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Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)).

Kiss H, Nett M, Domin N, Martin K, Maresca JA, Copeland A, Lapidus A, Lucas S, Berry KW, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Detter JC, Schmutz J, Brettin T, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Klenk HP, Bryant DA - Stand Genomic Sci (2011)

Bottom Line: H. aurantiacus cells are organized in filaments which can rapidly glide.The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes.The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

View Article: PubMed Central - PubMed

ABSTRACT
Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95(T) is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

No MeSH data available.


Related in: MedlinePlus

Chromosome of H. aurantiacus strain 114-95T oriented to the dnaA gene (top). The inner ring shows a normalized plot of GC skew, while the center ring shows a normalized plot of GC content. The outer circle shows the distribution of secondary metabolite gene clusters. Biosynthetic gene clusters associated with thiotemplate-based assembly (PKS, NRPS) are depicted in red and bacteriocin loci are marked in black.
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f6: Chromosome of H. aurantiacus strain 114-95T oriented to the dnaA gene (top). The inner ring shows a normalized plot of GC skew, while the center ring shows a normalized plot of GC content. The outer circle shows the distribution of secondary metabolite gene clusters. Biosynthetic gene clusters associated with thiotemplate-based assembly (PKS, NRPS) are depicted in red and bacteriocin loci are marked in black.

Mentions: The genome consists of a circular chromosome (6,346,587 bp) and two circular plasmids, pHAU01 (339,639 bp) and pHAU02 (88,204 bp), respectively with an overall G+C content of 50.9% (Table 3, Figure 3, Figure 4, Figure 5 and Figure 6). These are the only plasmids that have been identified to date among the seventeen Chloroflexi strains whose genomes have been sequenced. Interestingly, the GC content of the chromosome (50.7%) is notably lower than that of pHAU01 (53.7%) or pHAU02 (53.1%). Plasmid pHAU02 is predicted to encode 71 proteins, and pHAU01 is predicted to encode 231 potential proteins, which included a variety of transposases, phage recombinases and integrases, a CRISPR and CRISPR-associated gene cluster, and a variety of predicted transcription regulators. Neither plasmid encodes a product known to be essential for cell viability. Of the 5,654 genes predicted, 5,577 were protein-coding genes, and 77 encoded RNAs; 82 pseudogenes were identified. The majority of the protein-coding genes (67.4%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.


Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)).

Kiss H, Nett M, Domin N, Martin K, Maresca JA, Copeland A, Lapidus A, Lucas S, Berry KW, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Detter JC, Schmutz J, Brettin T, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Klenk HP, Bryant DA - Stand Genomic Sci (2011)

Chromosome of H. aurantiacus strain 114-95T oriented to the dnaA gene (top). The inner ring shows a normalized plot of GC skew, while the center ring shows a normalized plot of GC content. The outer circle shows the distribution of secondary metabolite gene clusters. Biosynthetic gene clusters associated with thiotemplate-based assembly (PKS, NRPS) are depicted in red and bacteriocin loci are marked in black.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368417&req=5

f6: Chromosome of H. aurantiacus strain 114-95T oriented to the dnaA gene (top). The inner ring shows a normalized plot of GC skew, while the center ring shows a normalized plot of GC content. The outer circle shows the distribution of secondary metabolite gene clusters. Biosynthetic gene clusters associated with thiotemplate-based assembly (PKS, NRPS) are depicted in red and bacteriocin loci are marked in black.
Mentions: The genome consists of a circular chromosome (6,346,587 bp) and two circular plasmids, pHAU01 (339,639 bp) and pHAU02 (88,204 bp), respectively with an overall G+C content of 50.9% (Table 3, Figure 3, Figure 4, Figure 5 and Figure 6). These are the only plasmids that have been identified to date among the seventeen Chloroflexi strains whose genomes have been sequenced. Interestingly, the GC content of the chromosome (50.7%) is notably lower than that of pHAU01 (53.7%) or pHAU02 (53.1%). Plasmid pHAU02 is predicted to encode 71 proteins, and pHAU01 is predicted to encode 231 potential proteins, which included a variety of transposases, phage recombinases and integrases, a CRISPR and CRISPR-associated gene cluster, and a variety of predicted transcription regulators. Neither plasmid encodes a product known to be essential for cell viability. Of the 5,654 genes predicted, 5,577 were protein-coding genes, and 77 encoded RNAs; 82 pseudogenes were identified. The majority of the protein-coding genes (67.4%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Bottom Line: H. aurantiacus cells are organized in filaments which can rapidly glide.The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes.The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

View Article: PubMed Central - PubMed

ABSTRACT
Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95(T) is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

No MeSH data available.


Related in: MedlinePlus