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Network Biology, 2021, 11(4): 295-314
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Article

Shedding light on the dark proteome of Hepatitis E Virus

Zoya Shafat1, Anwar Ahmed2, Mohammad K. Parvez3, Shama Parveen1
1Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
2Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
3Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia

Received 11 August 2021;Accepted 18 September 2021;Published 1 December 2021
IAEES

Abstract
Hepatitis E virus (HEV) is a quasi-enveloped RNA virus of the family Hepeviridae. HEV is the chief cause of acute hepatitis worldwide, causing approximately 20 million infections annually, which results in 60,000 deaths. Due to insufficiency in appropriate HEV in vitro cell culture systems, our knowledge of its pathogenesis is inadequately understood. HEV encodes three open reading frames (ORFs): ORF1 (replicative machinery), ORF2 (viral capsid) essential for (infectious particles formation) and ORF3 (viral release). The presence of known and unknown coding and non-coding regions of HEV ORFs are still debated. Viral proteins entail disordered regions which are linked with the infectivity and pathogenicity of virus. Thus, we examined the dark proteome of HEV through analyzing intrinsically disordered protein regions (IDPRs) present in the ORFs by exploiting computational methodologies. Our findings suggested that ORF3 had the highest prevalence of disordered regions. The ORF3 region was followed by ORF2, which had comparatively lesser fraction of intrinsic disorder. The ORF1 had the least number of disordered residues in the HEV proteome. Our intrinsic disorder analysis results revealed that ORF1 polyprotein consists of mostly ordered domains, i.e., proteins having significant level of well-defined structures, with the exclusion of Pro and PCP domains. The analysis reveals Pro domain as a highly disordered protein while PCP domain as an intrinsic disordered protein. MoRF analysis revealed that HEV proteome contains multiple MoRFs across all ORFs. IDPRs are characterized by remarkable conformational flexibility and structural plasticity resulting in their engagement in several biological processes. Due to possession of MoRF in the HEV proteins, these regions can be used for protein-protein interactions due to the structural flexibility. IDPRs are characterized by remarkable conformational flexibility and structural plasticity resulting in their engagement in several biological processes. Due to possession of MoRF in the HEV proteins, these regions can be used for protein-protein interactions due to the structural flexibility. These extensive findings on the HEV proteome will have significant implications in understanding the deeper functioning of structural as well as non-structural biology of HEV proteins.

Keywords HEV;ORF1;ORF2;ORF3;intrinsically disordered proteins;protein-binding propensity;DNA-binding propensity;RNA-binding propensity.


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