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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

Phylogenetic analysis of Paenibacillus sp. JDR-2 was performed using MEGA4 [9] with the Neighbor-Joining method (bootstrap: 2,000 replicates). The species and GenBank accession numbers are: Paenibacillus larvae subsp. pulvifaciens DSM 3615 (AB073204); Bacillus halodurans C-125 (BA000004); Bacillus subtilis subsp. subtilis str. 168 (AL009126); Bacillus clausii KSM-K16 (AP006627); Bacillus licheniformis DSM 13 (AE017333); Bacillus megaterium str. KL-197 (AY030338); Bacillus stearothermophilus (AB021196); Paenibacillus lentimorbus (AB110988); Paenibacillus popilliae str. ATCC14706(T), (AF071859); Paenibacillus thiaminolyticus (D78475); Paenibacillus nematophilus str. NEM1b (AF480937); Paenibacillus polymyxa (AF355463); Paenibacillus peoriae DSM 8320 (AB073186); Paenibacillus polymyxa SC2 (CP002213); Paenibacillus sp. JDR-2 (CP001656); Paenibacillus sp. Y412MC10 (CP001793); “Paenibacillus vortex” str. V453 (HQ005270); Clostridium difficile 630 (AM180355); Clostridium polysaccharolyticum DSM 1801 (X71858); Clostridium acetobutylicum DSM 1731 (X78071); Clostridium pasteurianum (M23930); Microbacterium testaceum StLB037 (AP012052); Microbacterium laevaniformans str. C820 (NR_036839); Microbacterium luteolum DSM 20143 (Y17235); Cellulosimicrobium cellulans str. ZFJ-17 (EU931556).
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f1: Phylogenetic analysis of Paenibacillus sp. JDR-2 was performed using MEGA4 [9] with the Neighbor-Joining method (bootstrap: 2,000 replicates). The species and GenBank accession numbers are: Paenibacillus larvae subsp. pulvifaciens DSM 3615 (AB073204); Bacillus halodurans C-125 (BA000004); Bacillus subtilis subsp. subtilis str. 168 (AL009126); Bacillus clausii KSM-K16 (AP006627); Bacillus licheniformis DSM 13 (AE017333); Bacillus megaterium str. KL-197 (AY030338); Bacillus stearothermophilus (AB021196); Paenibacillus lentimorbus (AB110988); Paenibacillus popilliae str. ATCC14706(T), (AF071859); Paenibacillus thiaminolyticus (D78475); Paenibacillus nematophilus str. NEM1b (AF480937); Paenibacillus polymyxa (AF355463); Paenibacillus peoriae DSM 8320 (AB073186); Paenibacillus polymyxa SC2 (CP002213); Paenibacillus sp. JDR-2 (CP001656); Paenibacillus sp. Y412MC10 (CP001793); “Paenibacillus vortex” str. V453 (HQ005270); Clostridium difficile 630 (AM180355); Clostridium polysaccharolyticum DSM 1801 (X71858); Clostridium acetobutylicum DSM 1731 (X78071); Clostridium pasteurianum (M23930); Microbacterium testaceum StLB037 (AP012052); Microbacterium laevaniformans str. C820 (NR_036839); Microbacterium luteolum DSM 20143 (Y17235); Cellulosimicrobium cellulans str. ZFJ-17 (EU931556).

Mentions: A phylogenetic tree was constructed using the Neighbor-Joining method [9] for complete sequences of genes encoding 16S rRNA derived from sequenced genomes of Paenibacillus spp., along with the sequences of some members of the Bacillus spp., Microbacterium spp. and Clostridium spp, is presented in Figure 1. The sequence of the gene encoding 16S rRNA (AF355462) from Paenibacillus polymyxa PKB1 is included as representative of the type species of the genus [10].


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)

Phylogenetic analysis of Paenibacillus sp. JDR-2 was performed using MEGA4 [9] with the Neighbor-Joining method (bootstrap: 2,000 replicates). The species and GenBank accession numbers are: Paenibacillus larvae subsp. pulvifaciens DSM 3615 (AB073204); Bacillus halodurans C-125 (BA000004); Bacillus subtilis subsp. subtilis str. 168 (AL009126); Bacillus clausii KSM-K16 (AP006627); Bacillus licheniformis DSM 13 (AE017333); Bacillus megaterium str. KL-197 (AY030338); Bacillus stearothermophilus (AB021196); Paenibacillus lentimorbus (AB110988); Paenibacillus popilliae str. ATCC14706(T), (AF071859); Paenibacillus thiaminolyticus (D78475); Paenibacillus nematophilus str. NEM1b (AF480937); Paenibacillus polymyxa (AF355463); Paenibacillus peoriae DSM 8320 (AB073186); Paenibacillus polymyxa SC2 (CP002213); Paenibacillus sp. JDR-2 (CP001656); Paenibacillus sp. Y412MC10 (CP001793); “Paenibacillus vortex” str. V453 (HQ005270); Clostridium difficile 630 (AM180355); Clostridium polysaccharolyticum DSM 1801 (X71858); Clostridium acetobutylicum DSM 1731 (X78071); Clostridium pasteurianum (M23930); Microbacterium testaceum StLB037 (AP012052); Microbacterium laevaniformans str. C820 (NR_036839); Microbacterium luteolum DSM 20143 (Y17235); Cellulosimicrobium cellulans str. ZFJ-17 (EU931556).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3368403&req=5

f1: Phylogenetic analysis of Paenibacillus sp. JDR-2 was performed using MEGA4 [9] with the Neighbor-Joining method (bootstrap: 2,000 replicates). The species and GenBank accession numbers are: Paenibacillus larvae subsp. pulvifaciens DSM 3615 (AB073204); Bacillus halodurans C-125 (BA000004); Bacillus subtilis subsp. subtilis str. 168 (AL009126); Bacillus clausii KSM-K16 (AP006627); Bacillus licheniformis DSM 13 (AE017333); Bacillus megaterium str. KL-197 (AY030338); Bacillus stearothermophilus (AB021196); Paenibacillus lentimorbus (AB110988); Paenibacillus popilliae str. ATCC14706(T), (AF071859); Paenibacillus thiaminolyticus (D78475); Paenibacillus nematophilus str. NEM1b (AF480937); Paenibacillus polymyxa (AF355463); Paenibacillus peoriae DSM 8320 (AB073186); Paenibacillus polymyxa SC2 (CP002213); Paenibacillus sp. JDR-2 (CP001656); Paenibacillus sp. Y412MC10 (CP001793); “Paenibacillus vortex” str. V453 (HQ005270); Clostridium difficile 630 (AM180355); Clostridium polysaccharolyticum DSM 1801 (X71858); Clostridium acetobutylicum DSM 1731 (X78071); Clostridium pasteurianum (M23930); Microbacterium testaceum StLB037 (AP012052); Microbacterium laevaniformans str. C820 (NR_036839); Microbacterium luteolum DSM 20143 (Y17235); Cellulosimicrobium cellulans str. ZFJ-17 (EU931556).
Mentions: A phylogenetic tree was constructed using the Neighbor-Joining method [9] for complete sequences of genes encoding 16S rRNA derived from sequenced genomes of Paenibacillus spp., along with the sequences of some members of the Bacillus spp., Microbacterium spp. and Clostridium spp, is presented in Figure 1. The sequence of the gene encoding 16S rRNA (AF355462) from Paenibacillus polymyxa PKB1 is included as representative of the type species of the genus [10].

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