The dnaB-pheA (256 -240 ) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism

Abstract

Within the framework of the international programme to sequence the genome of Baci//us subti/is strain 168, we were allocated the region between dna8 (256") and pheA (240"). The sequencing of this region is now complete and we report our primary analysis of the 114 kb region containing 114 ORFs. In addition to previously characterized genes, we have identified genes involved in the utilization of plant cell wall pOlySaCCharideS, stress responses and the metabolism of amino acids, cell walls, DNA and fatty acids. We also discuss various structural and physical features, including the orientation of genes with respect to replication, putative start and stop codons, ribosome binding sites and pindependent transcription terminators. I I

Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis

“…The primary structure of B. subtilis AbfA is very similar to that of the characterized AbfA from Geobacillus stearothermophilus T-6 [71 % identity (Gilead & Shoham, 1995)], AbfATK4 from Geobacillus caldoxylolyticus TK4 [70 % identity (Canakci et al, 2007)] and Araf51 from Clostridium thermocellum [63 % identity (Taylor et al, 2006)], and AF activity was reported for the B. subtilis abfA gene product (Wipat et al, 1996). The amino acid sequence of Abf2 displays high identity to characterized AFs from Bacillus pumilus, ArfA [65 % identity (Degrassi et al, 2003)], Thermobacillus xylanilyticus, AbfD3 [64 % identity (Debeche et al, 2000)], Clostridium cellulovorans, ArfA [60 % identity (Kosugi et al, 2002)] and Clostridium stercorarium ArfB [56 % identity (Zverlov et al, 1998)].…”

“…By primary amino acid sequence analysis, the abfA and abf2 genes from B. subtilis most probably encode AFs (EC 3.2.1.55) (Raposo et al, 2004;Wipat et al, 1996). The primary structure of B. subtilis AbfA is very similar to that of the characterized AbfA from Geobacillus stearothermophilus T-6 [71 % identity (Gilead & Shoham, 1995)], AbfATK4 from Geobacillus caldoxylolyticus TK4 [70 % identity (Canakci et al, 2007)] and Araf51 from Clostridium thermocellum [63 % identity (Taylor et al, 2006)], and AF activity was reported for the B. subtilis abfA gene product (Wipat et al, 1996).…”

Transcriptional Regulation of Genes Encoding Arabinan-Degrading Enzymes in Bacillus subtilis

“…The abfA and the xsa genes most probably encode AFs (EC 3.2.1.55). The amino acid sequence of AbfA displays a high level of identity (71%) to characterized AbfA from Geobacillus stearothermophilus T-6 (8), and AF activity was reported for the B. subtilis abfA gene product (40). Xsa is highly homologous to characterized AFs from Thermobacillus xylanilyticus AbfD3 (64% identity) (3), Clostridium cellulovorans ArfA (60% identity) (15), and Clostridium stercorarium ArfB (56% identity) (42).…”

“…Additionally, the ara regulon is subjected to carbon catabolite repression by glucose and glycerol (11). The last gene of the L-arabinose metabolic operon, abfA, and the xsa gene located 23 kb downstream from the operon (32,40) (Fig. 1) most probably encode AFs belonging to the glycosyl hydrolase (GH) family G51 (see the Carbohydrate-Active Enzymes website [http://afmb.cnrs-mrs.fr /ϳcazy/CAZY]).…”

“…1) most probably encode AFs belonging to the glycosyl hydrolase (GH) family G51 (see the Carbohydrate-Active Enzymes website [http://afmb.cnrs-mrs.fr /ϳcazy/CAZY]). The gene abnA, located immediately upstream from the metabolic operon (32,40) (Fig. 1), most likely en-codes an ABN grouped in the GH43 family (http://afmb.cnrs -mrs.fr/ϳcazy/CAZY).…”