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Complete genome sequence of Paenibacillus sp. strain JDR-2.

Chow V, Nong G, St John FJ, Rice JD, Dickstein E, Chertkov O, Bruce D, Detter C, Brettin T, Han J, Woyke T, Pitluck S, Nolan M, Pati A, Martin J, Copeland A, Land ML, Goodwin L, Jones JB, Ingram LO, Shanmugam KT, Preston JF - Stand Genomic Sci (2012)

Bottom Line: The genome of Paenibacillus sp.Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism.The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

View Article: PubMed Central - PubMed

ABSTRACT
Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of β-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

No MeSH data available.


Related in: MedlinePlus

Circular map of the genome of Paenibacillus sp JDR-2. Labeling from the outside circle towards the inside circles: circle 1. Nucleotide numbering system; circle 2 and 3. Predicted coding sequences on the forward strand and on the reverse strand with each gene colored by its assigned COG category; circle 4. RNA genes (tRNAs in green, rRNAs in red, other RNAs in black); circle 5. GC content; circle 6. GC skew.
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f3: Circular map of the genome of Paenibacillus sp JDR-2. Labeling from the outside circle towards the inside circles: circle 1. Nucleotide numbering system; circle 2 and 3. Predicted coding sequences on the forward strand and on the reverse strand with each gene colored by its assigned COG category; circle 4. RNA genes (tRNAs in green, rRNAs in red, other RNAs in black); circle 5. GC content; circle 6. GC skew.

Mentions: Genes were identified using Prodigal [37] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by manual curation using the JGI program GenePRIMP [38]. The predicted CDSs were translated and searched with the following databases to assign a product description for each predicted protein: the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [39], RNAMMer [38], Rfam [40], TMHMM [41], and SignalP [42]. Genome statistics are provided in Table 2, and a full circular map in Figure 3 below.


Complete genome sequence of Paenibacillus sp. strain JDR-2.

Chow V, Nong G, St John FJ, Rice JD, Dickstein E, Chertkov O, Bruce D, Detter C, Brettin T, Han J, Woyke T, Pitluck S, Nolan M, Pati A, Martin J, Copeland A, Land ML, Goodwin L, Jones JB, Ingram LO, Shanmugam KT, Preston JF - Stand Genomic Sci (2012)

Circular map of the genome of Paenibacillus sp JDR-2. Labeling from the outside circle towards the inside circles: circle 1. Nucleotide numbering system; circle 2 and 3. Predicted coding sequences on the forward strand and on the reverse strand with each gene colored by its assigned COG category; circle 4. RNA genes (tRNAs in green, rRNAs in red, other RNAs in black); circle 5. GC content; circle 6. GC skew.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368403&req=5

f3: Circular map of the genome of Paenibacillus sp JDR-2. Labeling from the outside circle towards the inside circles: circle 1. Nucleotide numbering system; circle 2 and 3. Predicted coding sequences on the forward strand and on the reverse strand with each gene colored by its assigned COG category; circle 4. RNA genes (tRNAs in green, rRNAs in red, other RNAs in black); circle 5. GC content; circle 6. GC skew.
Mentions: Genes were identified using Prodigal [37] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by manual curation using the JGI program GenePRIMP [38]. The predicted CDSs were translated and searched with the following databases to assign a product description for each predicted protein: the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [39], RNAMMer [38], Rfam [40], TMHMM [41], and SignalP [42]. Genome statistics are provided in Table 2, and a full circular map in Figure 3 below.

Bottom Line: The genome of Paenibacillus sp.Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism.The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

View Article: PubMed Central - PubMed

ABSTRACT
Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of β-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

No MeSH data available.


Related in: MedlinePlus