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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (9): 1365-1374.doi: 10.3724/SP.J.1006.2019.81087

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide characterization and transcriptional analysis of the protein disulfide isomerase-like genes in barley (Hordeum vulgare)

SHI Li-Jie1,2,JIANG Cong-Cong2,WANG Fang-Mei1,2,YANG Ping2,*(),FENG Zong-Yun1,*()   

  1. 1 Barley Research Center, Colleague of Agronomy, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
    2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2018-12-11 Accepted:2019-04-15 Online:2019-09-12 Published:2019-04-18
  • Contact: Ping YANG,Zong-Yun FENG E-mail:yangping@caas.cn;zyfeng49@126.com
  • Supported by:
    This study was supported by the Fundamental Research Funds for Central Non-Profit of Chinese Academy of Agricultural Sciences(S2018YC01);This study was supported by the Fundamental Research Funds for Central Non-Profit of Chinese Academy of Agricultural Sciences(S2018PY03);the China Agriculture Research System(CARS-05)

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Abstract:

Protein disulfide isomerase (PDI) and PDI-like proteins (PDILs) belong to a protein family that are usually located on endoplasmic reticulum and highly conserved across eukaryotes. The main function of PDILs is catalyzing the redox and isomerization of disulfide bonds in protein precursors via the thioredoxin (TRX) domain. PDILs have been also reported as chaperones in folding and unfolding of proteins, thus being important in growth and development, as well as biotic or abiotic stress responses of plant. In this study, we identified by bioinformatics analysis 10 members of barley PDILs (HvPDILs), which were subjected for analyzing the physical location, protein structure and subcellular localization. The phylogenetic analysis revealed eight sub-branches of plant PDILs, and barley PDILs showed a high sequence homology with wheat PDILs. The transcriptional analysis revealed large variation of the transcription abundance of PDILs in different tissues and development stages. Notably, mechanical inoculation of Barley mild mosaic virus (BaMMV) resulted in transcriptional re-programming of several HvPDILs. This result suggests the association between PDILs and BaMMV infection, despite that the functional mechanism remains largely unknown and needs further studies.

Key words: barley, protein disulfide isomerase, gene family, barley yellow mosaic virus disease

Table 1

Identified PDI genes in barley genome"

基因名称
Gene name		 水稻同源基因
Rice orthologous gene		 NCBI登录号
Acc. ID		 基因ID
Gene ID		 染色体位置
Chromosomal location		 cDNA全长
Full length cDNA
HvPDIL1-1 OsPDIL1_1 AK357991.1 HORVU4Hr1G043910.1 4H:350262817-350266613 1542
HvPDIL1-2 OSPDIL1_2 AK368066.1 HORVU2Hr1G076390.6 2H:549859450-549862026 1554
HvPDIL1-3 OSPDIL1_4 AK370108.1 HORVU6Hr1G001700.1 6H:5173471-5182932 1764
HvPDIL1-4 OSPDIL1_5 AK366963.1 HORVU7Hr1G026030.2 7H:44299270-44302170 1635
HvPDIL2-1 OSPDIL2_1 AK249580.1 HORVU1Hr1G022810.1 1H:98741192-98744845 1104
HvPDIL2-2 OSPDIL2_3 AK353639.1 HORVU5Hr1G067570.1 5H:513285275-513290639 1323
HvPDIL5-1 OSPDIL5_1 AK250421.1 HORVU4Hr1G056730.1 4H:476590992-476593244 456
HvPDIL5-2 OSPDIL5_2 AK251979.1 HORVU2Hr1G075810.4 2H:545243929-545244816 1245
HvPDIL5-3 OSPDIL5_3 AK249445.1 HORVU6Hr1G059710.3 6H:395564404-395567220 1257
HvPDIL5-4 OSPDIL5_4 AK251501.1 HORVU2Hr1G046000.3 2H:243330620-243337299 1458

Fig. 1

Chromosomal location of HvPDILs The six bars represent the six chromosomes of barley. The gene names and physical locations (Mb) are marked at the right and left side of each chromosome respectively. The chromosome 3H is not shown as PDILs is not identified on it."

