Proteomics of Animal Viruses

Behera, Suchismita; Suryawanshi, Amol Ratnakar

doi:10.1007/978-3-031-21630-5_3

Suchismita Behera^7,8 &
Amol Ratnakar Suryawanshi^7,8

Part of the book series: Sustainable Agriculture Reviews ((SARV,volume 59))

224 Accesses

Abstract

Viruses are obligate parasites, and therefore are dependent upon host’s cellular machinery for their survival. Alterations in several cellular pathways occur due to viral infections where viral proteins share contributions in host-cell interactions. The study of these altered proteins and their role in viral infection is crucial to understand a biological system or disease progression, to identify markers for diagnosis and prognosis, and to develop therapeutic strategies to control the viral infections. In recent years, advancements in proteomics technologies and approaches have created an opportunity to study alterations in host/viral proteins due to viral infections in high throughput manner.

In this review, we first describe proteomics technologies and approaches. We review viral proteomics studies on common animal viruses, categorized as animal viruses, human viruses and zoonotic viruses, to understand the role of proteins altered during viral infection. This review also provides a list of proteins altered during virus infections and their probable role in viral pathogenesis.

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Abbreviations

¹³C:

Carbon-13

¹⁵N:

Nitrogen-15

²H:

Hydrogen-2 or Deuterium

1D-PAGE:

One-dimensional polyacrylamide gel electrophoresis

2D-DIGE:

Two-dimensional differential gel electrophoresis

2D-PAGE:

Two-dimensional polyacrylamide gel electrophoresis

AHA:

Azidohomoalanine

AMPK:

Adenosine monophosphate-activated protein kinase

Annexin A2:

Annexin 2

AP-LC-MS/MS:

Affinity purification liquid chromatography-tandem mass spectrometry

Apo A-I:

Apolipoprotein A-I

AQUA:

Absolute Quantification

Arl3:

ADP-ribosylation factor-like protein 3

ARSs:

Aminocyl-tRNA synthetases

ATP:

Adenosine triphosphate

BHK-21:

Baby hamster kidney 21

BHV-1:

Bovine herpesvirus 1

BONCAT:

Bioorthogonal noncanonical amino acid tagging

Caco-2:

Cancer-coli 2

CAMK2:

Calcium-calmodulin protein kinase II

CAMKIIA:

Calcium-calmodulin protein kinase II A

CD4:

Cluster of differentiation 4

CDK1:

Cyclin-dependent kinase 1

CDK7:

Cyclin-dependent kinase 7

CFR:

Curved-field reflectron

CHIKF:

Chikungunya fever

CHIKV:

Chikungunya virus

CI:

Chemical Ionization

CRM1:

Chromosomal maintenance 1

CRMP2:

Collapsing response mediator protein 2

CRP:

C-reactive protein

CSFV:

Classical swine fever virus

Cy:

Cyanine

DDX1:

DEAD box helicase 1

DDX17:

DEAD box helicase 17

DDX3:

DEAD box helicase 3

DDX3X:

DEAD-box helicase 3 X-linked

DEAD:

Aspartate-glutamate-alanine-aspartate

DENV:

Dengue virus

DNA:

Deoxyribonucleic acid

DNAH12:

Dynein heavy chain 12

DNAH5:

Dynein heavy chain 5

DNAJC7:

DnaJ homology subfamily C member 7

dUTPases:

deoxyuridine-triphosphatases

EBOV:

Ebola virus

EBV:

Epstein-Barr virus

EI:

Electron Impact ionization

ENO1:

Alpha enolase

ERK/MAPK:

Extracellular-signal-regulated kinase/ mitogen activated protein kinase

ESCRT:

Endosomal sorting complex required for transport

ESI:

Electrospray Ionization

F9:

Coagulation factor IX

FABP3:

Fatty acid-binding protein 3

FGL1:

Fibrinogen-like protein 1

FMDV:

Foot-and-mouth disease virus

FTIR:

Fourier transform ion cyclotron resonance

GAPDH:

Glyceraldehyde 3-phosphate dehydrogenase

GDI2:

Guanosine diphosphate dissociation inhibitor alpha 2

Ge-LC-MS/MS:

