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In-depth proteomic profiling of the Singapore grouper iridovirus virion

  • Defu Yao
  • Yingfu Liu
  • Xiuli Chen
  • Teck Kwang Lim
  • Lili Wang
  • Jude Juventus Aweya
  • Yueling ZhangEmail author
  • Qingsong LinEmail author
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Abstract

Singapore grouper iridovirus (SGIV) is a lethal grouper virus containing 162 predicted ORFs. Previous proteomic studies led to identification of 73 SGIV structural proteins. Here, SDS-assisted tube-gel digestion and DOC-assisted in-solution digestion coupled with LC-ESI-MS/MS were applied to further profile the SGIV structural proteome. We identified a total of 90 SGIV structural proteins including 24 newly reported proteins. Additionally, several PTMs were identified, including 26 N-terminal acetylated proteins, three phosphorylated proteins, and one myristoylated protein. Importantly, 47 of the proteins that were identified are predicted to contain conserved domains. Our work greatly expands the repertoire of the SGIV structural proteome and provides more insight into the biology of SGIV.

Abbreviations

ACN

acetonitrile

APS

ammonium persulfate

DOC

sodium deoxycholate

ESI

electrospray ionization

FA

formic acid

iTRAQ

relative and absolute quantification

LC

liquid chromatography

MS

mass spectrometry

MS/MS

tandem mass spectrometry

MALDI

matrix-assisted laser desorption ionization

MMTS

methyl methanethiosulfonate

ORF

open reading frame

PTM

post-translational modification

SDS

sodium dodecyl sulfate

TEAB

triethylammonium bicarbonate

TECP

tris-(2-carboxyethyl) phosphine

TFA

trifluoroacetic acid

TEMED

N,N,N′,N′-tetramethylethylenediamine

1-DE

one-dimensional gel electrophoresis

Notes

Acknowledgements

We acknowledge Dr. Jinlu Wu of the National University of Singapore for kindly providing us with grouper embryonic cells and SGIV. This work was sponsored by the National Natural Science Foundation of China (no. 31702387) and the China Postdoctoral Science Foundation (no. 2018M630973).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The research reported here did not involve experimentation with human participants or animals.

Supplementary material

705_2019_4264_MOESM1_ESM.doc (362 kb)
Supplementary material 1 (DOC 362 kb)
705_2019_4264_MOESM2_ESM.doc (223 kb)
Supplementary material 2 (DOC 223 kb)
705_2019_4264_MOESM3_ESM.doc (140 kb)
Supplementary material 3 (DOC 139 kb)

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Defu Yao
    • 1
    • 2
  • Yingfu Liu
    • 3
  • Xiuli Chen
    • 4
  • Teck Kwang Lim
    • 2
  • Lili Wang
    • 2
  • Jude Juventus Aweya
    • 1
  • Yueling Zhang
    • 1
    Email author
  • Qingsong Lin
    • 2
    Email author
  1. 1.Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Faculty of ScienceShantou UniversityShantouChina
  2. 2.Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
  3. 3.Department of Basic Medical Sciences, School of medicineXiamen UniversityXiamenChina
  4. 4.Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy AquacultureGuangxi Academy of Fishery SciencesNanningChina

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