Fig. 2

Graphic representation of barley PDIL-likes proteins"

Table 2

Characteristics of barley PDILs protein"

Fig. 3

Phylogenetic tree of PDIL homologous proteins from barley, wheat, rice, maize, and Arabidopsis"

Fig. 4

Transcriptional abundance of HvPDILs in different tissues EMB: embryos; ROO1: roots from seedlings; LEA: shoots from seedlings; INF2: developing inflorescences; NOD, developing tillers, 3rd internode; CAR5: developing grain (5 DAP); CAR15: developing grain (15 DAP); ETI: etiolated seedling, dark cond; LEM: inflorescences, lemma; LOD: inflorescences, lodicule; PAL: dissected inflorescences, palea; EPI: epidermal strips; RAC: Inflorescences, rachis; ROO2: roots; SEN: senescing leaves."

Table 3

Primers used for qPCR and length of amplified fragments"

引物名称
Primer name		 引物序列
Sequence (5'-3')		 退火温度
Tm (°C)		 扩增片段大小
Size of
amplicon (bp)		 备注
Remarks
HvUBC-F AAGCAGCCAGAATGTACAGCGAGAAC 63 152 内参基因
Reference gene
HvUBC-R GGTACAGACCAGCAAAGCCAGAAATG
BaMMV-F GGCACTTTGTGTTATGCAATGG 63 138 检测BaMMV
Check the presence of BaMMV
BaMMV-R TGCCACCCTCAGGTAGGATTAG
HvPDIL1_1-F CGTTGCTTGGTTGAAGGATT 60 199 检测基因表达
Check the expression of HvPDIL1-1
HvPDIL1_1-R GATGGGTGCTAGCTTCTTGC
HvPDIL1_2-F CAGACCCGACCAACCATAAG 60 194 检测基因表达
Check the expression of HvPDIL1-2
HvPDIL1_2-R ATACTCGAAGGCACGGTCAG
引物名称
Primer name		 引物序列
Sequence (5'-3')		 退火温度
Tm (°C)		 扩增片段大小
Size of amplicon (bp)		 备注
Remarks
HvPDIL1_3-F GTGTGGCCATTGTCAGTCAC 60 200 检测基因表达
Check the expression of HvPDIL1-3
HvPDIL1_3-R CCCCCTCGAAAGTTATAGGC
HvPDIL1_4-F AGTTGGCCAAGCATTTCAGT 60 198 检测基因表达
Check the expression of HvPDIL1-4
HvPDIL1_4-R CTGCAGCTTCTCCTTGATGA
HvPDIL2_1-F CGGGACTTGGATGACTTTGT 60 200 检测基因表达
Check the expression of HvPDIL2-1
HvPDIL2_1-R AGGACCACTGAGCTTTGCAG
HvPDIL2_2-F CTAGCGCAGATGTGATGGAA 60 198 检测基因表达
Check the expression of HvPDIL2-2
HvPDIL2_2-R GCTTCTCCAGATCAGCTTGC
HvPDIL5_1-F CGAAGAGACCTTCTCCGACA 60 200 检测基因表达
Check the expression of HvPDIL5-1
HvPDIL5_1-R GAATGTCCACCTTTGAGCAGA
HvPDIL5_2-F CCCCGAGTTAGATGAAGCTG 60 199 检测基因表达
Check the expression of HvPDIL5-2
HvPDIL5_2-R AAGATTGCGGACAAGCAAGT
HvPDIL5_3-F GAAACTTCCATGCGGTTGAT 60 199 检测基因表达
Check the expression of HvPDIL5-3
HvPDIL5_3-R CCAAACTCTCCAAACCCTCA
HvPDIL5_4-F CCTGAAATGGATGGCAGAAT 60 200 检测基因表达
Check the expression of HvPDIL5-4
HvPDIL5_4-R TCCATAGCCGCGACTAAACT

Fig. 5

Relative expression level of HvPDILs in leaves of virus-infected plants The significance of difference was evaluated by t-test (*P < 0.05; **P < 0.01). Error bar: the standard error."

