The <i>Bacillus subtilis</i> Minimal Genome Compendium

Michalik, Stephan; Reder, Alexander; Richts, Björn; Faßhauer, Patrick; Mäder, Ulrike; Pedreira, Tiago; Heel, Auke J. van; Tilburg, Amanda Y van; Altenbuchner, Josef; Klewing, Anika; Reuß, Daniel R.; Daniel, Rolf; Commichau, Fabian M.; Kuipers, Oscar P.; Hamoen, Leendert W.; Völker, Uwe; Stülke, Jörg

doi:10.1021/acssynbio.1c00339

Cited by 30 publications

(26 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…To increase our understanding of the biophysical basis of FMMs and their constituent lipids, we performed a detailed lipidomic analysis of FMMs in two academically and industrially relevant B. subtilis host strains: B . subtilis 168 and mini Bacillus PG10 (Reuß et al ., 2017 ; Michalik et al ., 2021 ). B. subtilis 168 is a commonly used laboratory strain, whereas mini Bacillus PG10 is a genome‐minimized (by 36%) derivative of B. subtilis 168.…”

Section: Introductionmentioning

confidence: 99%

Membrane composition and organization of Bacillus subtilis 168 and its genome‐reduced derivative miniBacillus PG10

Tilburg

Warmer

Heel

et al. 2021

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

Summary A form of lateral membrane compartmentalization in bacteria is represented by functional membrane microdomains (FMMs). FMMs are important for various cellular processes and offer application possibilities in microbial biotechnology. We designed a lipidomics method to directly measure relative abundances of lipids in detergent‐resistant and detergent‐sensitive membrane fractions of the model bacterium Bacillus subtilis 168 and the biotechnologically attractive mini Bacillus PG10 strain. Our study supports previous work suggesting that cardiolipin and prenol lipids are enriched in FMMs of B. subtilis . Additionally, structural analysis of acyl chains of major phospholipids indicated that FMMs display increased order and thickness compared with the surrounding bilayer. Despite the 36% genome reduction, membrane and FMM integrity are largely preserved in mini Bacillus PG10, as supported by analysis of membrane fluidity, flotillin distribution and gene expression data. The novel insights in FMM architecture reported here will contribute to further explore the biological significance of FMMs and the means by which FMMs can be exploited as heterologous production platforms. Moreover, our lipidomics method enables comparative FMM lipid profiling between different bacteria.

show abstract

Section: Introductionmentioning

confidence: 99%

Membrane composition and organization of Bacillus subtilis 168 and its genome‐reduced derivative miniBacillus PG10

Tilburg

Warmer

Heel

et al. 2021

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Some of these strains have already been proven superior for biotechnological applications such as the production and secretion of difficult proteins and lantibiotics ( 16 , 17 ). The MiniBacillus Compendium section ( http://www.subtiwiki.uni-goettingen.de/v4/minibacillus ) ( 18 ) contains a table listing the name of each strain, the respective download link of Geneious and GenBank files, genomic details (genome size, deletion steps and percentage of genome reduction) and a list of publications associated with the respective strain.…”

Section: New Data Integrationmentioning

confidence: 99%

The current state of SubtiWiki, the database for the model organism Bacillus subtilis

Pedreira

Elfmann

Stülke

2021

Nucleic Acids Research

Self Cite

137

141

View full text Add to dashboard Cite

Bacillus subtilis is a Gram-positive model bacterium with extensive documented annotation. However, with the rise of high-throughput techniques, the amount of complex data being generated every year has been increasing at a fast pace. Thus, having platforms ready to integrate and give a representation to these data becomes a priority. To address it, SubtiWiki (http://subtiwiki.uni-goettingen.de/) was created in 2008 and has been growing in data and viewership ever since. With millions of requests every year, it is the most visited B. subtilis database, providing scientists all over the world with curated information about its genes and proteins, as well as intricate protein–protein interactions, regulatory elements, expression data and metabolic pathways. However, there is still a large portion of annotation to be unveiled for some biological elements. Thus, to facilitate the development of new hypotheses for research, we have added a Homology section covering potential protein homologs in other organisms. Here, we present the recent developments of SubtiWiki and give a guided tour of our database and the current state of the data for this organism.

show abstract

“… 9 In the case of B. subtilis GP10, despite acquiring a trait for effective production, genome reduction results in decreased growth rate compared with that of the parental strain, even when grown in a rich medium, likely resulting from deletion of a ribosomal RNA gene. 10 , 11 In the genome reduction process of E. coli DGF-298, further deletion became difficult due to the problems in growth fitness and cell yield when the genome size approached 3 Mb, and construction of the DGF-298 strain required restoration of the proVWX hyperosmolarity regulator genes to maintain growth. 7 Thus, given that large/extensive genome reduction is associated with tradeoffs of undesirable phenotypes caused by gene deletion and changes in gene expression, there is likely an optimal reduction size for creating beneficial strains, which can be used for research and technology development.…”

Section: Introductionmentioning

confidence: 99%

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production

et al. 2022

View full text Add to dashboard Cite

Partial bacterial genome reduction by genome engineering can improve the productivity of various metabolites, possibly via deletion of non-essential genome regions involved in undesirable metabolic pathways competing with pathways for the desired end products. However, such reduction may cause growth defects. Genome reduction of Bacillus subtilis MGB874 increases the productivity of cellulases and proteases but reduces their growth rate. Here, we show that this growth defect could be restored by silencing redundant or less important genes affecting exponential growth by manipulating the global transcription factor AbrB. Comparative transcriptome analysis revealed that AbrB-regulated genes were upregulated and those involved in central metabolic pathway and synthetic pathways of amino acids and purine/pyrimidine nucleotides were downregulated in MGB874 compared with the wild-type strain, which we speculated were the cause of the growth defects. By constitutively expressing high levels of AbrB, AbrB regulon genes were repressed, while glycolytic flux increased, thereby restoring the growth rate to wild-type levels. This manipulation also enhanced the productivity of metabolites including γ-polyglutamic acid. This study provides the first evidence that undesired features induced by genome reduction can be relieved, at least partly, by manipulating a global transcription regulation system. A similar strategy could be applied to other genome engineering-based challenges aiming toward efficient material production in bacteria.

show abstract

The Bacillus subtilis Minimal Genome Compendium

Cited by 30 publications

References 19 publications

Membrane composition and organization of Bacillus subtilis 168 and its genome‐reduced derivative miniBacillus PG10

Membrane composition and organization of Bacillus subtilis 168 and its genome‐reduced derivative miniBacillus PG10

The current state of SubtiWiki, the database for the model organism Bacillus subtilis

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production

Contact Info

Product

Resources

About