title: Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T.
abstract: Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T) that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal its divergence from other myxobacterial species and support its taxonomic characterization into a separate family Sandaracinaceae, within the suborder Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved in starch, agar, chitin, and cellulose degradation. We identified 16 α-amylases and two γ-amylases in the S. amylolyticus genome that likely play a role in starch degradation. While many of the amylases are seen conserved in other δ-proteobacteria, we notice several novel amylases acquired via horizontal transfer from members belonging to phylum Deinococcus-Thermus, Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in the S. amylolyticus genome. Interestingly, several putative β-glucosidases and endoglucanases proteins involved in cellulose degradation were identified. However, the absence of cellobiohydrolases/exoglucanases corroborates with the lack of cellulose degradation by this bacteria.
authors.affiliation: Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, India.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sharma
authors.affiliation: Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, India.
authors.forename: Indu
authors.initials: I
authors.lastname: Khatri
authors.affiliation: Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, India krishna@imtech.res.in.
authors.forename: Srikrishna
authors.initials: S
authors.lastname: Subramanian
mesh_terms: D000681:Amylases / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D017124:Conserved Sequence; D019175:DNA Methylation; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D013213:Starch / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D012335:RNA, Ribosomal; D013213:Starch; D012343:RNA, Transfer; D000681:Amylases
keywords: CAZyme; agarase; amylase; cellulase; methylome; phylogeny