[1] Freedman R B, Hirst T R, Tuite M F . Protein disulphide isomerase: building bridges in protein folding. Trends Biochem Sci, 1994,19:331-336.
[2] Wu H, Wensley E, Bhave M . Identification and analysis of genes encoding a novel ER-localised cyclophilin B in wheat potentially involved in storage protein folding. Plant Sci, 2009,176:420-432.
[3] Quan H, Fan G, Wang C C . Independence of the chaperone activity of protein disulfide isomerase from its thioredoxin-like active site. J Biol Chem, 1995,270:17078-17080.
[4] Jacquot J P, Gelhaye E, Rouhier N, Corbier C, Didierjean C, Aubry A . Thioredoxins and related proteins in photosynthetic organisms: molecular basis for thiol dependent regulation. Biochem Pharmacol, 2002,64:1065-1069.
[5] Darby N J, Kemmink J, Creighton T E . Identifying and characterizing a structural domain of protein disulfide isomerase. Biochemistry, 1996,35:10517-10528.
[6] Kemmink J, Darby N J, Dijkstra K, Nilges M, Creighton T E . The folding catalyst protein disulfide isomerase is constructed of active and inactive thioredoxin modules. Curr Biol, 1997,7:239-245.
[7] Klappa P, Ruddock L W, Darby N J, Freedman R B . The b' domain provides the principal peptide-binding site of protein disulfide isomerase but all domains contribute to binding of misfolded proteins. EMBO J, 1998,17:927-935.
[8] Lucero H A, Kaminer B . The role of calcium on the activity of ERcalcistorin/protein-disulfide isomerase and the significance of the C-terminal and its calcium binding. A comparison with mammalian protein-disulfide isomerase. J Biol Chem, 1999,274:3243-3251.
[9] Denecke J, De Rycke R, Botterman J . Plant and mammalian sorting signals for protein retention in the endoplasmic reticulum contain a conserved epitope. EMBO J, 1992,11:2345-2355.
[10] Selles B, Jacquot J P, Rouhier N . Comparative genomic study of protein disulfide isomerases from photosynthetic organisms. Genomics, 2011,97:37-50.
[11] 陈珍, 江琼, 朱诚 . 植物中的蛋白质二硫键异构酶及其类蛋白. 植物生理学报, 2013,49:715-721.
Chen J, Jiang Q, Zhu C . Protein disulfide isomerise and PDI-like proteins in plant. Plant Physiol J, 2013,49:715-721 (in Chinese with English abstract).
[12] Houston N L, Fan C, Xiang J Q, Schulze J M, Jung R, Boston R S . Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. Plant Physiol, 2005,137:762-778.
[13] Narindrasorasak S, Yao P, Sarkar B . Protein disulfide isomerase, a multifunctional protein chaperone, shows copper-binding activity. Biochem Biophys Res Commun, 2003,311:405-414.
[14] Andeme Ondzighi C, Christopher D A, Cho E J, Chang S C, Staehelin L A . Arabidopsis protein disulfide isomerase-5 inhibits cysteine proteases during trafficking to vacuoles before programmed cell death of the endothelium in developing seeds. Plant Cell, 2008,20:2205-2220.
[15] Levitan A, Trebitsh T, Kiss V, Pereg Y, Dangoor I, Danon A . Dual targeting of the protein disulfide isomerase RB60 to the chloroplast and the endoplasmic reticulum. Proc Natl Acad Sci USA, 2005,102:6225-6230.
[16] Wang H, Boavida L C, Ron M, McCormick S . Truncation of a protein disulfide isomerase, PDIL2-1, delays embryo sac maturation and disrupts pollen tube guidance in Arabidopsis thaliana. Plant Cell, 2008,20:3300-3311.
[17] Johnson J C, Appels R, Bhave M . The PDI genes of wheat and their syntenic relationship to the esp2 locus of rice. Funct Integr Genomics, 2006,6:104-121.
[18] Takemoto Y, Coughlan S J, Okita T W, Satoh H, Ogawa M, Kumamaru T . The rice mutant esp2 greatly accumulates the glutelin precursor and deletes the protein disulfide isomerase. Plant Physiol, 2002,128:1212-1222.
[19] Han X, Wang Y, Liu X, Jiang L, Ren Y, Liu F, Peng C, Li J, Jin X, Wu F, Wang J, Guo X, Zhang X, Cheng Z, Wan J . The failure to express a protein disulphide isomerase-like protein results in a floury endosperm and an endoplasmic reticulum stress response in rice. J Exp Bot, 2012,63:121-130.
