Genome-wide identification and abiotic stress responses of DGK gene family in maize

Original Article

Abstract

Diacylglycerol kinase (DGK) is a kind of phosphokinase that catalyzes the formation of signaling molecule phosphatidic acid. In this study, seven maize (Zea mays) DGK gene family members were identified by an exploration of maize genome via multiple online databases, and designated as ZmDGK1-7, respectively. The proteins encoded by ZmDGKs ranged from 487 to 716 amino acids, and had a molecular weight (MWs) between 54.6 and 80.2 kDa. Phylogenetic analysis revealed that ZmDGKs grouped into three clusters as described for known plant DGK families: Cluster I was composed of three maize DGKs, ZmDGK1, ZmDGK4 and ZmDGK5, cluster II contained ZmDGK6, and the isoforms ZmDGK2, ZmDGK3 and ZmDGK7 fell into cluster III. ZmDGK proteins featured the typical functional domains, while all seven ZmDGKs have a conserved catalytic domain DGKc, only the cluster I ZmDGKs have the DAG/PE binding domain. Most ZmDGK genes showed ubiquitous expression profiles at various developmental stages, while a high relative expression was observed at the tasseling stage. ZmDGK genes exhibited differential expression patterns in response to abiotic stresses including cold, salinity and drought, and all ZmDGK genes were found obviously up-regulated by cold. The distinct roles of ZmDGKs in cold response was also supported by the finding that an accumulation of DGK products–PA under low temperature. This study will help to better understand the roles of DGKs in the development and abiotic stress responses in major crops.

Keywords

Diacylglycerol kinase (DGK) Phosphatidic acid (PA) Lipid signaling Abiotic stress Maize (Zea mays

Abbreviations

DAG

Diacylglycerol

DGK

Diacylglycerol kinase

PA

Phosphatidic acid

PC

Phosphatidylcholine

PE

Phosphatidylethanolamine

PLD

Phospholipase D

PLC

Phospholipase C

Notes

Acknowledgement

This work was supported by National science and technology support plan (2015BAD23B05-04); Natural Science Foundation of Heilongjiang Province(C201446); National science and technology support plan of china (2013BAD07B01); Heilongjiang Bayi Agricultural University graduate student innovation fund projects (YJSCX2015-Z01).

Compliance with ethical standards

Conflict of interest

The authors declare no competing financial interests.

