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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

Circular Representation of the Chromosome of A. aurescens TC1Each concentric circle is numbered from the outermost circle to the inner most circle and represents genomic data for A. aurescens strain TC1 chromosome. The first and second circles represent the predicted coding sequences on the plus and minus strands, respectively, colored by functional role categories: salmon, amino acid biosynthesis; light blue, biosynthesis of cofactors and prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; green, energy metabolism; purple, fatty acid and phospholipid metabolism; pink, protein fate and synthesis; orange, purines, pyrimidines, nucleosides, and nucleotides; blue, regulatory functions; grey, transcription; teal, transport and binding proteins; and black, hypothetical and conserved hypothetical proteins. The third circle displays the G + C skew: positive G + C skew in magenta and negative G + C skew in green. The fourth circle displays the rRNAs (red), sRNAs (blue), and tRNAs (green). The fifth circle displays repeated sequences of at least 50 bp long (at least 97% identity between two repeats); each color/tick size represents a different repeat. Prophage (blue ticks) and transposon (dark green ticks) genes are displayed on the sixth circle. The seventh circle displays the percentage of similarity (BLASTP searches) between TC1 and Arthrobacter sp. FB24 ORFs: >95%, full-sized black ticks; 85%–95%, three-quarter sized brown ticks; 75%–85%, three-quarter sized red ticks; 65%–75%, half-sized gold ticks; 55%–65%, half-sized yellow ticks. The eighth and ninth circles display the organism best match: L. xili (blue ticks), S. coelicolor (green ticks), and S. avermitilis (gold ticks) on circle 8. N. farcinica (red ticks), T. fusca (brown ticks), M. avium (cyan ticks), and C. efficiens (black ticks) on circle 9. The tenth circle shows the regions of atypical composition (χ2 analysis).
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pgen-0020214-g001: Circular Representation of the Chromosome of A. aurescens TC1Each concentric circle is numbered from the outermost circle to the inner most circle and represents genomic data for A. aurescens strain TC1 chromosome. The first and second circles represent the predicted coding sequences on the plus and minus strands, respectively, colored by functional role categories: salmon, amino acid biosynthesis; light blue, biosynthesis of cofactors and prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; green, energy metabolism; purple, fatty acid and phospholipid metabolism; pink, protein fate and synthesis; orange, purines, pyrimidines, nucleosides, and nucleotides; blue, regulatory functions; grey, transcription; teal, transport and binding proteins; and black, hypothetical and conserved hypothetical proteins. The third circle displays the G + C skew: positive G + C skew in magenta and negative G + C skew in green. The fourth circle displays the rRNAs (red), sRNAs (blue), and tRNAs (green). The fifth circle displays repeated sequences of at least 50 bp long (at least 97% identity between two repeats); each color/tick size represents a different repeat. Prophage (blue ticks) and transposon (dark green ticks) genes are displayed on the sixth circle. The seventh circle displays the percentage of similarity (BLASTP searches) between TC1 and Arthrobacter sp. FB24 ORFs: >95%, full-sized black ticks; 85%–95%, three-quarter sized brown ticks; 75%–85%, three-quarter sized red ticks; 65%–75%, half-sized gold ticks; 55%–65%, half-sized yellow ticks. The eighth and ninth circles display the organism best match: L. xili (blue ticks), S. coelicolor (green ticks), and S. avermitilis (gold ticks) on circle 8. N. farcinica (red ticks), T. fusca (brown ticks), M. avium (cyan ticks), and C. efficiens (black ticks) on circle 9. The tenth circle shows the regions of atypical composition (χ2 analysis).

Mentions: The genome of A. aurescens TC1 is comprised of three molecules: a single circular chromosome of 4,597,686 bp (locus tag: AAur) and two plasmids: pTC1 (locus tag: AAur_pTC1) and pTC2 (locus tag: AAur_pTC2) of 328,237 and 300,725 bp, respectively (Figure 1; Figure 2; Table 1). Since the pTC1 contains six identical copies of a 16-kb repeat region, the final molecule size is approximately 408 kb (see below and Materials and Methods). Overall, the chromosome and plasmids of the A. aurescens genome contain 4,708 open reading frames (ORFs), of which 3,071 (65.2%) could be assigned a putative function. Approximately 13.2% (623 hypothetical proteins) of the A. aurescens TC1 genome appears to be unique to this bacterium, with no matches to any known sequence.


