Computational protocol: Complete Genome Sequence of Bacillus horikoshii Strain 20a from Cuatro Cienegas, Coahuila, Mexico

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Protocol publication

[…] Bacillus horikoshii is an alkaliphilic, aerobic, endospore-forming bacterium, initially isolated from soil samples (). We report the genome of B. horikoshii strain 20a isolated from shallow-water sediment collected in the Churince system in the Cuatro Cienegas Basin, Coahuila, Mexico (). Bacillus horikoshii 20a has been studied to better understand how microbial assembly in communities is influenced by antagonistic interactions (). Thus, it is important to identify genes involved in coping with this oligotrophic environment and genes related to defense responses. The 20a genome was sequenced with the PacBio RSII system, assembled with Canu v.1.3 (), and circularized with Circlator v.1.3 (). This assembly resulted in two contigs representing the chromosome (4,277,585 bp, 192.75× mean coverage) and an extrachromosomal feature (18,297 bp, 122.28× mean coverage). The contigs were annotated with RAST (), which identified 24 rRNAs, 72 tRNAs, and 4,366 protein-coding sequences in 457 functional subsystems. Alignment of the 16S rRNA gene against the type strains in the RDP database () returned a 0.991 similarity score between B. horikoshii 20a and B. horikoshii DSM 8719. However, in the B. horikoshii 20a genome, there are 533 genes that are not found in any of the two B. horikoshii published genomes (strains DSM 8719 and FJAT-14233). RAST annotated 12 genes coding for bacteriocins and ribosomally synthesized antibacterial peptides, 48 genes related to resistance to antibiotics and toxic compounds, and 139 genes involved in dormancy and sporulation.Interestingly, three genes located in tandem were annotated as genes for cyanophycin synthetase (CphA), and two other regions located 2.76 Mb upstream were identified as genes for cyanophycinase and isoaspartyl dipeptidase, respectively. These are enzymes involved in the metabolism of cyanophycin, a branched, nonribosomally synthesized polypeptide consisting of aspartic acid in the backbone and arginine in the side chain (). Cyanophycin was originally described in Cyanobacteria, where it accumulates under conditions of intense light, high carbon dioxide concentration, or phosphate or sulfur starvation (). Given its high nitrogen content and water insolubility, cyanophycin has been suggested to constitute a reserve material (, ). Cyanophycin synthetase has also been found in Firmicutes, like Clostridium perfringens, where it possibly plays a role in spore assembly as a matrix material giving spores their normal morphology (). Both cyanophycin functions, as a nitrogen and carbon reserve and as a spore material, might be relevant for the survival of B. horikoshii 20a in its oligotrophic environment. We carried out PSI-BLAST () of one of the B. horikoshii 20a putative CphAs and evaluated the conservation of amino acid residues of the active sites for cyanophycin synthesis (). An alignment including the three B. horikoshii 20a putative CphAs plus the PSI-BLAST results showed that the CphAs have the essential residues involved in the incorporation of aspartate but lack the essential residues for the incorporation of arginine. This composition is similar to those of cyanobacterial enzymes classified as CphA2 and CphA2′ (). Cyanobacterial CphA2 contributes to the synthesis of cyanophycin in N2-fixing Cyanobacteria, where cyanophycin seems to play a role in nitrogen storage (). Our transcriptome data show expression of the CphA, cyanophycinase, and isoaspartyl dipeptidase genes in B. horikoshi 20a. […]

Pipeline specifications

Software tools Canu, Circlator, RAST, BLASTP
Application De novo sequencing analysis