Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T)

Abstract

Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216(T), which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.

Keywords: Bacillus smithii; Biotechnology; Genome sequence; Lactic acid; Thermophile; Thermophilic bacillus.

Fig. 1

Scanning electron micrographs of B. smithii DSM 4216^T

Fig. 2

Phylogenetic tree based on 16S rRNA gene sequences (left) and protein domains (right). A comparison is included (horizontal lines) between the two trees, showing the position of Bacillus smithii DSM 4216^T relative to other Bacillus strains, as well as several industrially important Lactic Acid Bacterium strains. Only strains were used for which a complete genome sequence is available (as on 18 September 2014) in order to be able to perform the domain-based analysis. The 16S sequences were aligned using DECIPHER (R) [29] and the distance analysis was performed using a Jukes-Cantor correction. Phylogenetic analysis of all domains was performed by re-annotation of all proteins from selected genomes using InterProScan 5-RC7 and transformed into a absence-presence matrix. Distance was calculated using a standard Euclidean distance and clustering was performed by complete method using hclust. Tree comparison was performed by dendextend. Note that “unique” nodes between the 16S and domain-based tree are indicated with dashed lines (i.e. the order is the same but the subclustering is not). GenBank IDs of used whole genome sequences in order from top to bottom: AE016877.1, AL009126.3, CP000002.3, BA000004.3, CP012024.1, CP002472.1, CP002835.1, CP002293.1, CP001638.1, CP000557.1, CP006254.2, CP002442.1, CP002050.1, CP004008.1, CP003125.1, BA000043.1, CP000922.1, CP002222.1, CP001617.1

Fig. 3

Chromosome and plasmid map of B. smithii DSM 4216^T. The outer circle represents base pair numbers; red are genes on the forward strand and blue on the reverse; the inner circle represents GC skew in which red is a positive GC content and green a negative

Fig. 4

Reconstruction of central carbon metabolism of B. smithii DSM 4216^T. Blue lines indicate pathways of which the EC-number was identified only via domainome analysis; grey lines indicate pathways unidentified by both RAST annotation and domainome analysis. Abbreviations: XI: xylose isomerase; XK: xylulokinase; PTS: phosphotransferase system; GK: glucokinase; glpF: glycerol facilitator; glyK: glycerol kinase; Gly3P-DH: glycerol-3-phosphate dehydrogenase; PGI: glucose-6-phosphate isomerase; G6PDH: glucose-6-phosphate dehydrogenase; 6PGDH: 6-phosphogluconate dehydrogenase; RPI: phosphopentose isomerase; RPE: phosphopentose epimerase; TKL: transketolase; TAL: transaldolase; FBP: fructose bisphosphatase; PFK: phosphofructokinase; FBA: fructose bis-phosphate aldolase; TPI: triosephosphate isomerase; GAP: glyceraldehyde 3-phosphate dehydrogenase; PGK: phosphoglycerate kinase; PGM: phosphoglycerate mutase; ENO: enolase; PCK: phosphoenol pyruvate carboxykinase; PPC: phosphoenol pyruvate carboxylase; PYK: pyruvate kinase; PYC: pyruvate carboxylase; PDHC: pyruvate dehydrogenase complex; ME: malic enzyme; MDH: malate dehydrogenase; MQO: malate:quinone oxidoreductase; CS: citrate synthase; ACN: aconitase; ICL: isocitrate lyase; MS: malate synthase; ICD: isocitrate dehydrogenase; OOR: 2-oxoglutarate reductase; ODH: 2-oxoglutratae dehydrogenase; SCS: succinyl-CoA synthetase; SDH: succinate dehydrogenase; FH: fumarate hydratase; ALS: acetolactate synthase; NOD: non-enzymatic oxidative decarboxylation; BDH: butanediol dehydrogenase; ACH: acetoin dehydrogenase; LDHL: L-lactate dehydrogenase; ACDH: acetyl-CoA dehydrogenase; ADH: alcohol dehydrogenase; ACS: acetyl-CoA synthetase; MGS: methylglyoxal synthase; MGR: methylglyoxal reductase; GLXI: glyoxalase I; GLXII: glyoxalase II; LADH: lactaldehyde dehydrogenase