Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles
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Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles. / Garrett, Roger Antony; Prangishvili, David; Shah, Shiraz Ali; Reuter, Monika; Stetter, Karl O; Peng, Xu.
I: Environmental Microbiology, Bind 12, Nr. 11, 01.11.2010, s. 2918-30.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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
VL - 12
SP - 2918
EP - 2930
JO - Environmental Microbiology
JF - Environmental Microbiology
SN - 1462-2912
IS - 11
ER -
ID: 33493754