Sequencing and functional analysis of the genome of <i>Bacillus subtilis</i> strain 168

Harwood, Colin R.; Wipat, Anil

doi:10.1016/0014-5793(96)00524-8

Cited by 77 publications

(36 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This was at the core of the European effort to set up two major consortia for sequencing microbial genomes, the Saccharomyces cerevisiae consortium and the B. subtilis consortium (Simpson, 2001). Joined by Japanese investigators in 1990, the consortium extended to some 30 groups (including two US and a Korean group, joining later on) which sequenced and annotated chromosomal segments covering the whole B. subtilis genome (Harwood & Wipat, 1996). …”

Section: Introductionmentioning

confidence: 99%

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

et al. 2009

View full text Add to dashboard Cite

Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches, among which the Firmicutes occupy a considerable space. Bacillus subtilis has been the model of Firmicutes for decades and its genome has been a reference for more than 10 years. Sequencing the genome involved more than 30 laboratories, with different expertises, in a attempt to make the most of the experimental information that could be associated with the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high-level annotation platforms, motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that B. subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.

show abstract

Section: Introductionmentioning

confidence: 99%

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

et al. 2009

View full text Add to dashboard Cite

show abstract

“…12 Because it is single copy and chromosomally integrated it is much more stable than when we would have placed it on a multi-copy plasmid. The improved variant relates to the higher production due to improved translation by adding of a heptameric N-terminal tail as described by Veening et al 12 Sequencing and functional analysis of the genome of B. subtilis strain 168 has been reported, 13 also effects of gene expression and phosphorelay perturbations on architecture, sporulation and spore resistance. 14,15 For cultivation and maintenance of the bacterial strain, a complex growth medium (1% tryptone, 0.5% yeast extract, 1% NaCl) supplemented with chloramphenicol (5 μg ml − 1 ) for mutant selection was used.…”

Section: Test Organism and Its Cultivationmentioning

confidence: 95%

A fluorescence-based bioassay for antibacterials and its application in screening natural product extracts

et al. 2015

View full text Add to dashboard Cite

The reliable assessment of the biological activity of a minor component embedded in a complex matrix of several hundred compounds is a difficult but common task in the search for natural product-based antibiotics, for example, by bioassay-guided fractionation. To quantify the antibiotic properties, it is necessary to assess the cell viability. Direct measurements use CFU counts, OD measurements or detection via fluorescent or reducible dyes. However, natural extracts often already possess intrinsic dye, fluorescent, reducing or protein denaturing properties, or they contain insoluble compounds or general protein-binding (tanning) polyphenols as disturbing features, while at the same time very little of the selective antibiotic sought after is present. A promising alternative is provided by intrinsically produced bright fluorescent proteins. In this paper, a rapid, robust and concentration-dependent assay for screening antibiotics with genetically modified mutants of Bacillus subtilis 168 (PabrB-iyfp) is presented. The Gram-positive bacteria exhibit a native fluorescence during their exponential growth phase due to the expression of improved yellow fluorescent protein. To demonstrate the applicability in the field of natural product research, several compounds and extracts were screened for antibacterial activity, with an emphasis on those from the fungal genus Hygrophorus (waxy caps).

show abstract

“…The genome sequence of B. subtilis 168 was published in 1997 by a consortium mainly formed by European and Japanese laboratories (Harwood and Wipat, 1996; Kunst et al ., 1997). At the time, sequencing was very hard work because it primarily rested on cloning fragments of DNA into an E. coli recipient host before sequencing, under conditions where at least 15% of the sequences failed to be cloned.…”

Section: Introductionmentioning

confidence: 99%

Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement

Borriss

Danchin

Harwood

et al. 2017

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

SummaryGenome annotation is, nowadays, performed via automatic pipelines that cannot discriminate between right and wrong annotations. Given their importance in increasing the accuracy of the genome annotations of other organisms, it is critical that the annotations of model organisms reflect the current annotation gold standard. The genome of Bacillus subtilis strain 168 was sequenced twenty years ago. Using a combination of inductive, deductive and abductive reasoning, we present a unique, manually curated annotation, essentially based on experimental data. This reveals how this bacterium lives in a plant niche, while carrying a paleome operating system common to Firmicutes and Tenericutes. Dozens of new genomic objects and an extensive literature survey have been included for the sequence available at the INSDC (AccNum AL009126.3). We also propose an extension to Demerec's nomenclature rules that will help investigators connect to this type of curated annotation via the use of common gene names.

show abstract

Sequencing and functional analysis of the genome of Bacillus subtilis strain 168

Cited by 77 publications

References 36 publications

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

A fluorescence-based bioassay for antibacterials and its application in screening natural product extracts

Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement

Contact Info

Product

Resources

About