Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp.
            <i>subtilis</i>
            Strain SP1

Richts, Björn; Hertel, Robert; Potot, Sébastien; Daniel, Rolf; Schyns, Ghislain; Prágai, Zoltán; Commichau, Fabian M.

doi:10.1128/mra.00825-20

Cited by 6 publications

(5 citation statements)

References 17 publications

(18 reference statements)

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“…The B. subtilis strain SP1 is a prototrophic derivative of the laboratory strain 168 that has been used throughout this study. Due to its prototrophy, this strain is of interest for biotechnological applications ( 40 ). SP1 lacking the ansAB operon (strain BP269) is also sensitive to l -Asn, even on complex medium.…”

Section: Resultsmentioning

confidence: 99%

Control of asparagine homeostasis in Bacillus subtilis : identification of promiscuous amino acid importers and exporters

Meißner,

Königshof,

Wrede

et al. 2024

J Bacteriol

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The Gram-positive model bacterium B. subtilis is able to import all proteinogenic amino acids from the environment as well as to synthesize them. However, the players involved in the acquisition of asparagine have not yet been identified for this bacterium. In this work, we used d -asparagine as a toxic analog of l -asparagine to identify asparagine transporters. This revealed that d - but not l -asparagine is taken up by the malate/lactate antiporter MleN. Specific strains that are sensitive to the presence of l -asparagine due to the lack of the second messenger cyclic di-AMP or due to the intracellular accumulation of this amino acid were used to isolate and characterize suppressor mutants that were resistant to the presence of otherwise growth-inhibiting concentrations of l -asparagine. These screens identified the broad-spectrum amino acid importers AimA and BcaP as responsible for the acquisition of l -asparagine. The amino acid exporter AzlCD allows detoxification of l -asparagine in addition to 4-azaleucine and histidine. This work supports the idea that amino acids are often transported by promiscuous importers and exporters. However, our work also shows that even stereo-enantiomeric amino acids do not necessarily use the same transport systems. IMPORTANCE Transport of amino acid is a poorly studied function in many bacteria, including the model organism Bacillus subtilis . The identification of transporters is hampered by the redundancy of transport systems for most amino acids as well as by the poor specificity of the transporters. Here, we apply several strategies to use the growth-inhibitive effect of many amino acids under defined conditions to isolate suppressor mutants that exhibit either reduced uptake or enhanced export of asparagine, resulting in the identification of uptake and export systems for l -asparagine. The approaches used here may be useful for the identification of transporters for other amino acids both in B. subtilis and in other bacteria.

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Section: Resultsmentioning

confidence: 99%

Control of asparagine homeostasis in Bacillus subtilis : identification of promiscuous amino acid importers and exporters

Meißner,

Königshof,

Wrede

et al. 2024

J Bacteriol

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“…To identify the mutation(s) conferring heat inducibility of SPβ c2, we re-sequenced the SPβ c2 genome. Sequence variations were identified through a direct alignment with the SPβ genome of the B. subtilis laboratory strain SP1 [Richts et al, 2020]. We identified four sequence variations in the yorN - yorM intergenic region and in the yoqA , yopR and yokI genes.…”

Section: Resultsmentioning

confidence: 99%

“…The sequencing reads were mapped onto the genome of the B. subtilis strain SP1 and mutations were identified using the applications bowtie2 and breseq [Langmead and Salzberg, 2012; Deatherage and Barrick, 2014]. SP1 is prototrophic for tryptophan and a derivative of the laboratory strain 168 [Richts et al, 2020]. All identified mutations were verified by PCR and Sanger sequencing.…”

Section: Methodsmentioning

confidence: 99%

Structural and functional analysis of YopR and identification of an additional key component of the SPβ phage lysis-lysogeny management system

Kohm

Jalomo-Khayrova

Basu

et al. 2022

Preprint

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Prophages need to tightly control their lifestyle to either be maintained within the host genome or enter the lytic cycle. The SPβ prophage present in the genome ofBacillus subtilis168 was recently shown to possess anarbitriumsystem defining its replication stage. Using an historicB. subtilisstrain harboring the heat-sensitive SPβ c2 mutant, we analyzed a key component of the lysis-lysogeny decision system called YopR, which is crucial for maintenance of lysogeny. Here, we demonstrate that the heat-sensitive SPβ c2 phenotype is due to a single nucleotide exchange in theyopRgene, rendering the encoded YopRG136Eprotein temperature sensitive. Structural characterization of YopR revealed that the protein is a DNA-binding protein with an overall fold like tyrosine recombinases. Biochemical and functional analyses indicate that YopR has lost the recombinase function and the G136E exchange impairs its higher order structure and DNA binding activity. We also show that the serine recombinase SprA and its accessory factor SprB are not required for the heat-dependent induction of the lytic cycle of the SPβ c2 prophage. Finally, an evolution experiment with aB. subtilisstrain carrying SPβ c2 identified YosL as a novel component of the lysis-lysogeny management system, as the presence ofyosLis crucial for the induction of the lytic cycle of SPβ.

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“…It is expected that these isolates of the reference strain 168 did not evolve while staying in the repositories. However, isolates used regularly in the laboratory keep evolving (Richts et al, 2020 ; Shiwa et al, 2013 ), and consequently clonal genome sequences should be checked regularly. This is important since the sequencing of individual laboratory isolates often identifies SNP variants that in some cases can reveal additional knowledge (Zhao et al, 2019 ).…”

Section: Key Annotation Resources Used To Create the International Nu...mentioning

confidence: 99%

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Bremer

Calteau

Danchin

et al. 2023

Microbial Biotechnology

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The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).

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Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1

Cited by 6 publications

References 17 publications

Control of asparagine homeostasis in Bacillus subtilis : identification of promiscuous amino acid importers and exporters

Control of asparagine homeostasis in Bacillus subtilis : identification of promiscuous amino acid importers and exporters

Structural and functional analysis of YopR and identification of an additional key component of the SPβ phage lysis-lysogeny management system

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

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