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Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China.

Pagaling E, Haigh RD, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S - BMC Genomics (2007)

Bottom Line: ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified.Evidence for viral integration was obtained.Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Infection Immunity and Inflammation, University of Leicester, University Road, Leicester, LE1 9HN, UK. eulyn_pagaling@hotmail.com

ABSTRACT

Background: We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus.

Results: Haloarchaeal strains with 16S rRNA gene sequences 98% identical to Halorubrum saccharovorum were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content ofapproximately 65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained.

Conclusion: The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system.

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Top panel. Diagram of the BJ1 genome drawn in a circular form. The major features are shown including the predicted ORFs, blue arrows in the forward direction, green arrows in the reverse. The tRNA gene is in red. ORFs mentioned in the text are numbered. The outer scale bar is in base pairs. The inner curved arrows indicate entirely hypothetical operons. The bottom panel shows the cumulative GC skew.
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Figure 4: Top panel. Diagram of the BJ1 genome drawn in a circular form. The major features are shown including the predicted ORFs, blue arrows in the forward direction, green arrows in the reverse. The tRNA gene is in red. ORFs mentioned in the text are numbered. The outer scale bar is in base pairs. The inner curved arrows indicate entirely hypothetical operons. The bottom panel shows the cumulative GC skew.

Mentions: See Figure 4 and Table 1. The double stranded genomic DNA isolated from virus particles is shown as a circular sequence 42, 271 bp long with a G+C content of 64.8 mol% [EMBL: AM419438]. Exonuclease III susceptibility showed that the DNA is linear but sequence assembly indicated it to be circular. This indicates that the genome is terminally redundant (and may be circularly permuted). It is unclear if the BJ1 genome ever forms a circular molecule but if it does then cos sites are unlikely to be involved as digests with three infrequent cutting restriction enzymes (HindIII, EcoRV and EcoRI) followed by melting at 80°C failed to show any change in the number of bands compared to un-melted digests (data not shown).


Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China.

Pagaling E, Haigh RD, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S - BMC Genomics (2007)

Top panel. Diagram of the BJ1 genome drawn in a circular form. The major features are shown including the predicted ORFs, blue arrows in the forward direction, green arrows in the reverse. The tRNA gene is in red. ORFs mentioned in the text are numbered. The outer scale bar is in base pairs. The inner curved arrows indicate entirely hypothetical operons. The bottom panel shows the cumulative GC skew.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194725&req=5

Figure 4: Top panel. Diagram of the BJ1 genome drawn in a circular form. The major features are shown including the predicted ORFs, blue arrows in the forward direction, green arrows in the reverse. The tRNA gene is in red. ORFs mentioned in the text are numbered. The outer scale bar is in base pairs. The inner curved arrows indicate entirely hypothetical operons. The bottom panel shows the cumulative GC skew.
Mentions: See Figure 4 and Table 1. The double stranded genomic DNA isolated from virus particles is shown as a circular sequence 42, 271 bp long with a G+C content of 64.8 mol% [EMBL: AM419438]. Exonuclease III susceptibility showed that the DNA is linear but sequence assembly indicated it to be circular. This indicates that the genome is terminally redundant (and may be circularly permuted). It is unclear if the BJ1 genome ever forms a circular molecule but if it does then cos sites are unlikely to be involved as digests with three infrequent cutting restriction enzymes (HindIII, EcoRV and EcoRI) followed by melting at 80°C failed to show any change in the number of bands compared to un-melted digests (data not shown).

Bottom Line: ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified.Evidence for viral integration was obtained.Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Infection Immunity and Inflammation, University of Leicester, University Road, Leicester, LE1 9HN, UK. eulyn_pagaling@hotmail.com

ABSTRACT

Background: We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus.

Results: Haloarchaeal strains with 16S rRNA gene sequences 98% identical to Halorubrum saccharovorum were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content ofapproximately 65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained.

Conclusion: The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system.

Show MeSH
Related in: MedlinePlus