scholarly journals Responses of Bacillus subtilis to Hypotonic Challenges: Physiological Contributions of Mechanosensitive Channels to Cellular Survival

2008 ◽  
Vol 74 (8) ◽  
pp. 2454-2460 ◽  
Author(s):  
Tamara Hoffmann ◽  
Clara Boiangiu ◽  
Susanne Moses ◽  
Erhard Bremer
Keyword(s):  
Bacillus Subtilis ◽  
Mutational Analysis ◽  
Mechanosensitive Channels ◽  
High Osmolarity ◽  
Cellular Survival ◽  
Genes Encoding ◽  
Quadruple Mutant ◽  
Rapid Transition ◽  
A Minor ◽  
Small Conductance

ABSTRACT Mechanosensitive channels are thought to function as safety valves for the release of cytoplasmic solutes from cells that have to manage a rapid transition from high- to low-osmolarity environments. Subsequent to an osmotic down-shock of cells grown at high osmolarity, Bacillus subtilis rapidly releases the previously accumulated compatible solute glycine betaine in accordance with the degree of the osmotic downshift. Database searches suggest that B. subtilis possesses one copy of a gene for a mechanosensitive channel of large conductance (mscL) and three copies of genes encoding proteins that putatively form mechanosensitive channels of small conductance (yhdY, yfkC, and ykuT). Detailed mutational analysis of all potential channel-forming genes revealed that a quadruple mutant (mscL yhdY yfkC ykuT) has no growth disadvantage in high-osmolarity media in comparison to the wild type. Osmotic down-shock experiments demonstrated that the MscL channel is the principal solute release system of B. subtilis, and strains with a gene disruption in mscL exhibited a severe survival defect upon an osmotic down-shock. We also detected a minor contribution of the SigB-controlled putative MscS-type channel-forming protein YkuT to cellular survival in an mscL mutant. Taken together, our data revealed that mechanosensitive channels of both the MscL and MscS types play pivotal roles in managing the transition of B. subtilis from hyper- to hypo-osmotic environments.

scholarly journals Bacillus subtilis 168 Contains Two Differentially Regulated Genes Encoding l-Asparaginase

2002 ◽  
Vol 184 (8) ◽  
pp. 2148-2154 ◽  
Author(s):  
Susan H. Fisher ◽  
Lewis V. Wray
Keyword(s):  
Transcription Factor ◽  
Bacillus Subtilis ◽  
Mutational Analysis ◽  
Limited Growth ◽  
Mobility Shift ◽  
Regulatory Factors ◽  
Bacillus Subtilis 168 ◽  
Dnase I Footprinting ◽  
Genes Encoding ◽  
Gel Mobility Shift

ABSTRACT Expression of the two Bacillus subtilis genes encoding l-asparaginase is controlled by independent regulatory factors. The ansZ gene (formerly yccC) was shown by mutational analysis to encode a functional l-asparaginase, the expression of which is activated during nitrogen-limited growth by the TnrA transcription factor. Gel mobility shift and DNase I footprinting experiments indicate that TnrA regulates ansZ expression by binding to a DNA site located upstream of the ansZ promoter. The expression of the ansA gene, which encodes the second l-asparaginase, was found to be induced by asparagine. The ansA repressor, AnsR, was shown to negatively regulate its own expression.

scholarly journals Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2688
Author(s):  
Tobias Goris ◽  
Rafael R. C. Cuadrat ◽  
Annett Braune
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Health Impact ◽  
Gut Bacteria ◽  
Human Gut ◽  
Positive Health ◽  
Human Gut Microbiome ◽  
Nutritional Recommendations ◽  
Genes Encoding ◽  
A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

scholarly journals 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David J. Young ◽  
Sezen Meydan ◽  
Nicholas R. Guydosh
Keyword(s):  
Protein Synthesis ◽  
Neurological Disease ◽  
Ribosome Profiling ◽  
Minor Role ◽  
Stop Codons ◽  
Genes Encoding ◽  
Ribosome Footprinting ◽  
A Minor ◽  
And Control ◽  
In Cells

AbstractThe recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we used a 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.

scholarly journals Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Catarina Leal ◽  
Florence Fontaine ◽  
Aziz Aziz ◽  
Conceiçao Egas ◽  
Christophe Clément ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Vitis Vinifera ◽  
Genome Sequence ◽  
Draft Genome ◽  
Rhizospheric Soil ◽  
Bioactive Substances ◽  
Protein Coding ◽  
Genes Encoding ◽  
Stimulate Plant Growth ◽  
Biocontrol Potential

Abstract Background Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity. Results The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes. Conclusions Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.

scholarly journals Spo0A-Dependent Activation of an Extended −10 Region Promoter in Bacillus subtilis

2006 ◽  
Vol 188 (4) ◽  
pp. 1411-1418 ◽  
Author(s):  
Guangnan Chen ◽  
Amrita Kumar ◽  
Travis H. Wyman ◽  
Charles P. Moran
Keyword(s):  
Bacillus Subtilis ◽  
Base Pair ◽  
Promoter Activity ◽  
Mutational Analysis ◽  
Dna Binding Protein ◽  
Base Pairs ◽  
Dnase I Footprinting ◽  
Level Of Activity ◽  
High Level ◽  
Activity Dependent

