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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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Electron micrograph images of BJ1; the scale bar is 500 nm, top panel and 200 nm bottom panel. A schematic diagram of BJ1 annotated with discernible features and the size of these features is also shown. The standard deviation (SD) of measurements from twenty six different particles was determined.
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Figure 2: Electron micrograph images of BJ1; the scale bar is 500 nm, top panel and 200 nm bottom panel. A schematic diagram of BJ1 annotated with discernible features and the size of these features is also shown. The standard deviation (SD) of measurements from twenty six different particles was determined.

Mentions: Virus BJ1 has an icosahedral head, collar and tail, (Fig. 2). The icosahedral head usually has an electron dense shadowing in the centre. The sizes of these features are shown in the schematic diagram Fig 2. The length of a single vertex is 28 nm. The average length of an entire virus particle is about 127 nm. The virus appears to be non-contractile and can be tentatively assigned to the Siphoviridae family, (see the Discussion).


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)

Electron micrograph images of BJ1; the scale bar is 500 nm, top panel and 200 nm bottom panel. A schematic diagram of BJ1 annotated with discernible features and the size of these features is also shown. The standard deviation (SD) of measurements from twenty six different particles was determined.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Electron micrograph images of BJ1; the scale bar is 500 nm, top panel and 200 nm bottom panel. A schematic diagram of BJ1 annotated with discernible features and the size of these features is also shown. The standard deviation (SD) of measurements from twenty six different particles was determined.
Mentions: Virus BJ1 has an icosahedral head, collar and tail, (Fig. 2). The icosahedral head usually has an electron dense shadowing in the centre. The sizes of these features are shown in the schematic diagram Fig 2. The length of a single vertex is 28 nm. The average length of an entire virus particle is about 127 nm. The virus appears to be non-contractile and can be tentatively assigned to the Siphoviridae family, (see the Discussion).

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