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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

Phylogenetic tree highlighting the position of Saprospira grandis strain Lewin relative to other type and non-type strains within the Saprospiraceae. The tree was inferred from 1,350 aligned characters of the 16S rRNA gene sequence using maximum likelihood method. The branch lengths indicate the expected number of substitutions per site and the numbers adjacent to the branches are support values from 1,000 bootstrap replicates. Bootstrap values are indicated only if they are larger than 60%. Best topology of the tree was inferred by the phylogenetic analysis tool RAxML using GTR (General Time Reversible) model of substitution with the gamma model of rate heterogeneity [21]. Chitinophaga pinensis 16S rRNA gene was used to root the tree.
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f1: Phylogenetic tree highlighting the position of Saprospira grandis strain Lewin relative to other type and non-type strains within the Saprospiraceae. The tree was inferred from 1,350 aligned characters of the 16S rRNA gene sequence using maximum likelihood method. The branch lengths indicate the expected number of substitutions per site and the numbers adjacent to the branches are support values from 1,000 bootstrap replicates. Bootstrap values are indicated only if they are larger than 60%. Best topology of the tree was inferred by the phylogenetic analysis tool RAxML using GTR (General Time Reversible) model of substitution with the gamma model of rate heterogeneity [21]. Chitinophaga pinensis 16S rRNA gene was used to root the tree.

Mentions: There are three identical copies of the 16S rRNA gene in the Saprospira grandis str. Lewin genome and one copy was chosen to search against the nucleotide database using NCBI BLAST [19]. It has the highest sequence identity to Saprospira grandis SS98-5 (99.7%, AB088636) isolated from Kagoshima Bay, Japan in 1998 [10], 99.4% identity to Saprospira grandis DSM 2844, and 98.0% identity to the type strain Gross [20]. S. grandis DSM 2844 is the only other strain with a draft genome sequence currently available from the Joint Genome Institute (JGI). Figure 1 shows the phylogenetic neighborhood of S. grandis str. Lewin in relation to type and non-type strains within the genus Saprospiraceae. Chitinophaga pinensis was used as an outgroup to root the tree.


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)

Phylogenetic tree highlighting the position of Saprospira grandis strain Lewin relative to other type and non-type strains within the Saprospiraceae. The tree was inferred from 1,350 aligned characters of the 16S rRNA gene sequence using maximum likelihood method. The branch lengths indicate the expected number of substitutions per site and the numbers adjacent to the branches are support values from 1,000 bootstrap replicates. Bootstrap values are indicated only if they are larger than 60%. Best topology of the tree was inferred by the phylogenetic analysis tool RAxML using GTR (General Time Reversible) model of substitution with the gamma model of rate heterogeneity [21]. Chitinophaga pinensis 16S rRNA gene was used to root the tree.
© Copyright Policy
Related In: Results  -  Collection

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

f1: Phylogenetic tree highlighting the position of Saprospira grandis strain Lewin relative to other type and non-type strains within the Saprospiraceae. The tree was inferred from 1,350 aligned characters of the 16S rRNA gene sequence using maximum likelihood method. The branch lengths indicate the expected number of substitutions per site and the numbers adjacent to the branches are support values from 1,000 bootstrap replicates. Bootstrap values are indicated only if they are larger than 60%. Best topology of the tree was inferred by the phylogenetic analysis tool RAxML using GTR (General Time Reversible) model of substitution with the gamma model of rate heterogeneity [21]. Chitinophaga pinensis 16S rRNA gene was used to root the tree.
Mentions: There are three identical copies of the 16S rRNA gene in the Saprospira grandis str. Lewin genome and one copy was chosen to search against the nucleotide database using NCBI BLAST [19]. It has the highest sequence identity to Saprospira grandis SS98-5 (99.7%, AB088636) isolated from Kagoshima Bay, Japan in 1998 [10], 99.4% identity to Saprospira grandis DSM 2844, and 98.0% identity to the type strain Gross [20]. S. grandis DSM 2844 is the only other strain with a draft genome sequence currently available from the Joint Genome Institute (JGI). Figure 1 shows the phylogenetic neighborhood of S. grandis str. Lewin in relation to type and non-type strains within the genus Saprospiraceae. Chitinophaga pinensis was used as an outgroup to root the tree.

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