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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."

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