In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein.

Dickson Kinyanyi,Stephen Mwaniki,George Obiero,Mark Wamalwa,Peris Amwayi,George F.O Obiero

doi:10.7717/peerj.4396

Dickson Kinyanyi, Stephen Mwaniki + Show 4 more

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https://doi.org/10.7717/peerj.4396

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Journal: PeerJ	Publication Date: Feb 22, 2018
Citations: 13	License type: CC BY 4.0

Affiliation: Technical University of Kenya, Kenyatta University

Abstract

African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published; however, about half of ASFV open reading frames have not been characterized in terms of their structure and function despite being essential for our understanding of ASFV pathogenicity. The present study reports the three-dimensional structure and function of uncharacterized protein, pB263R (NP_042780.1), an open reading frame found in all ASFV strains. Sequence-based profiling and hidden Markov model search methods were used to identify remote pB263R homologs. Iterative Threading ASSEmbly Refinement (I-TASSER) was used to model the three-dimensional structure of pB263R. The posterior probability of fold family assignment was calculated using TM-fold, and biological function was assigned using TM-site, RaptorXBinding, Gene Ontology, and TM-align. Our results suggests that pB263R has the features of a TATA-binding protein and is thus likely to be involved in viral gene transcription.

Highlights

African swine fever virus (ASFV) is a large enveloped double-stranded DNA virus and the sole member of the family Asfarviridae (Dixon et al, 2004), which belongs to the nucleo-cytoplasmic large DNA virus (NCLDV) superfamily, an apparently monophyletic class of viruses with eukaryotic hosts
NCLDVs partially replicate in the cytoplasm, with varying degrees of dependence on the host nucleus (Dixon et al, 2013); members of the superfamily have been classified to belong to the proposed new order named Megavirales, some include, Poxviridae, Iridoviridae, Mimiviridae, Phycodnaviridae, Marseilleviridae, and Ascoviridae (Colson et al, 2012; Colson et al, 2013)
The identified sequences were putative proteins conserved among ASFV and faustovirus, another member of the NCLDV superfamily (Oliveira et al, 2017)

Summary

Introduction

African swine fever virus (ASFV) is a large enveloped double-stranded DNA virus and the sole member of the family Asfarviridae (Dixon et al, 2004), which belongs to the nucleo-cytoplasmic large DNA virus (NCLDV) superfamily, an apparently monophyletic class of viruses with eukaryotic hosts. NCLDVs partially replicate in the cytoplasm, with varying degrees of dependence on the host nucleus (Dixon et al, 2013); members of the superfamily have been classified to belong to the proposed new order named Megavirales, some include, Poxviridae, Iridoviridae, Mimiviridae, Phycodnaviridae, Marseilleviridae, and Ascoviridae (Colson et al, 2012; Colson et al, 2013). The natural hosts of ASFVs include bush pigs, warthogs, and argasid ticks of the genus Ornithodoros (Carrillo et al, 1994; Rodríguez & Salas, 2013) in these hosts, infection by the virus is not fatal. There is currently no vaccine against ASFV (Donnell et al, 2015; Reis et al, 2016), making it a major threat to the global pork industry

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