Journal article
Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter
Applied and environmental microbiology, Vol.74(9), pp.2852-2863
05/2008
Handle:
https://hdl.handle.net/2376/113064
PMCID: PMC2394895
PMID: 18326675
Abstract
The alphaproteobacterium
Nitrobacter hamburgensis
X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the
Nitrobacter hamburgensis
X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between
N. hamburgensis
and the finished and draft genome sequences of
Nitrobacter winogradskyi
and
Nitrobacter
sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to
N. hamburgensis
and encode a variety of functions (central metabolism, energy conservation, conjugation, and heavy metal resistance), yet ∼21 kb of a ∼28-kb “autotrophic” island on the largest plasmid was conserved in the chromosomes of
Nitrobacter winogradskyi
Nb-255 and
Nitrobacter
sp. strain Nb-311A. The
N. hamburgensis
chromosome also harbors many unique genes, including those for heme-copper oxidases, cytochrome
b
561
, and putative pathways for the catabolism of aromatic, organic, and one-carbon compounds, which help verify and extend its mixotrophic potential. A
Nitrobacter
“subcore” genome was also constructed by removing homologs found in strains of the closest evolutionary relatives,
Bradyrhizobium japonicum
and
Rhodopseudomonas palustris
. Among the
Nitrobacter
subcore inventory (116 genes), copies of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes associated with a dissimilatory nitrite reductase (NirK), PII-like regulators, and polysaccharide formation were identified. Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in
Nitrobacter
.
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Details
- Title
- Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter
- Creators
- Shawn R Starkenburg - Oregon State University, Corvallis, Oregon 97331Frank W Larimer - Oregon State University, Corvallis, Oregon 97331Lisa Y Stein - Oregon State University, Corvallis, Oregon 97331Martin G Klotz - Oregon State University, Corvallis, Oregon 97331Patrick S. G Chain - Oregon State University, Corvallis, Oregon 97331Luis A Sayavedra-Soto - Oregon State University, Corvallis, Oregon 97331Amisha T Poret-Peterson - Oregon State University, Corvallis, Oregon 97331Mira E Gentry - Oregon State University, Corvallis, Oregon 97331Daniel J Arp - Oregon State University, Corvallis, Oregon 97331Bess Ward - Oregon State University, Corvallis, Oregon 97331Peter J Bottomley - Oregon State University, Corvallis, Oregon 97331
- Publication Details
- Applied and environmental microbiology, Vol.74(9), pp.2852-2863
- Academic Unit
- Molecular Biosciences, School of
- Publisher
- American Society for Microbiology (ASM)
- Identifiers
- 99900547735301842
- Language
- English
- Resource Type
- Journal article