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

. 2011 Dec 31;5(3):356-70.

doi: 10.4056/sigs.2194987. Epub 2011 Dec 23.

Markus Nett, Nicole Domin, Karin Martin, Julia A Maresca, Alex Copeland, Alla Lapidus, Susan Lucas, Kerrie W Berry, Tijana Glavina Del Rio, Eileen Dalin, Hope Tice, Sam Pitluck, Paul Richardson, David Bruce, Lynne Goodwin, Cliff Han, John C Detter, Jeremy Schmutz, Thomas Brettin, Miriam Land, Loren Hauser, Nikos C Kyrpides, Natalia Ivanova, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Donald A Bryant

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

Hajnalka Kiss et al. Stand Genomic Sci. 2011.

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.

Keywords: Chemoorganoheterotrophic; Chloroflexi; DOEM2005; Gram-negative; Herpetosiphonaceae; ensheathed filaments; free-living; gliding; predator.

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Figures

Figure 1

Figure 1

Phylogenetic tree highlighting the position of H. aurantiacus relative to the other type strains within the phylum Chloroflexi. The tree was inferred from 1,350 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 100 ML bootstrap replicates [15] (left) and from 1,000 maximum parsimony bootstrap replicates [16] (right) if the value is larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, and those also listed as 'Complete and Published' with two asterisks (see [18,19] and AP012029 for Anaerolinea thermophila, CP002084 for Dehalogenimonas lykanthroporepellens, CP001337 for Chloroflexus aggregans, CP000909 C. aurantiacus, and CP000804 for Roseiflexus castenholzii).

Figure 2

Figure 2

Scanning electron micrograph of a multicellular filament of H. aurantiacus 114-95T.

Figure 3

Figure 3

Graphical circular map of the chromosome (not drawn to scale with plasmids). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 4

Figure 4

Graphical circular map of the plasmid pHAU01. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 5

Figure 5

Graphical circular map of the plasmid pHAU02 (not drawn to scale with chromosome). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 6

Figure 6

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.

References

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