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)

Circular Representation of the Chromosome of A. aurescens TC1Each concentric circle is numbered from the outermost circle to the inner most circle and represents genomic data for A. aurescens strain TC1 chromosome. The first and second circles represent the predicted coding sequences on the plus and minus strands, respectively, colored by functional role categories: salmon, amino acid biosynthesis; light blue, biosynthesis of cofactors and prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; green, energy metabolism; purple, fatty acid and phospholipid metabolism; pink, protein fate and synthesis; orange, purines, pyrimidines, nucleosides, and nucleotides; blue, regulatory functions; grey, transcription; teal, transport and binding proteins; and black, hypothetical and conserved hypothetical proteins. The third circle displays the G + C skew: positive G + C skew in magenta and negative G + C skew in green. The fourth circle displays the rRNAs (red), sRNAs (blue), and tRNAs (green). The fifth circle displays repeated sequences of at least 50 bp long (at least 97% identity between two repeats); each color/tick size represents a different repeat. Prophage (blue ticks) and transposon (dark green ticks) genes are displayed on the sixth circle. The seventh circle displays the percentage of similarity (BLASTP searches) between TC1 and Arthrobacter sp. FB24 ORFs: >95%, full-sized black ticks; 85%–95%, three-quarter sized brown ticks; 75%–85%, three-quarter sized red ticks; 65%–75%, half-sized gold ticks; 55%–65%, half-sized yellow ticks. The eighth and ninth circles display the organism best match: L. xili (blue ticks), S. coelicolor (green ticks), and S. avermitilis (gold ticks) on circle 8. N. farcinica (red ticks), T. fusca (brown ticks), M. avium (cyan ticks), and C. efficiens (black ticks) on circle 9. The tenth circle shows the regions of atypical composition (χ2 analysis).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0020214-g001: Circular Representation of the Chromosome of A. aurescens TC1Each concentric circle is numbered from the outermost circle to the inner most circle and represents genomic data for A. aurescens strain TC1 chromosome. The first and second circles represent the predicted coding sequences on the plus and minus strands, respectively, colored by functional role categories: salmon, amino acid biosynthesis; light blue, biosynthesis of cofactors and prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; green, energy metabolism; purple, fatty acid and phospholipid metabolism; pink, protein fate and synthesis; orange, purines, pyrimidines, nucleosides, and nucleotides; blue, regulatory functions; grey, transcription; teal, transport and binding proteins; and black, hypothetical and conserved hypothetical proteins. The third circle displays the G + C skew: positive G + C skew in magenta and negative G + C skew in green. The fourth circle displays the rRNAs (red), sRNAs (blue), and tRNAs (green). The fifth circle displays repeated sequences of at least 50 bp long (at least 97% identity between two repeats); each color/tick size represents a different repeat. Prophage (blue ticks) and transposon (dark green ticks) genes are displayed on the sixth circle. The seventh circle displays the percentage of similarity (BLASTP searches) between TC1 and Arthrobacter sp. FB24 ORFs: >95%, full-sized black ticks; 85%–95%, three-quarter sized brown ticks; 75%–85%, three-quarter sized red ticks; 65%–75%, half-sized gold ticks; 55%–65%, half-sized yellow ticks. The eighth and ninth circles display the organism best match: L. xili (blue ticks), S. coelicolor (green ticks), and S. avermitilis (gold ticks) on circle 8. N. farcinica (red ticks), T. fusca (brown ticks), M. avium (cyan ticks), and C. efficiens (black ticks) on circle 9. The tenth circle shows the regions of atypical composition (χ2 analysis).
Mentions: The genome of A. aurescens TC1 is comprised of three molecules: a single circular chromosome of 4,597,686 bp (locus tag: AAur) and two plasmids: pTC1 (locus tag: AAur_pTC1) and pTC2 (locus tag: AAur_pTC2) of 328,237 and 300,725 bp, respectively (Figure 1; Figure 2; Table 1). Since the pTC1 contains six identical copies of a 16-kb repeat region, the final molecule size is approximately 408 kb (see below and Materials and Methods). Overall, the chromosome and plasmids of the A. aurescens genome contain 4,708 open reading frames (ORFs), of which 3,071 (65.2%) could be assigned a putative function. Approximately 13.2% (623 hypothetical proteins) of the A. aurescens TC1 genome appears to be unique to this bacterium, with no matches to any known sequence.

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