Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general

Abstract

Fuselloviridae are ubiquitous crenarchaeal viruses found in high-temperature acidic hot springs worldwide. The type virus, Sulfolobus spindle-shaped virus 1 (SSV1), has a double-stranded DNA genome that contains 34 open reading frames (ORFs). Fuselloviral genomes show little similarity to other organisms, generally precluding functional predictions. However, tertiary protein structure can provide insight into protein function. We have thus undertaken a systematic investigation of the SSV1 proteome and report here on the F112 gene product. Biochemical, proteomic and structural studies reveal a monomeric intracellular protein that adopts a winged helix DNA binding fold. Notably, the structure contains an intrachain disulfide bond, prompting analysis of cysteine usage in this and other hyperthermophilic viral genomes. The analysis supports a general abundance of disulfide bonds in the intracellular proteins of hyperthermophilic viruses, and reveals decreased cysteine content in the membrane proteins of hyperthermophilic viruses infecting Sulfolobales. The evolutionary implications of the SSV1 distribution are discussed.

The Crystal Structure of D212 from Sulfolobus Spindle-Shaped Virus Ragged Hills Reveals a New Member of the PD-(D/E)XK Nuclease Superfamily

“…Alternatively, D212 may function in a DNA repair pathway, and expression of D212 might play a role in correcting replication defects or other damage to the viral genome. In this light, it is interesting that SSV1 D244, a D212 ortholog, is thought to be packaged within the SSV1 viral particle (33). The presence of D212 in the viral particle could ensure availability upon infection of a new host cell, helping to protect the integrity of the viral genome from the acidic, hyperthermal environments in which these viruses reside.…”

“…VP1 and VP3 are structural proteins (51), while VP2 is thought to function as a small, packaged, DNA binding protein (52,58). More recently, two additional components that copurify with the viral particle have also been identified, C792 and D244 (33). C792 is a predicted membrane protein and thus likely to serve a structural role, while D244 is a soluble protein of unknown function (33).…”

“…More recently, two additional components that copurify with the viral particle have also been identified, C792 and D244 (33). C792 is a predicted membrane protein and thus likely to serve a structural role, while D244 is a soluble protein of unknown function (33). Structural studies have also contributed to our understanding of the SSV1 proteome, with crystal structures of D63, F112, and F93 revealing distant evolutionary relationships and potential functions for these proteins (26,27,29,33).…”

“…C792 is a predicted membrane protein and thus likely to serve a structural role, while D244 is a soluble protein of unknown function (33). Structural studies have also contributed to our understanding of the SSV1 proteome, with crystal structures of D63, F112, and F93 revealing distant evolutionary relationships and potential functions for these proteins (26,27,29,33). Unfortunately, attempts to crystallize D244 for structural annotation have been unproductive, despite significant efforts (B. J. Eilers and C. M. Lawrence, unpublished data).…”

Crystal Structure of Novel Dye-linked l-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix

“…In addition, the common use of disulfides in thermostable proteins of hyperthermophiles has been evaluated at both the structural and genomic levels (31,(33)(34)(35). We therefore compared the numbers of hydrophobic interactions, ion pairs, and disulfide bonds within the structures of ApeLPDH and PDH1 (Table 2).…”