Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles

TY - JOUR

T1 - Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles

AU - Garrett, Roger Antony

AU - Prangishvili, David

AU - Shah, Shiraz Ali

AU - Reuter, Monika

AU - Stetter, Karl O

AU - Peng, Xu

N1 - © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

PY - 2010/11/1

Y1 - 2010/11/1

N2 - Two novel viral genomes and four plasmids were assembled from an environmental sample collected from a hot spring at Yellowstone National Park, USA, and maintained anaerobically in a bioreactor at 85°C and pH 6. The double-stranded DNA viral genomes are linear (22.7 kb) and circular (17.7 kb), and derive apparently from archaeal viruses HAV1 and HAV2. Genomic DNA was obtained from samples enriched in filamentous and tadpole-shaped virus-like particles respectively. They yielded few significant matches in public sequence databases reinforcing, further, the wide diversity of archaeal viruses. Several variants of HAV1 exhibit major genomic alterations, presumed to arise from viral adaptation to different hosts. They include insertions up to 350 bp, deletions up to 1.5 kb, and genes with extensively altered sequences. Some result from recombination events occurring at low complexity direct repeats distributed along the genome. In addition, a 33.8 kb archaeal plasmid pHA1 was characterized, encoding a possible conjugative apparatus, as well as three cryptic plasmids of thermophilic bacterial origin, pHB1 of 2.1 kb and two closely related variants pHB2a and pHB2b, of 5.2 and 4.8 kb respectively. Strategies are considered for assembling genomes of smaller genetic elements from complex environmental samples, and for establishing possible host identities on the basis of sequence similarity to host CRISPR immune systems.

AB - Two novel viral genomes and four plasmids were assembled from an environmental sample collected from a hot spring at Yellowstone National Park, USA, and maintained anaerobically in a bioreactor at 85°C and pH 6. The double-stranded DNA viral genomes are linear (22.7 kb) and circular (17.7 kb), and derive apparently from archaeal viruses HAV1 and HAV2. Genomic DNA was obtained from samples enriched in filamentous and tadpole-shaped virus-like particles respectively. They yielded few significant matches in public sequence databases reinforcing, further, the wide diversity of archaeal viruses. Several variants of HAV1 exhibit major genomic alterations, presumed to arise from viral adaptation to different hosts. They include insertions up to 350 bp, deletions up to 1.5 kb, and genes with extensively altered sequences. Some result from recombination events occurring at low complexity direct repeats distributed along the genome. In addition, a 33.8 kb archaeal plasmid pHA1 was characterized, encoding a possible conjugative apparatus, as well as three cryptic plasmids of thermophilic bacterial origin, pHB1 of 2.1 kb and two closely related variants pHB2a and pHB2b, of 5.2 and 4.8 kb respectively. Strategies are considered for assembling genomes of smaller genetic elements from complex environmental samples, and for establishing possible host identities on the basis of sequence similarity to host CRISPR immune systems.

KW - Archaea

KW - Archaeal Viruses

KW - Bacteria

KW - Base Sequence

KW - DNA, Intergenic

KW - Databases, Nucleic Acid

KW - Genetic Variation

KW - Genome, Viral

KW - Hot Springs

KW - Hot Temperature

KW - Inverted Repeat Sequences

KW - Metagenomics

KW - Microscopy, Electron

KW - Mutagenesis, Insertional

KW - Plasmids

KW - Repetitive Sequences, Nucleic Acid

KW - Sequence Analysis, DNA

KW - Sequence Deletion

KW - Wyoming

U2 - 10.1111/j.1462-2920.2010.02266.x

DO - 10.1111/j.1462-2920.2010.02266.x

M3 - Journal article

C2 - 20545752

SN - 1462-2912

VL - 12

SP - 2918

EP - 2930

JO - Environmental Microbiology

JF - Environmental Microbiology

IS - 11

ER -