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Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.

Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ - PLoS Genet. (2006)

Bottom Line: Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils.The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways.The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.

View Article: PubMed Central - PubMed

Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America.

ABSTRACT
Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.

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Related in: MedlinePlus

Maximum Likelihood Bootstrap Majority-Rule Consensus Tree for 16S rRNA Gene Sequences from 19 Strains Phylogenetically Related to A. aurescens TC1Numbers adjacent to branch points are bootstrap percentages (n = 100 replicates). The bar represents 10% sequence divergence.
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pgen-0020214-g005: Maximum Likelihood Bootstrap Majority-Rule Consensus Tree for 16S rRNA Gene Sequences from 19 Strains Phylogenetically Related to A. aurescens TC1Numbers adjacent to branch points are bootstrap percentages (n = 100 replicates). The bar represents 10% sequence divergence.

Mentions: In agreement with phylogeny based on analysis of 16S rRNA (Figure 5), the genome of A. aurescens TC1 shares coding sequences, (>40% amino acid–sequence identity) with Streptomyces coelicolor A3(2) (668 genes, 14.2% of the TC1 genome) and Leifsonia xyli subsp. xyli str. CTCB07 (232 genes, 4.9% of the TC1 genome) (Figure S2). However, A. aurescens TC1 contains a large number of unique ORFs (3,413) relative to these bacteria, suggesting that this bacterium has diverged from its phylogenetic neighbors. Overall, genome comparisons with respect to genes involved in survival reflect, to some degree, the lifestyle of each organism. For example, the intracellular pathogens Tropheryma and Leifsonia have relatively few genes (three and 38 genes, respectively; Table 2) involved in stress responses, while the bacteria that live in soil, S. avermitilis (147 genes), P. putida (68 genes), A. aurescens TC1 (112 genes), and Arthobacter sp. FB24 (113 genes) have a relatively large number of genes encoding stress-related proteins. Interestingly, however, the industrially important soil bacterium Corynebacterium glutamicum has relatively few genes (39 genes) involved in survival in response to oxidative damage and other stresses (Table 2). As expected, organisms that have both a soil- and animal-host phase, such as the pathogenic Mycobacterium sp. strains, have a number of stress-related ORFs that are intermediate between these two extremes.


Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.

Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ - PLoS Genet. (2006)

Maximum Likelihood Bootstrap Majority-Rule Consensus Tree for 16S rRNA Gene Sequences from 19 Strains Phylogenetically Related to A. aurescens TC1Numbers adjacent to branch points are bootstrap percentages (n = 100 replicates). The bar represents 10% sequence divergence.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1713258&req=5

pgen-0020214-g005: Maximum Likelihood Bootstrap Majority-Rule Consensus Tree for 16S rRNA Gene Sequences from 19 Strains Phylogenetically Related to A. aurescens TC1Numbers adjacent to branch points are bootstrap percentages (n = 100 replicates). The bar represents 10% sequence divergence.
Mentions: In agreement with phylogeny based on analysis of 16S rRNA (Figure 5), the genome of A. aurescens TC1 shares coding sequences, (>40% amino acid–sequence identity) with Streptomyces coelicolor A3(2) (668 genes, 14.2% of the TC1 genome) and Leifsonia xyli subsp. xyli str. CTCB07 (232 genes, 4.9% of the TC1 genome) (Figure S2). However, A. aurescens TC1 contains a large number of unique ORFs (3,413) relative to these bacteria, suggesting that this bacterium has diverged from its phylogenetic neighbors. Overall, genome comparisons with respect to genes involved in survival reflect, to some degree, the lifestyle of each organism. For example, the intracellular pathogens Tropheryma and Leifsonia have relatively few genes (three and 38 genes, respectively; Table 2) involved in stress responses, while the bacteria that live in soil, S. avermitilis (147 genes), P. putida (68 genes), A. aurescens TC1 (112 genes), and Arthobacter sp. FB24 (113 genes) have a relatively large number of genes encoding stress-related proteins. Interestingly, however, the industrially important soil bacterium Corynebacterium glutamicum has relatively few genes (39 genes) involved in survival in response to oxidative damage and other stresses (Table 2). As expected, organisms that have both a soil- and animal-host phase, such as the pathogenic Mycobacterium sp. strains, have a number of stress-related ORFs that are intermediate between these two extremes.

Bottom Line: Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils.The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways.The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.

View Article: PubMed Central - PubMed

Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America.

ABSTRACT
Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.

Show MeSH
Related in: MedlinePlus