The predicted CDSs were translated and searched with the followin

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 protein inhibitor 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. Table 2 Genomic Statistics Figure 3 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 …

Insights from genome sequencing Utilization of lignocellulosics The nucleotide sequence of a cluster of genes which included the ��-glucuronidase gene served as a marker for the sequenced genome. The sequence of this cluster was previously determined in a cosmid clone of the genomic DNA of Pjdr2. The presence of this unique contiguous sequence in a single copy without orthologs or paralogs supported the final genomic sequence as representative of a single genome from a pure culture. This aldouronate-utilization gene cluster, in conjunction with the distal gene encoding a multimodular cell-associated GH10 endoxylanase, constitutes a xylan-utilization regulon as previously defined [3].

The coordinate expression of the genes in this regulon supports a process in which assimilation of the aldouronate, 4-0-methylglucuronoxylotriose, generated by a cell-associated GH10 endoxylanase, is coupled to extracellular depolymerization, facilitating depolymerization, assimilation and metabolism as previously described [4]. The sequencing of the genome of Paenibacillus sp. strain JDR-2 has allowed further analysis of its xylan-utilization regulon and the identification of similar regulons involved in the depolymerization and utilization of soluble ��-glucans. A noteworthy feature of the genome of Pjdr2 is the large number (874) of genes involved in carbohydrate metabolism and transport constituting 17% of the genome (Table 3). This characteristic contrasted with 9% and 291 genes in Bacillus subtilis subtilis 168 and 11% and 481 genes in Paenibacillus polymyxa E861.

The recently completed genome Paenibacillus sp. Y412MC10, however, is quite similar to Pjdr2 and contains 16% and 828 genes Cilengitide in this category. Table 3 Number of genes associated with the general COG functional categories Acknowledgements We thank the Electron Microscopy and Bio-Imaging laboratory, Interdisciplinary Center for Biotechnology Research, University of Florida for their assistance in preparing the scanning electron micrographs of Strain Pjdr2.

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