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Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

Saw JH, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa S, Alam M - Stand Genomic Sci (2012)

Bottom Line: Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases.The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented.A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

View Article: PubMed Central - PubMed

ABSTRACT
Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

No MeSH data available.


Related in: MedlinePlus

Circular maps of the S. grandis str. Lewin genome. (A) Chromosome. From the inside to outside: GC skew, GC content, genomic islands, rRNA and tRNA coding genes, CRISPR repeat regions, protein coding genes in positive and negative strands colored according to COG categories. (B) Plasmid. From inside to outside: GC skew, GC content, protein coding genes in positive and negative strands colored according to COG categories.
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f2: Circular maps of the S. grandis str. Lewin genome. (A) Chromosome. From the inside to outside: GC skew, GC content, genomic islands, rRNA and tRNA coding genes, CRISPR repeat regions, protein coding genes in positive and negative strands colored according to COG categories. (B) Plasmid. From inside to outside: GC skew, GC content, protein coding genes in positive and negative strands colored according to COG categories.

Mentions: The genome contains a single circular chromosome of 4,345,237 bases and a circular plasmid of 54,948 bases. The circular genomic maps of the S. grandis str. Lewin chromosome and plasmid are shown in Figure 2A and Figure 2B, respectively, and the general genome features are listed in Table 3. The G+C% of the genome is 46.36%. A total of 4,251 ORFs with an average length of 886 bp were predicted. Protein coding genes with known functions account for 50.4% of the genes identified and 34.8% of the gene products have no known function associated with them, i.e., annotated as hypothetical proteins. Conserved hypothetical proteins account for 14.7% of the coding sequences. The distribution of genes into COG functional categories is listed in Table 4. There are 3 ribosomal RNA operons and 48 tRNA genes. The IslandViewer web server predicted 18 putative genomic islands within the genome (Figure 2A).


Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

Saw JH, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa S, Alam M - Stand Genomic Sci (2012)

Circular maps of the S. grandis str. Lewin genome. (A) Chromosome. From the inside to outside: GC skew, GC content, genomic islands, rRNA and tRNA coding genes, CRISPR repeat regions, protein coding genes in positive and negative strands colored according to COG categories. (B) Plasmid. From inside to outside: GC skew, GC content, protein coding genes in positive and negative strands colored according to COG categories.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368406&req=5

f2: Circular maps of the S. grandis str. Lewin genome. (A) Chromosome. From the inside to outside: GC skew, GC content, genomic islands, rRNA and tRNA coding genes, CRISPR repeat regions, protein coding genes in positive and negative strands colored according to COG categories. (B) Plasmid. From inside to outside: GC skew, GC content, protein coding genes in positive and negative strands colored according to COG categories.
Mentions: The genome contains a single circular chromosome of 4,345,237 bases and a circular plasmid of 54,948 bases. The circular genomic maps of the S. grandis str. Lewin chromosome and plasmid are shown in Figure 2A and Figure 2B, respectively, and the general genome features are listed in Table 3. The G+C% of the genome is 46.36%. A total of 4,251 ORFs with an average length of 886 bp were predicted. Protein coding genes with known functions account for 50.4% of the genes identified and 34.8% of the gene products have no known function associated with them, i.e., annotated as hypothetical proteins. Conserved hypothetical proteins account for 14.7% of the coding sequences. The distribution of genes into COG functional categories is listed in Table 4. There are 3 ribosomal RNA operons and 48 tRNA genes. The IslandViewer web server predicted 18 putative genomic islands within the genome (Figure 2A).

Bottom Line: Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases.The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented.A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

View Article: PubMed Central - PubMed

ABSTRACT
Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

No MeSH data available.


Related in: MedlinePlus