Supplementary material

13562_2017_424_MOESM1_ESM.tif (328 kb)
Fig. S1 Gene structural analysis of maize DGK genes. (a) Phylogenetic clusters. (b) Exon-intron architecture of ZmDGKs. Genome sequences of ZmDGK genes were analyzed, and a diagram of the exon-intron distribution was generated by the online PIECE program. The blue boxes represent exons, and the gray lines represent the introns. The number 0, 1, 2 indicate the phase of the introns. (TIFF 327 kb)
13562_2017_424_MOESM2_ESM.tif (916 kb)
Fig. S2 Chromosomal localization of maize DGK genes. All non-redundant maize DGK genes were mapped on the 10 maize chromosomes and a sketch map was created with MapDraw. (TIFF 916 kb)
13562_2017_424_MOESM3_ESM.tif (2.5 mb)
Fig. S3 Multiple sequence alignment and conserved domain analysis of maize and Arabidopsis DGKs. (a) DGKc: Diacylglycerol kinase catalytic domain in maize and Arabidopsis. (b) DAG/PE-binding domain in maize, rice, apple and Arabidopsis. The consensus GXGXXG sequence in ATP-binding site in DGKc domain was boxed. (The accession numbers of all the plant DGKs are listed in Table S1). (TIFF 2569 kb)
13562_2017_424_MOESM4_ESM.tif (2.9 mb)
Fig. S4 Multiple sequence alignment and conserved domain analysis of maize and Arabidopsis DGKs. (a) DGKa: Diacylglycerol kinase accessory domain in maize and Arabidopsis. (b) DAG/PE-binding domain c in maize, rice, apple and Arabidopsis. Multiple sequences alignments were conducted using DNAMAN software (The accession numbers of all the DGKs are listed in Table S1). (TIFF 2948 kb)
13562_2017_424_MOESM5_ESM.tif (289 kb)
Fig. S5 Analysis of Cis- elements in the promoter regions of ZmDGKs. The Scale bar -1500 to -1 represents the upstream region of the promoter of ZmDGKs. The regulatory elements analyzed are LTR (low temperature responsive), C-repeat/DRE (cold/dehydration responsive), ABRE (abscisic acid responsive), MBS (MYB binding site), and TC-rich repeat (defense/ stress responsive). (TIFF 288 kb)
13562_2017_424_MOESM6_ESM.tif (271 kb)
Fig. S6 Expression analysis of ZmDGKs genes in different tissues/developmental stages. Quantitive real-time PCR was conducted with the specific primers designed according to individual ZmDGK gene sequence, and the expression profile of maize DGKs was detected in various maize tissues/developmental stages, including L1: Seedling Stage, L2: Elongation Stage, L3: Huge Bellbottom Period, L4: Tasseling Stage, ST: Stem, ES: Endosperm, SE: Seed. The maize 18s-rRNA gene was used as an endogenous control, and values from roots were normalized to 0 as experimental control. Mean values were obtained from 3 replicates. Vertical bars indicate standard deviation. Lowercase letter on top of the error bars indicate the significant difference (α=0.05) compared with DGK genes. (TIFF 270 kb)
13562_2017_424_MOESM7_ESM.pdf (192 kb)
Table S1 Accession numbers of all the DGK genes in this study. (PDF 191 kb)
13562_2017_424_MOESM8_ESM.pdf (146 kb)
Table S2 Primers used for quantitive real-time PCR. (PDF 145 kb)
13562_2017_424_MOESM9_ESM.pdf (219 kb)
Table S3 Accession numbers of genes in PLD and PLC/DGK pathway. (PDF 219 kb)
13562_2017_424_MOESM10_ESM.pdf (223 kb)
Table S4 Sequences producing significant alignments (AtDGK1). (PDF 222 kb)
13562_2017_424_MOESM11_ESM.pdf (230 kb)
Table S5 Sequences producing significant alignments (AtDGK2). (PDF 229 kb)
13562_2017_424_MOESM12_ESM.pdf (228 kb)
Table S6 Sequences producing significant alignments (AtDGK3). (PDF 228 kb)
13562_2017_424_MOESM13_ESM.pdf (225 kb)
Table S7 Sequences producing significant alignments (AtDGK4). (PDF 225 kb)
13562_2017_424_MOESM14_ESM.pdf (210 kb)
Table S8 Sequences producing significant alignments (AtDGK5). (PDF 209 kb)
13562_2017_424_MOESM15_ESM.pdf (202 kb)
Table S9 Sequences producing significant alignments (AtDGK6). (PDF 202 kb)
13562_2017_424_MOESM16_ESM.pdf (246 kb)
Table S10 Sequences producing significant alignments (AtDGK7). (PDF 246 kb)
13562_2017_424_MOESM17_ESM.pdf (142 kb)
Table S11 List of PF00130 found in phytozome and NCBI databases. (PDF 142 kb)
13562_2017_424_MOESM18_ESM.pdf (153 kb)
Table S12 List of PF00781 found in phytozome database. (PDF 153 kb)
13562_2017_424_MOESM19_ESM.pdf (144 kb)
Table S13 List of PF00609 found in phytozome database. (PDF 144 kb)

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2017

Authors and Affiliations

  • Yingnan Gu
    • 1
    • 2
  • Changjiang Zhao
    • 1
  • Lin He
    • 1
  • Bowei Yan
    • 1
  • Jiejing Dong
    • 1
  • Zuotong Li
    • 1
  • Kejun Yang
    • 1
  • Jingyu Xu
    • 1
  1. 1.Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of AgricultureHeilongjiang Bayi Agricultural UniversityDaqingPeople’s Republic of China
  2. 2.Heilongjiang Academy of Agricultural SciencesHarbinPeople’s Republic of China

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