Extensive in silico analysis of Mimivirus coded Rab GTPase homolog suggests a possible role in virion membrane biogenesis

Amrutraj Zade,Malavi Sengupta,Kiran Kondabagil

doi:10.3389/fmicb.2015.00929

Amrutraj Zade, Malavi Sengupta + Show 1 more

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https://doi.org/10.3389/fmicb.2015.00929

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Abstract

Rab GTPases are the key regulators of intracellular membrane trafficking in eukaryotes. Many viruses and intracellular bacterial pathogens have evolved to hijack the host Rab GTPase functions, mainly through activators and effector proteins, for their benefit. Acanthamoeba polyphaga mimivirus (APMV) is one of the largest viruses and belongs to the monophyletic clade of nucleo-cytoplasmic large DNA viruses (NCLDV). The inner membrane lining is integral to the APMV virion structure. APMV assembly involves extensive host membrane modifications, like vesicle budding and fusion, leading to the formation of a membrane sheet that is incorporated into the virion. Intriguingly, APMV and all group I members of the Mimiviridae family code for a putative Rab GTPase protein. APMV is the first reported virus to code for a Rab GTPase (encoded by R214 gene). Our thorough in silico analysis of the subfamily specific (SF) region of Mimiviridae Rab GTPase sequences suggests that they are related to Rab5, a member of the group II Rab GTPases, of lower eukaryotes. Because of their high divergence from the existing three isoforms, A, B, and C of the Rab5-family, we suggest that Mimiviridae Rabs constitute a new isoform, Rab5D. Phylogenetic analysis indicated probable horizontal acquisition from a lower eukaryotic ancestor followed by selection and divergence. Furthermore, interaction network analysis suggests that vps34 (a Class III PI3K homolog, coded by APMV L615), Atg-8 and dynamin (host proteins) are recruited by APMV Rab GTPase during capsid assembly. Based on these observations, we hypothesize that APMV Rab plays a role in the acquisition of inner membrane during virion assembly.

Highlights

With a particle size of about 750 nm, Acanthamoeba polyphaga mimivirus (APMV) is one of the largest viruses known so far (La Scola et al, 2003; Claverie et al, 2006)
All Members of the Group I Mimiviridae Family Encode for Rab GTPase A thorough BLASTP search of the NCBI GenBank database, with APMV R214 gene, that was annotated as a probable small GTPase protein (Raoult et al, 2004) as the query sequence against all members of the nucleo-cytoplasmic large DNA viruses (NCLDV) superfamily, revealed that only Moumouvirus, Mamavirus, Lentille virus, Hirudovirus, Courdo virus, Samba virus, and Megavirus code for R214 homolog (Table 1)
A phylogenetic tree, constructed using the DNA polymerase B, with representative sequences from all NCLDVs, suggests that Rab GTPase was acquired by an ancestor of group I Mimiviridae lineages (Figure 1)

Summary

Introduction

With a particle size of about 750 nm, Acanthamoeba polyphaga mimivirus (APMV) is one of the largest viruses known so far (La Scola et al, 2003; Claverie et al, 2006). APMV is a cytoplasmically replicating virus that carries out viral genome replication transcription, protein synthesis and the subsequent stages of particle formation and virus budding in the giant cytosplasmic structures known as viral factories. Regular budding of ∼70 nm vesicles from the cellular cisternae have been observed around the viral factories at earlier PI times (Mutsafi et al, 2013). Continuous fusion of smaller vesicles leads to the formation of multivesicular bodies followed by its fissure to form large membrane sheets that are incorporated into the viral progenies (Mutsafi et al, 2013). A consistent membrane overhang that prevents the premature closure of the capsid is trimmed off upon completion of the capsid assembly, leaving a ∼20 nm nonvertex transient opening for genome packaging (Mutsafi et al, 2013)

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