology,2004,135(3):1269-1279.
[16]Wu P Z,Li J,Qian W,et al.Cloning and functional characterization of an acyl-acyl carrier protein thioesterase(Jc FATB1)from Jatropha curcas[J].Tree Physiology,2009,29(10):1299-1305.
[17]李璐,梁倩,安茜,等.紫苏脂肪酸硫酯酶基因Pf Fat A生物信息学及其表达特性分析[J].华北农学报,2017,32(2):104-108.
[18]肖勇,杨耀东,夏薇,等.椰子Acyl-ACP硫酯酶相关基因的克隆及其表达分析[J].广东农业科学,2013,40(12):149-152.
[19]Sánchez-García A,Moreno-Pérez A J,Muro-Pastor A M,et al.Acyl-ACP thioesterases from castor(Ricinus communis L.):an enzymatic system appropriate for high rates of oil synthesis and accumulation[J].Phytochemistry,2010,71(9):860-869.
[20]Tan K W M,Yuan K L.Expression of the heterologous Dunaliella tertiolecta,fatty acyl-ACP thioesterase leads to increased lipid production in Chlamydomonas reinhardtii[J].Journal of Biotechnology,2017,247:60-67.
[21]Mayer K M,Shanklin J.Identification of amino acid residues involved in substrate specificity of plant acyl-ACP thioesterases using a bioinformatics-guided approach[J].BMC Plant Biology,2007,7(1):1.
[22]Dong S,Liu Y,Xiong B,et al.Transcriptomic analysis of a potential bioenergy tree,Pistacia chinensis Bunge,and identification of candidate genes involved in the biosynthesis of oil[J].Bioenergy Research,2016,9(3):740-749.
[23]程涛,杨建明,刘辉,等.拟南芥硫酯酶基因(atfata)在大肠杆菌中的表达及其对游离脂肪酸合成的影响[J].应用与环境生物学报,2011,17(4):568-571.
[24]陈高.多不饱和脂肪酸生物合成途径相关酶基因的克隆及在集胞藻PCC6803中的表达研究[D].济南:山东师范大学,2012.
[25]D9rmann P,Voelker T A,Ohlrogge J B.Accumulation of palmitate in Arabidopsis mediated by the acyl-acyl carrier protein thioesterase FATB1[J].Plant Physiology,2000,123(2):637-644.
[26]张小茜.花生Ah FAD2基因的RNAi抑制表达遗传转化研究[D].济南:山东师范大学,2007.
[27]李晓斐.花生脂肪酸合成关键酶(KASI、Fat B)基因的克隆、序列分析与ah FAD2B遗传转化的研究[D].泰安:山东农业大学,2011.
[28]Moreno-Pérez A J,Venegas-Calerón M,Vaistij F E,et al.Reduced expression of Fat A thioesterases in Arabidopsis affects the oil content and fatty acid composition of the seeds[J].Planta,2012,235(3):629-639.
[29]Huynh T T,Pirtle R M,Chapman K D.Expression of a Gossypium hirsutum c DNA encoding a Fat B palmitoyl-acyl carrier protein thioesterase in Escherichia coli[J].Plant Physiology&Biochemistry,2002,40(1):1-9.
[30]李昊远,郝翠翠,潘丽娟,等.花生酰基载体蛋白硫酯酶(FATB2)基因的克隆与表达分析[J].花生学报,2017,46(4):7-14.
[31]Ramanouskaya T V,Grinev V V.The determinants of alternative RNA splicing in human cells[J].Molecular Genetics&Genomics,2017(3):1-21.
[32]周晏秋.几种经济植物可变剪接预测及分析[D].武汉:中南民族大学,2015.
[33]Wang Q,Silver P A.Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation[J].Cell Cycle,2010,9(22):4419-4421.
[34]Zhang X N,Mount S M.Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development[J].Plant Physiology,2009,150(3):1450-1458.
[2]Chen G,Peng Z Y,Shan L,et al.Cloning of acyl-ACP thioesterase Fat A from Arachis hypogaea L.and its expression in Escherichia coli[J].Journal of Biomedicine&Biotechnology,2012,2012(2):161-177.
[3]Wen Q,Lei Y,Huang J,et al.Molecular cloning and characterization of an acyl-ACP thioesterase gene(Ah Fat B1)from allotetraploid peanut(Arachis hypogaea L.)[J].African Journal of Biotechnology,2012,11(77):14123-14131.
[4]Salas J J,Ohlrogge J B.Characterization of substrate specificity of plant Fat A and Fat B acyl-ACP thioesterases[J].Archives of Biochemistry&Biophysics,2002,403(1):25-34.
[5]Harwood J.Fatty acid biosynthesis[M]//Murphy D J.Plant lipids:biology,utilization and manipulation.Oxford:Blackwell Publishing,2005:27-66.
[6]刘美兰,龙洪旭,谭晓风.油桐Vf FATB1基因的克隆及其功能的初步分析[J].植物生理学报,2016,52(6):895-904.
[7]王威浩,谭晓风.植物脂酰-酰基载体蛋白硫酯酶研究综述[J].经济林研究,2009,27(2):118-124.
[8]Salas J J,Martínez-Force E,Harwood J L,et al.Biochemistry of high stearic sunflower,a new source of saturated fats[J].Progress in Lipid Research,2014,55(7):30-42.
