Home > Archive>Volume 26, Issue 2, 2018 >107-115. DOI:10.11926/jtsb.3804
PDF HTML XML Export Cite reminder
Bioinformatics Analysis of PEPC Gene Family in Arachis duranensis
Author:
  • Article
    • | |
  • Metrics
    • |
  • Reference [29]
    • |
  • Related [20]
    • |
  • Cited by
    • | |
  • Comments
    Abstract:

    To understand the function of phosphoenolpyruvate carboxylase (PEPC) in peanut, PEPC sequences of the diploid progenitor Arachis duranensis genome database were analyzed. Nine gene family members were found, and their sequence lengths ranged from 3 584 to 12 956 bp with 702-3 168 bp open reading frame (ORF), distributed in the 3, 5, 7, 8, 9, and 10th chromosomes. In the amino acid sequences of AdPEPC proteins, there were conserved domains, such as HCO3- binding sites and PEP binding sites, et al. According to the sequence characteristics, AdPEPC proteins could be divided into 3 groups as plant type, bacterium type and short sequence type. Protein homologies of the same type were high, and the number of intron and exon in gene structures was similar. Gene expression analysis showed that the expressions of most members were high in flowers or stems. AdPEPC1;2 and AdPEPC4;2 had the highest expression in stem. Other family members, especially AdPEPC2, AdPEPC1;5 and AdPEPC1;3, expressions were significantly higher in flower than other tissues. AdPEPC1;5 expression was not detected in leaf. No expression of AdPEPC3 was detected in root, stem, leaf and flower, and it was presumed to be pseudogenes based on its gene structure. These would lay a foundation for further study on the functions of AdPEPC family genes.

    Reference
    [1] O'Leary B, Rao S K, Plaxton W C. Phosphorylation of bacterial-type phosphoenolpyruvate carboxylase at Ser425 provides a further tier of enzyme control in developing castor oil seeds[J]. Biochem J, 2011, 433(1):65-74. doi:10.1042/BJ20101361.
    [2] IZUI K, MATSUMURA H, FURUMOTO T, et al. Phosphoenol pyruvate carboxylase:A new era of structural biology[J]. Annu Rev Plant Biol, 2004, 55:69-84. doi:10.1146/annurev.arplant.55.031903.141619.
    [3] GUAN J J, CHEN J Q, WANG X F. Bioinformatic analysis on bacterial-type phosphoenolpyruate carboxylase in plants[J]. Acta Agric Zhejiang, 2011, 23(2):203-208. doi:10.3969/j.issn.1004-1524.2011.02.002. 关晶晶, 陈锦清, 汪小福. 植物细菌型磷酸烯醇式丙酮酸羧化酶基因的生物信息学分析[J]. 浙江农业学报, 2011, 23(2):203-208. doi:10.3969/j.issn.1004-1524.2011.02.002.
    [4] WANG N, ZHONG X J, CONG Y H, et al. Genome-wide analysis of phosphoenolpyruvate carboxylase gene family and their response to abiotic stresses in soybean[J]. Sci Rep, 2016, 6:38448. doi:10.1038/srep38448.
    [5] MURAMATSU M, SUZUKI R, YAMAZAKI T, et al. Comparison of plant-type phosphoenolpyruvate carboxylases from rice:Identification of two plant-specific regulatory regions of the allosteric enzyme[J]. Plant Cell Physiol, 2015, 56(3):468-480. doi:10.1093/pcp/pcu189.
    [6] SÁNCHEZ R, CEJUDO F J. Identification and expression analysis of a gene encoding a bacterial-type phosphoenolpyruvate carboxylase from Arabidopsis and rice[J]. Plant Physiol, 2003, 132(2):949-957. doi:10.1104/pp.102.019653.
    [7] DONG L Y, MASUDA T, KAWAMURA T, et al. Cloning, expression, and characterization of a root-form phosphoenolpyruvate carboxylase from Zea mays:Comparison with the C4-form enzyme[J]. Plant Cell Physiol, 1998, 39(8):865-873. doi:10.1093/oxfordjournals.pcp.a029446.
    [8] BESNARD G, PINÇON G, D'HONT A, et al. Characterisation of the phosphoenolpyruvate carboxylase gene family in sugarcane (Saccharum spp.)[J]. Theor Appl Genet, 2003, 107(3):470-478. doi:10.1007/s00122-003-1268-2.
