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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

Comparative Linear Display Representing the Sequence Homologies between the A. aurescens pTC1 Plasmid, the Pseudomonas sp. pADP-1 Plasmid, and the A. nicotinivorans pAO1 PlasmidOnly selected regions for each of the three plasmids are shown. The percent of protein identity is indicated by the color of the connecting lines (legend on the bottom left side of the figure). For clarity, the locus tags (AAur_pTC1 for the pTC1 plasmid, AAK for the pADP-1 plasmid, and CAD for the pAO1 plasmid) were removed from the ORF numbers.
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pgen-0020214-g004: Comparative Linear Display Representing the Sequence Homologies between the A. aurescens pTC1 Plasmid, the Pseudomonas sp. pADP-1 Plasmid, and the A. nicotinivorans pAO1 PlasmidOnly selected regions for each of the three plasmids are shown. The percent of protein identity is indicated by the color of the connecting lines (legend on the bottom left side of the figure). For clarity, the locus tags (AAur_pTC1 for the pTC1 plasmid, AAK for the pADP-1 plasmid, and CAD for the pAO1 plasmid) were removed from the ORF numbers.

Mentions: Genes on pTC1 showed limited homology to those on other sequenced plasmids, including plasmid sequences reported for Arthrobacter sp. FB24. The genes on pTC1 involved in atrazine degradation were initially discovered by homology to genes carried by plasmid pADP-1 from Pseudomonas sp. strain ADP [46]. The greatest relationship between pADP1 and pTC1, with an amino-acid similarity of 83.3%–100%, seems to be limited to the region delimited by 17 pTC1-encoded ORFS (AAur_pTC10202 through AAur_pTC10225; Table S4) containing the atrazine degradation genes atzB and atzC and several transposases (Figure 4). Outside this region, there were 14 additional genes showing more limited similarity (30%–43%) between plasmids pTC1 and pADP1, primarily encoding transposases, IS elements, and mercury-resistance proteins. However, two additional ORFs (AAur_pTC10210 and AAur_pTC10215) had significant amino acid similarity (81%–100%) to ORFs on pADP-1 encoding a putative transporter and a dihydrolipoamide dehydrogenase homolog, respectively (Table S4).


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)

Comparative Linear Display Representing the Sequence Homologies between the A. aurescens pTC1 Plasmid, the Pseudomonas sp. pADP-1 Plasmid, and the A. nicotinivorans pAO1 PlasmidOnly selected regions for each of the three plasmids are shown. The percent of protein identity is indicated by the color of the connecting lines (legend on the bottom left side of the figure). For clarity, the locus tags (AAur_pTC1 for the pTC1 plasmid, AAK for the pADP-1 plasmid, and CAD for the pAO1 plasmid) were removed from the ORF numbers.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0020214-g004: Comparative Linear Display Representing the Sequence Homologies between the A. aurescens pTC1 Plasmid, the Pseudomonas sp. pADP-1 Plasmid, and the A. nicotinivorans pAO1 PlasmidOnly selected regions for each of the three plasmids are shown. The percent of protein identity is indicated by the color of the connecting lines (legend on the bottom left side of the figure). For clarity, the locus tags (AAur_pTC1 for the pTC1 plasmid, AAK for the pADP-1 plasmid, and CAD for the pAO1 plasmid) were removed from the ORF numbers.
Mentions: Genes on pTC1 showed limited homology to those on other sequenced plasmids, including plasmid sequences reported for Arthrobacter sp. FB24. The genes on pTC1 involved in atrazine degradation were initially discovered by homology to genes carried by plasmid pADP-1 from Pseudomonas sp. strain ADP [46]. The greatest relationship between pADP1 and pTC1, with an amino-acid similarity of 83.3%–100%, seems to be limited to the region delimited by 17 pTC1-encoded ORFS (AAur_pTC10202 through AAur_pTC10225; Table S4) containing the atrazine degradation genes atzB and atzC and several transposases (Figure 4). Outside this region, there were 14 additional genes showing more limited similarity (30%–43%) between plasmids pTC1 and pADP1, primarily encoding transposases, IS elements, and mercury-resistance proteins. However, two additional ORFs (AAur_pTC10210 and AAur_pTC10215) had significant amino acid similarity (81%–100%) to ORFs on pADP-1 encoding a putative transporter and a dihydrolipoamide dehydrogenase homolog, respectively (Table S4).

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