[20] Satoh-Cruz M, Crofts A J, Takemoto-Kuno Y, Sugino A., Washida H, Crofts N, Okita T W, Ogawa M, Satoh H, Kumamaru T . Protein disulfide isomerase like 1-1 participates in the maturation of proglutelin within the endoplasmic reticulum in rice endosperm. Plant Cell Physiol, 2010,51:1581-1593.
[21] Onda Y, Nagamine A, Sakurai M, Kumamaru T, Ogawa M, Kawagoe Y . Distinct roles of protein disulfide isomerase and P5 sulfhydryl oxidoreductases in multiple pathways for oxidation of structurally diverse storage proteins in rice. Plant Cell, 2011,23:210-223.
[22] Li C P, Larkins B A . Expression of protein disulfide isomerase is elevated in the endosperm of the maize floury-2 mutant. Plant Mol Biol, 1996,30:873-882.
[23] Lu D P, Christopher D A . Endoplasmic reticulum stress activates the expression of a sub-group of protein disulfide isomerase genes and AtbZIP60 modulates the response in Arabidopsis thaliana. Mol Genet Genomics, 2008,280:199-210.
[24] 刘颖慧, 王秀堂, 石云素, 石云素, 黄亚群, 宋燕春, 王天宇, 黎裕 . 玉米蛋白质二硫键异构酶(PDI)基因的特征和表达. 中国生物化学与分子生物学报, 2009,25:229-234.
Liu Y H, Wang X T, Shi Y S, Huang Y Q, Song Y C, Wang T Y, Li Y . Expression and characterization of a protein disulfideisomerases in maize (Zea mays L.). Chin J Biochem Mol Biol, 2009,25:229-234 (in Chinese with English abstract).
[25] Chauhan H, Khurana N, Tyagi A K, Khurana J, Khurana P . Identification and characterization of high temperature stress responsive genes in bread wheat (Triticum aestivum L.) and their regulation at various stages of development. Plant Mol Biol, 2011,75:35-51.
[26] Ray S, Anderson J M, Urmeev F I, Goodwin S B . Rapid induction of a protein disulfide isomerase and defense-related genes in wheat in response to the hemibiotrophic fungal pathogen Mycosphaerella graminicola. Plant Mol Biol, 2003,53:701-714.
[27] Faheem M, Li Y, Arshad M, Jiangyue C, Jia Z, Wang Z, Xiao J, Wang H, Cao A, Xing L, Yu F, Zhang R, Xie Q, Wang X . A disulphide isomerase gene (PDI-V) from Haynaldia villosa contributes to powdery mildew resistance in common wheat. Sci Rep, 2016,6:24227.
[28] Kanyuka K, Ward E, Adams M J . Polymyxa graminis and the cereal viruses it transmits: a research challenge. Mol Plant Pathol, 2003,4:393-406.
[29] Kuhne T . Soil-borne viruses affecting cereals: known for long but still a threat. Virus Res, 2009,141:174-183.
[30] Yang P, Lupken T, Habekuss A, Goetz H, Burkhard S, Benjamin K, Ruvini A, Axel H, Jochen K, Uwe S, Frank O, Nils S . PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc Natl Acad Sci USA, 2014,111:2104-2109.
[31] d’Aloisio E, Paolacci A R, Dhanapal A P, Tanzarella O A, Porceddu E, Ciaffi M . The protein disulfide isomerase gene family in bread wheat (T. aestivum L.). BMC Plant Biol, 2010,10:101.
[32] Zhu C, Luo N, He M, Chen G, Zhu J, Yin G, Li X, Hu Y, Li J, Yan Y . Molecular characterization and expression profiling of the protein disulfide isomerase gene family in Brachypodium distachyon L. PLoS One, 2014,9:e94704.
[33] Ordon F, Friedt W . Mode of inheritance and genetic diversity of BaMMV resistance of exotic barley germplasms carrying genes different from ‘ym4’. Theor Appl Genet, 1993,86:229-233.
[34] Roustan V, Roustan P J, Weidinger M, Reipert S, Kapusi E, Shabrangy A, Stoger E, Weckwerth W, Ibl V . Microscopic and proteomic analysis of dissected developing barley endosperm layers reveals the starchy endosperm as prominent storage tissue for ER-derived hordeins alongside the accumulation of barley protein disulfide isomerase (HvPDIL1-1). Front Plant Sci, 2018,9:1248.
[35] Jeong W, Lee D Y, Park S, Rhee S G . ERp16, an endoplasmic reticulum-resident thiol-disulfide oxidoreductase: biochemical properties and role in apoptosis induced by endoplasmic reticulum stress. J Biol Chem, 2008,283:25557-25566.
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