[9]Inaba Y,Nakahigashi K,Ito T,et al.Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium-chain-specific thioesterase and acyl carrier protein[J].Phycological Research,2017,65(1):94-99.
[10]元冬娟,吴湃,江黎明.高等植物的酰基-ACP硫酯酶研究进展[J].中国油料作物学报,2009,31(1):103-108.
[11]Ghosh S K,Bhattacharjee A,Jha J K,et al.Characterization and cloning of a stearoyl/oleoyl specific fatty acyl-acyl carrier protein thioesterase from the seeds of Madhuca longifolia(latifolia)[J].Plant Physiology&Biochemistry,2007,45(12):887-897.
[12]Serrano-Vega M,Garces R F E.Cloning,characterization and structural model of a Fat A-type thioesterase from sunflower seeds(Helianthus annuus L.)[J].Planta,2005,221(6):868-880.
[13]Dong S,Huang J,Li Y,et al.Cloning,characterization,and expression analysis of acyl-acyl carrier protein(ACP)-thioesterase B from seeds of Chinese Spicehush(Lindera communis)[J].Gene,2014,542(1):16-22.
[14]Zhou Z,Zhang D Q,Lu M Z.Cloning and expression analysis of Pt FATB gene encoding the acyl-acyl carrier protein thioesterase in Populus tomentosa Carr.[J].Journal of Genetics and Genomics,2007,34(3):267-273.
[15]Bonaventure G,Bao X,Ohlrogge J,et al.Metabolic responses to the reduction in palmitate caused by disruption of the FATB gene in Arabidopsis[J].Plant Physiology,2004,135(3):1269-1279.
[16]Wu P Z,Li J,Qian W,et al.Cloning and functional characterization of an acyl-acyl carrier protein thioesterase(Jc FATB1)from Jatropha curcas[J].Tree Physiology,2009,29(10):1299-1305.
[17]李璐,梁倩,安茜,等.紫苏脂肪酸硫酯酶基因Pf Fat A生物信息学及其表达特性分析[J].华北农学报,2017,32(2):104-108.
[18]肖勇,杨耀东,夏薇,等.椰子Acyl-ACP硫酯酶相关基因的克隆及其表达分析[J].广东农业科学,2013,40(12):149-152.
[19]Sánchez-García A,Moreno-Pérez A J,Muro-Pastor A M,et al.Acyl-ACP thioesterases from castor(Ricinus communis L.):an enzymatic system appropriate for high rates of oil synthesis and accumulation[J].Phytochemistry,2010,71(9):860-869.
[20]Tan K W M,Yuan K L.Expression of the heterologous Dunaliella tertiolecta,fatty acyl-ACP thioesterase leads to increased lipid production in Chlamydomonas reinhardtii[J].Journal of Biotechnology,2017,247:60-67.
[21]Mayer K M,Shanklin J.Identification of amino acid residues involved in substrate specificity of plant acyl-ACP thioesterases using a bioinformatics-guided approach[J].BMC Plant Biology,2007,7(1):1.
[22]Dong S,Liu Y,Xiong B,et al.Transcriptomic analysis of a potential bioenergy tree,Pistacia chinensis Bunge,and identification of candidate genes involved in the biosynthesis of oil[J].Bioenergy Research,2016,9(3):740-749.
[23]程涛,杨建明,刘辉,等.拟南芥硫酯酶基因(atfata)在大肠杆菌中的表达及其对游离脂肪酸合成的影响[J].应用与环境生物学报,2011,17(4):568-571.
[24]陈高.多不饱和脂肪酸生物合成途径相关酶基因的克隆及在集胞藻PCC6803中的表达研究[D].济南:山东师范大学,2012.
[25]D9rmann P,Voelker T A,Ohlrogge J B.Accumulation of palmitate in Arabidopsis mediated by the acyl-acyl carrier protein thioesterase FATB1[J].Plant Physiology,2000,123(2):637-644.
[26]张小茜.花生Ah FAD2基因的RNAi抑制表达遗传转化研究[D].济南:山东师范大学,2007.
[27]李晓斐.花生脂肪酸合成关键酶(KASI、Fat B)基因的克隆、序列分析与ah FAD2B遗传转化的研究[D].泰安:山东农业大学,2011.
[28]Moreno-Pérez A J,Venegas-Calerón M,Vaistij F E,et al.Reduced expression of Fat A thioesterases in Arabidopsis affects the oil content and fatty acid composition of the seeds[J].Planta,2012,235(3):629-639.
[29]Huynh T T,Pirtle R M,Chapman K D.Expression of a Gossypium hirsutum c DNA encoding a Fat B palmitoyl-acyl carrier protein thioesterase in Escherichia coli[J].Plant Physiology&Biochemistry,2002,40(1):1-9.
[30]李昊远,郝翠翠,潘丽娟,等.花生酰基载体蛋白硫酯酶(FATB2)基因的克隆与表达分析[J].花生学报,2017,46(4):7-14.
[31]Ramanouskaya T V,Grinev V V.The determinants of alternative RNA splicing in human cells[J].Molecular Genetics&Genomics,2017(3):1-21.
[32]周晏秋.几种经济植物可变剪接预测及分析[D].武汉:中南民族大学,2015.
[33]Wang Q,Silver P A.Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation[J].Cell Cycle,2010,9(22):4419-4421.
[34]Zhang X N,Mount S M.Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development[J].Plant Physiology,2009,150(3):1450-1458.