Gel-enhanced liquid chromatography-mass spectrometry

GFAP:

Glial fibrillary acidic protein

GLUL:

Glutamate ammonia ligase

GOPC:

Golgi-associated PDZ and coiled-coil motif-containing protein

GRSF1:

G-rich sequence factor 1

GS:

Glutamine synthetase

GTPase:

Guanosine triphosphatases

HaCaT:

Human keratinocyte cells

HCMV:

Human cytomegalovirus

HFFFs:

Human fetal foreskin fibroblasts

HFFs:

Human foreskin fibroblasts

HFLS:

Human fibroblast-like synoviocytes

HIF-1:

Hypoxia-inducible factor 1

HIV-1:

Human immunodeficiency virus type 1

HNRNPH1:

Heterogenous nuclear ribonucleoprotein H1

HSP90AA1:

Heat shock protein 90 AA1

HSP90AB1:

Heat shock protein 90 AB1

HSV-1:

Herpes simplex virus 1

Huh7:

Hepatocyte-derived cellular carcinoma

ICAT:

Isotope-coded affinity tag

ICP0:

Infected-cell protein 0

ICP22:

Infected-cell protein 22

ICP4:

Infected-cell protein 4

IFITM3:

Interferon-induced transmembrane protein 3

IFV:

Influenza virus

IPG:

Immobilized pH gradient

IRF9:

Interferon regulatory factor 9

iTRAQ:

Isobaric tag for Relative and Absolute Quantitation

JAK1:

Janus kinase 1

JEV:

Japanese encephalitis virus

LC-MS:

Liquid chromatography-mass spectrometer

LC-MS/MS:

Liquid chromatography-tandem mass spectrometry

LMP1:

Latent membrane protein 1

LMP2A:

Latent membrane protein 2A

L-particles:

Light particles

LRG1:

Leucine-rich alpha-2-glycoprotein 1

LTQ:

Linear trap quadrupole

m/z:

mass-to-charge ratio

MALDI:

Matrix-assisted laser desorption ionization

MALDI-MS:

Matrix-assisted laser desorption ionization mass spectrometer

MALDI-TOF/MS:

Matrix-assisted laser desorption ionization-Time-of-Flight/Mass Spectrometer

MALDI-TOF/TOF:

Matrix-assisted laser desorption ionization-Time-of-Flight/Time-of-Flight

MCMV:

Murine cytomegalovirus

MDBK:

Madin-darby bovine kidney

MDCK:

Madin-darby canine kidney

MDMs:

Monocyte-derived macrophages

MEFs:

Mouse embryonic fibroblasts

mePROD:

Multiplexed enhanced protein dynamics

MFAP4:

Microfibril-associated glycoprotein 4

MHV68:

Murine gammaherpesvirus 68

MHVs:

Murine herpesviruses

MIB-MS:

Multiplexed kinase inhibitor bead-mass spectrometry

MIF:

Macrophage migration inhibitory factor

MRM:

Multiple Reaction Monitoring

MS:

Mass spectrometry

mTOR:

Mammalian target of rapamycin

MYO18A:

Myosin XVIII A

nanoLC-MS/MS:

Nanoscale liquid chromatography and tandem mass spectrometry

NEDD4:

Neural precursor cells expressed developmentally down-regulated protein 4

NHS:

N-hydroxy succinimide

NKRF:

Nuclear factor-kappa-B repressing factor

NSFL1C:

NSFL1 cofactor 47

OIE:

World Organization for Animal Health

ORF:

Open reading frame

PBMCs:

Peripheral Blood Mononuclear Cells

PCV:

Porcine circovirus

PDC6IP:

Programmed cell death 6 interacting protein

PDGFRα:

Platelet-derived growth factor receptor α

PDGFRβ:

Platelet-derived growth factor receptor β

PI3KC:

Phosphatidylinositol 3-kinase catalytic subunit type 3

PI4K2B:

Phosphatidylinositol 4-kinase type 2 beta

PK-15:

Porcine Kidney 15

PLAT:

Tissue-type plasminogen activator

PRM:

Parallel Reaction Monitoring

PRV:

Pseudorabies virus

PRV-Bartha:

Pseudo rabies virus

bartha

Prx-1:

