Similar vWA domain proteins have been reported previously in siphoviruses of haloarchaea: HCTV-2, HHTV-2 and HVTV-1. The encoding gene is situated next to a gene encoding an AAA ATPase (HrrHc1_240), an arrangement that is commonly found in bacteria and archaea. Such domains often function in protein–protein interactions.
The 711 aa protein HrrHc1_245 is predicted to carry a von Willebrand factor A domain (vWA) and a metal ion-dependent adhesion site (MIDAS) domain ( Table 5). Two other proteins specified by genes in the replication/accessory module of the genome have conserved functional domains. Upstream of terL is a dam gene ( hrrhc1_020) encoding a putative N-6-adenine-methyltransferase (Dam). The absence of genes for tail-sheath or base-plate J proteins is consistent with the VIRFAM prediction that Hardycor1 is a siphovirus. The close gene spacing and typical arrangement of viral genes identified this region as being responsible for DNA packaging, virus assembly and morphogenesis. MuF proteins have been reported to have a number of functions in different viruses, such as protecting the ends of viral DNA from nuclease attack when entering a host cell. A muf gene is found just downstream of the portal protein gene ( por), and specifies a MuF (SPP1 gp7) family protein of the longer type. The presence of conserved protein domains and characteristic VIRFAM profiles of virus proteins allowed functional assignments for eight proteins, revealing that the first 27 kb of the Hardycor1 genome carries genes encoding key proteins of caudoviruses, including the large subunit terminase (TerL), portal protein (Por), major capsid protein (Mcp) and tape measure protein (Tmp). An independently described algorithm, VICTOR, calculates similarities of viral genomes based on nucleotide or protein sequences, and in both cases, Hardycor1 was predicted to represent a novel species and novel genus ( Supplementary Table S2). Hardycor1 shows negligible similarity (0–2%) to the other 23 virus genomes and represents a novel species and genus. In this scheme, members of the same species share ≥95% nt similarity, while members of the same genus share more than about 70% nt similarity, although more recently, the ICTV have suggested a threshold of ~50% nt similarity for caudoviruses.
Values are calculated using the traditional algorithm recommended by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee. Figure 3 shows a heat map of intergenomic similarities of tailed haloviruses, produced using the VIRIDIC suite of programs. The low nucleotide sequence similarity of Hardycor1 to other tailed haloviruses prevents any meaningful alignment or phylogenetic inferences however, whole genome similarity values are useful to define viral taxa. This gene might play an important role in regulation of the temperate state. The attP sequences of many pleolipoproviruses were found to be embedded in a newly detected coding sequence, split in the provirus state, that spans between genes for integrase and a downstream CxxC-motif protein. volcanii showed little similarity (BLASTn) to known viruses and probably represents a novel virus group.
A re-examination of other similarly sequenced, archival virus stocks revealed induced proviruses of Haloferax volcanii, Haloferax gibbonsii and Haloarcula hispanica, three of which were pleolipoviruses. Unexpectedly, the sequenced virus stock HC1 also revealed two induced proviruses of the host: a siphovirus (Humcor1) and a pleolipovirus (Humcor2). No close relationship to other viruses was found using phylogenetic tree reconstructions based on TerL and Mcp. Hardycor1 was predicted to be a siphovirus (VIRFAM).
Six caudovirus-like proteins were encoded, including large subunit terminase (TerL), major capsid protein (Mcp) and tape measure protein (Tmp). Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in the NCBI nr protein database (E-value ≤ 10 −15). The genome showed little similarity (BLASTn) to known viruses. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense.
0 kommentar(er)