    [9] SULLIVAN S, JENKINS G I, NIMMO H G. Roots, cycles and leaves:Expression of the phosphoenolpyruvate carboxylase kinase gene family in soybean[J]. Plant Physiol, 2004, 135(4):2078-2087. doi:10.1104/pp.104.042762.
    [10] YU S L, PAN L J, YANG Q L, et al. Identification and expression analysis of the phosphoenolpyruvate carboxylase gene family in peanut (Arachis hypogaea L.)[J]. Agric Sci China, 2010, 9(4):477-487. doi:10.1016/S1671-2927(09)60120-6.
    [11] KANDOI D, MOHANTY S, GOVINDJEE, et al. Towards efficient photosynthesis:Overexpression of Zea mays phosphoenolpyruvate carboxylase in Arabidopsis thaliana[J]. Photosynth Res, 2016, 130(1/2/3):47-72. doi:10.1007/s11120-016-0224-3.
    [12] ZHANG X J, WANG G C, HE L W, et al. Cloning and analysis of the phosphoenolpyruvate carboxylase gene of Porphyra haitanesis (Rho-dophyta)[J]. Mar Sci, 2011, 35(4):70-76. 张晓娟, 王广策, 何林文, 等. 坛紫菜磷酸烯醇式丙酮酸羧化酶基因的克隆与序列分析[J]. 海洋科学, 2011, 35(4):70-76.
    [13] MASUMOTO C, MIYAZAWA S I, OHKAWA H, et al. Phospho-enolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation[J]. Proc Natl Acad Sci USA, 2010, 107(11):5226-5231. doi:10.1073/pnas.0913127107.
    [14] SUGIHARTO B, SUGIYAMA T. Effects of nitrate and ammonium on gene expression of phosphoenolpyruvate carboxylase and nitrogen metabolism in maize leaf tissue during recovery from nitrogen stress[J]. Plant Physiol, 1992, 98(4):1403-1408. doi:10.1104/pp.98.4.1403.
    [15] ZHANG Z Q, WANG J M, WANG X J, et al. The characteristics of PEPCase activity and accumulation of oil, protein and major protein subunits during seed development of rape (Brassica napus)[J]. Chin J Oil Crop Sci, 2009, 31(1):14-18. doi:10.3321/j.issn:1007-9084.2009.01.003. 张占琴, 王金梅, 王学军, 等. 油菜籽粒发育过程中PEPCase活性与油脂、蛋白及亚基积累的特点[J]. 中国油料作物学报, 2009, 31(1):14-18. doi:10.3321/j.issn:1007-9084.2009.01.003.
    [16] SEBEI K, OUERGHI Z, KALLEL H, et al. Evolution of phosphor-enolpyruvate carboxylase activity and lipid content during seed matu-ration of two spring rapeseed cultivars (Brassica napus L.)[J]. Compts Rendus Biol, 2006, 329(9):719-725. doi:10.1016/j.crvi.2006.06.002.
    [17] GENNIDAKIS S, RAO S, GREENHAM K, et al. Bacterial-and plant-type phosphoenolpyruvate carboxylase polypeptides interact in the hetero-oligomeric Class-2 PEPC complex of developing castor oil seeds[J]. Plant J, 2007, 52(5):839-849. doi:10.1111/j.1365-313X. 2007.03274.x.
    [18] PAN L J, YANG Q L, CHI X Y, et al. Functional analysis of the phosphoenolpyruvate carboxylase on the lipid accumulation of peanut (Arachis hypogaea L.) seeds[J]. J Integr Agric, 2013, 12(1):36-44. doi:10.1016/S2095-3119(13)60203-8.
    [19] ZHANG Y H, MENG Q L, JI C L, et al. Effects of aluminum stress on photosynthesis and active oxygen metabolism in C4 Ppc transgenic rice[J]. Biotechnol Bull, 2014(7):81-85. doi:10.13560/j.cnki.biotech.bull. 1985.2014.07.024. 张云华, 孟庆玲, 计成林, 等. 铝胁迫对转C4磷酸烯醇式丙酮酸羧化酶基因水稻光合作用和活性氧代谢的影响[J]. 生物技术通报, 2014(7):81-85. doi:10.13560/j.cnki.biotech.bull.1985.2014.07.024.
    [20] LIAO B S. Simple analysis of Chinese peanut oil industry competi-tiveness[J]. J Peanut Sci, 2003, 32(Sl):11-15. doi:10.14001/j.issn.1002-4093.2003.s1.003. 廖伯寿. 中国花生油脂产业竞争力浅析[J]. 花生学报, 2003, 32(S1):11-15. doi:10.14001/j.issn.1002-4093.2003.s1.003.
