Complete Genome Sequence of the Industrial Strain Bacillus megaterium WSH-002

Abstract

Bacillus megaterium, an industrial strain, has been widely used in protein production and the vitamin C industry. Here we reported a finished, annotated, and compared 4.14-Mbp high-quality genome sequence of B. megaterium WSH-002, which is the companion strain for Ketogulonicigenium vulgare in the vitamin C industry and is stocked in our laboratory.Bacillus megaterium, a potential industrial strain, has exhibited many advantages in the industrial production of recombinant proteins (1, 8) and vitamins (2). In this study, B. megaterium WSH-002, the companion strain to improve Ketogulonicigenium vulgare growth and 2-keto-L-gulonic acid synthesis in the vitamin C industry (12, 16), was sequenced.The B. megaterium WSH-002 genome was sequenced by a combined strategy of the Sanger shotgun approach and 454 single-end sequencing technology. A genomic library containing a 5-kb insert was constructed, and 9,604 single-end reads were generated using the Sanger shotgun method, giving 15.0-fold coverage of the genome. Using the 454 Newbler (454 Life Sciences, Branford, CT), about 97% of the 258,353 single-end reads were assembled into two large scaffolds, including 62 contigs. The relationship of the contigs was determined by multiplex PCR, and the gaps between the contigs were closed by PCR amplification, primer walking, or shotgun sequencing with an ABI 3730 sequencer. The complete genome of WSH-002 achieves an error rate of less than 1 in the range of a 10-kb sequence through sequence assembly and quality assessment by the Phred/Phrap/Consed software package (6). Protein-coding genes were predicted by combining the results obtained with Glimmer 3.02 (4) and ZCURVE (7), followed by manual inspection. Both tRNA and rRNA genes were identified by tRNAscan-SE (11) and RNAmmer (10

Isolation, Development, and Genomic Analysis ofBacillus megateriumSR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide

“…is consistent with previous studies establishing the propensity for B. megaterium strains to store large 530 extra chromosomal DNA in plasmids (Eppinger et al, 2011;Liu et al, 2011;Korneli et al, 2013b). 531…”

Expression Analysis of Ni- and V-Associated Resistance Genes in a Bacillus megaterium Strain Isolated from a Mining Site

“…Recently, B. megaterium has been characterized for an intrinsically high level of resistance to hostile conditions including 20 % of salinity [21,28] and metal exposition (e.g., mercury and nickel) [20,26]. Because of this capacity, B. megaterium has been used in the biological treatment of wastes with high metal content like nickel, vanadium, rhenium, and platinum [6,14,21]. Particularly, nickel is considered a hazardous metal which is part of several industrial wastes, including those from petrochemical process, thus creating serious problems in terms of environmental pollution due to their accumulation [1].…”

“…The V resistance in microorganisms is unclear, and few reports of vanadium resistance genes, including the VAN1 and VAN2 (also known as VRG4) identified in Saccharomyces cerevisiae, exist [8,9,25]. The B. megaterium genome contains predicted open reading frames of 110 genes involved in stress responses: 46 in oxidative stress-11 for protection from reactive oxygen species (ROS), 24 for oxidative stress, 2 for glutathione:non-redox reactions, 6 for redox-dependent regulation, 2 for glutaredoxins, and 1 for the CoA disulfide thiol-disulfide redox system-26 for osmotic stress, 14 for heat shock, 2 for cold shock, and 1 for detoxification [14], and some Ni-V resistance genes including proton efflux/ influx pumps. The genes nccA, hant (high-affinity nickel transporter), VAN2, and a metallothionein smtAB were previously identified by a polymerase chain reaction (PCR) approach in B. megaterium strain MNSH1-9K-1 (GenBank accession number KM654562.1) (Fierros-Romero G, unpublished data), which was isolated from a mining site located in Guanajuato, Mexico, and showed the ability to remove 141.5 mg/kg (33.1 %) of nickel and 1101.51 mg/ kg (50.8 %) of vanadium from a spent catalyst [9].…”

Engineering of Bacillus megaterium for improving PHA production from glycerol

“…According to antiSMASH (Medema et al, 2011), this genome contains at least 6 clusters associated with siderophores, terpenes, polyketide synthases (T3PKS) and phosphonates biosynthesis. Despite the average value of cluster in B. megaterium is 11, it is important to point out that the estimation is 6, according to the assessment of complete genomes of this strain (Liu et al, 2011;Eppinger et al, 2011;Johnson et al, 2015). Table S1 shows the genomic features of B. megaterium LVN01 in comparison to different strains of B. megaterium reported in public databases (last update: 29-11-2018).…”