Peroxiredoxin-1

PSD:

Post-source decay

PSMB1:

Proteasome subunit beta type-1

PSMB8:

Proteasome subunit beta type-8

PSMD2:

26S proteasome non-ATPase regulatory subunit 2

Q1:

Quadrupole 1

Q2:

Quadrupole 2

Q3:

Quadrupole 3

qTOF/MS:

Quadrupole time-of-flight mass spectrometer

RAB8B:

Ras-related protein Rab-8B

RABV:

Rabies virus

Ras:

GAP SH3

Ras-guanosine triphosphatase accelerating protein Src homology 3

RBP4:

Retinol-binding protein 4

Rev:

Regulator of viral protein expression

RNA:

Ribonucleic acid

RNH1:

Ribonuclease/angiogenin inhibitor 1

RPL18:

Ribosomal protein L18

RPL3:

Ribosomal protein L3

RPL5:

Ribososmal protein L5

RPS6:

Ribosomal protein S6

RRE:

Rev Response Element

SAA2:

Serum amyloid A2

SAMD9:

Sterile alpha motif domain-containing protein 9

SARS-CoV-2:

Severe acute respiratory syndrome coronavirus 2

SDS:

Sodium-dodecyl sulphate

SILAC:

Stable Isotope Labeling with Amino Acids in Cell Culture

siRNA:

Small interference RNA

STAT2:

Signal transducer and activator of transcription 2

SWATH:

Sequential Window Acquisition of all Theoretical Mass Spectra

TANK:

TRAF family member-associated nuclear factor-kappa-B

Tat:

Trans-activator of transcription

TGFBR1:

Transforming growth factor beta receptor 1

TGFBR2:

Transforming growth factor beta receptor 2

TLR2:

Toll-like receptor 2

TMT:

Tandem Mass Tag

TNF:

Tumor necrosis factor

TOF:

Time of flight

TOF/TOF:

Time-of-flight/time-of-flight

TQMS:

Triple-quadrupole-mass spectrometer

TRAF3:

Tumor necrosis factor receptor-associated factor 3

TUBA1C:

Tubulin alpha-1C chain

U_L:

Unique long region

US22:

Unique short region 22

Us3:

Unique short region 3

VAMP8:

Vesicle-associated membrane protein 8

VCAM1:

Vascular cell adhesion molecule-1

VLPs:

VP40-containing virus-like particles

VPS13D:

Vacuolar protein sorting-associated protein 13D

VPS24:

Vacuolar protein sorting-associated protein 24

VPS28:

Vacuolar protein sorting-associated protein 28

VPS37:

Vacuolar protein sorting-associated protein 37

VPS4A:

Vacuolar protein sorting-associated protein 4A

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Acknowledgements

We would like to convey our sincere thanks to Dr. Vinod Kumar Yata for his invitation to contribute this review for the book. We would like to acknowledge Dr. Ajay Parida, Director, Institute of Life Sciences, Bhubaneswar, Odisha, our lab members for their support.

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Autonomous Institute of the Department of Biotechnology, Clinical proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India
Suchismita Behera & Amol Ratnakar Suryawanshi
Regional Centre for Biotechnology, Faridabad, Haryana, India
Suchismita Behera & Amol Ratnakar Suryawanshi

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Suchismita Behera
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Amol Ratnakar Suryawanshi
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Correspondence to Amol Ratnakar Suryawanshi .

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Animal Biology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
Vinod Kumar Yata
ICAR-Indian Veterinary Research Institute, Mukteswar, India
Ashok Kumar Mohanty
Aix-Marseille University, Aix-en-Provence, France
Eric Lichtfouse

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Behera, S., Suryawanshi, A.R. (2023). Proteomics of Animal Viruses. In: Yata, V.K., Mohanty, A.K., Lichtfouse, E. (eds) Sustainable Agriculture Reviews 59. Sustainable Agriculture Reviews, vol 59. Springer, Cham. https://doi.org/10.1007/978-3-031-21630-5_3

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DOI: https://doi.org/10.1007/978-3-031-21630-5_3
Published: 08 February 2023
Publisher Name: Springer, Cham
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Online ISBN: 978-3-031-21630-5
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