    [21] CHEN X P, LI H J, PANDEY M K, et al. Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens[J]. Proc Natl Acad Sci USA, 2016, 113(24):6785-6790. doi:10.1073/pnas.1600899113.
    [22] SONG H, ZHAO S Z, HOU L, et al. Bioinformatics analysis on LOX genes related to disease resistance in whole genome of Arachis duranensis and Arachis ipaënsis[J]. Shandong Agric Sci, 2015, 47(10):1-7. doi:10.14083/j.issn.1001-4942.2015.10.001. 宋辉, 赵术珍, 侯蕾, 等. 野生花生全基因组抗病相关LOX基因的生物信息学分析[J]. 山东农业科学, 2015, 47(10):1-7. doi:10.14083/j.issn.1001-4942.2015.10.001.
    [23] DASH S, CANNON E K S, KALBERER S R, et al. Peanut base and other bioinformatic resources for peanut[M]//STALKER H T, WILSON R F. Peanuts Genetics, Processing, and Utilization. Boulder, Urbana:AOCS Press, 2016:241-252. doi:10.1016/B978-1-63067-038-2.00008-3.
    [24] GUO A Y, ZHU Q H, CHEN X, et al. GSDS:A gene structure display server[J]. Hereditas (Beijing), 2007, 29(8):1023-1026. doi:10.16288/j.yczz.2007.08.004. 郭安源, 朱其慧, 陈新, 等. GSDS:基因结构显示系统[J]. 遗传, 2007, 29(8):1023-1026. doi:10.16288/j.yczz.2007.08.004.
    [25] WANG Z H, TONG C B, YUAN W Z, et al. Bacterial-type PEPC genes identification and expression in developing seeds from four oil crops[J]. Chin J Oil Crop Sci, 2013, 35(1):8-16,23. doi:10.7505/j. issn.1007-9084.2013.01.002. 王志慧, 童超波, 袁午舟, 等. 四种油料作物中的细菌型PEPC基因的鉴定及在发育种子中的表达[J]. 中国油料作物学报, 2013, 35(1):8-16,23. doi:10.7505/j.issn.1007-9084.2013.01.002.
    [26] XU W X, AHMED S, MORIYAMA H, et al. The importance of the strictly conserved, C-terminal glycine residue in phosphoenolpyruvate carboxylase for overall catalysis:Mutagenesis and truncation of GLY-961 in the sorghum C4 leaf isoform[J]. J Biol Chem, 2006, 218(25):17238-17245. doi:http://dx.doi.org/10.1074/jbc.M602299200.
    [27] PAN L J, LIU F Z, WAN Y S, et al. Expression comparison of the phosphoenolpyruvate carboxylase gene in high oil-content peanut varieties Jihua 4 and its parent[J]. J Peanut Sci, 2015, 44(4):37-41. doi:10.14001/j.issn.1002-4093.2015.04.007. 潘丽娟, 刘风珍, 万勇善, 等. PEPC基因在高油品种吉花4号及其亲本中的表达比较[J]. 花生学报, 2015, 44(4):37-41. doi:10.14001/j.issn.1002-4093.2015.04.007.
    [28] MATSUMURA H, IZUI K, MIZUGUCHI K. A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase:A combined approach to structure-based alignment and model assessment[J]. Protein Eng Des Sel, 2006, 19(9):409-419. doi:10.1093/protein/gzl025.
    [29] IGAWA T, FUJIWARA M, TANAKA I, et al. Characterization of bacterial-type phosphoenolpyruvate carboxylase expressed in male gametophyte of higher plants[J]. BMC Plant Biol, 2010, 10:200. doi:10.1186/1471-2229-10-200.
    Cited by
    Comments
    Comments
    分享到微博
    Submit
Get Citation

涂嘉琦,甘璐,冯兰兰,袁良兵,黎茵.蔓花生PEPC基因家族的生物信息学分析[J].热带亚热带植物学报,2018,26(2):107~115

Copy
Share
Article Metrics
  • Abstract:
  • PDF:
  • HTML:
  • Cited by:
History
  • Received:August 16,2017
  • Revised:November 21,2017
  • Online: March 29,2018
Article QR Code
You are the first4646186 Visitors
Governing Body：中国科学院
Organizer：中国科学院华南植物园 广东省植物学会
Address：Xingke Road 723,Tianhe District,Guangzhou,China
Phone：+86 (0)20-3725 2514
Journal of Tropical and Subtropical Botany ® 2025 All Rights Reserved