ABSTRACT At the onset of endospore formation in Bacillus subtilis the DNA-binding protein Spo0A directly activates transcription from promoters of about 40 genes. One of these promoters, Pskf, controls expression of an operon encoding a killing factor that acts on sibling cells. AbrB-mediated repression of Pskf provides one level of security ensuring that this promoter is not activated prematurely. However, Spo0A also appears to activate the promoter directly, since Spo0A is required for Pskf activity in a ΔabrB strain. Here we investigate the mechanism of Pskf activation. DNase I footprinting was used to determine the locations at which Spo0A bound to the promoter, and mutations in these sites were found to significantly reduce promoter activity. The sequence near the −10 region of the promoter was found to be similar to those of extended −10 region promoters, which contain a TRTGn motif. Mutational analysis showed that this extended −10 region, as well as other base pairs in the −10 region, is required for Spo0A-dependent activation of the promoter. We found that a substitution of the consensus base pair for the nonconsensus base pair at position −9 of Pskf produced a promoter that was active constitutively in both ΔabrB and Δspo0A ΔabrB strains. Therefore, the base pair at position −9 of Pskf makes its activity dependent on Spo0A binding, and the extended −10 region motif of the promoter contributes to its high level of activity.

Gating and inactivation of mechanosensitive channels of small conductance: A continuum mechanics study

2019 ◽  
Vol 90 ◽  
pp. 502-514 ◽  
Author(s):  
Liangliang Zhu ◽  
Qiang Cui ◽  
Hang Xiao ◽  
Xiangbiao Liao ◽  
Xi Chen
Keyword(s):  
Continuum Mechanics ◽  
Mechanosensitive Channels ◽  
Small Conductance

scholarly journals Bioprecipitation of calcium carbonate by Bacillus subtilis and its potential to self-healing in cement-based materials

2020 ◽  
Vol 18 (5) ◽  
Author(s):  
Héctor Ferral Pérez ◽  
Mónica Galicia García
Keyword(s):  
Bacillus Subtilis ◽  
Calcium Carbonate ◽  
Building Materials ◽  
Soil Stabilization ◽  
Amorphous Material ◽  
Crystallinity Index ◽  
Self Healing ◽  
Semi Solid ◽  
A Minor ◽  
Novel Applications

In recent years, biological mineralization has been implemented as a viable option for the elaboration of new building materials, protection and repair of concrete by self-healing, soil stabilization, carbon dioxide capture, and drug delivery. Biogenic mineralization of calcium carbonate (CaCO3) induced by bacterial metabolism has been proposed as an effective method. The objective of the present study was to characterize the bioprecipitation of CaCO3 crystals by Bacillus subtilis in a semi-solid system. The results show that CaCO3 crystals were produced by day 3 of incubation. The prevalent crystalline polymorph was calcite, and in a minor proportion, vaterite. The presence of amorphous material was also detected (amorphous CaCO3 (ACC)). Finally, the crystallinity index was 81.1%. This biogenic calcium carbonate does not decrease pH and does not yield chloride formation. Contrary, it increases pH values up to 10, which constitutes and advantage for implementations at reinforced concrete. Novel applications for biogenic calcium carbonate derived from Bacillus subtilis addressing self-healing, biocementation processes, and biorestoration of monuments are presented.  

scholarly journals Landscape Of HOXA Genes Methylation in Colorectal Cancer

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Muhiddin Ishak ◽  
Rashidah Baharudin ◽  
Loh Teng-Hern Tan ◽  
Learn-Han Lee ◽  
Nurul-Syakima Ab Mutalib
Keyword(s):  
Colorectal Cancer ◽  
Cancer Susceptibility ◽  
Cpg Islands ◽  
Methylation Pattern ◽  
Gene Promoters ◽  
Normal Tissues ◽  
Genes Encoding ◽  
Hoxa Genes ◽  
A Minor ◽  
Hoxa Gene

Colorectal cancer (CRC) is among the most common cancers worldwide and the second leading cause of cancer-related death in Malaysia. The HOXA gene cluster is a family of Homeobox A genes encoding transcriptional regulators that play vital roles in cancer susceptibility and progression. Dysregulated HOXA expression influences various aspects of carcinogenesis processes. Therefore, this study aims to elucidate the methylation landscape of HOXA genes in CRC. Twelve pairs of CRC — adjacent normal tissues were subjected to Infinium DNA MethyEPIC array. Differentially methylatedregions were identified using the ChAMP Bioconductor and methylation levels of HOXA genes were manually curated. We identified 100 significantly differentially methylated probes annotated to HOXA genes. HOXA3 has the highest number of differentially methylated probes (n=27), followed by HOXA2 (n=20) and HOXA4 (n=14). The majority (43%) of the probes were located at the transcription start site (TSS) 200, which is one of the gene promoters. In respect to CpG islands (CGI), the probes were equally located in the island and shore regions (47% each) while a minor percentage was in the shelf (6%). Our work gave a comprehensive assessment of the DNA methylation pattern of HOXA genes and provide the first evidence of HOXA2, HOXA3 and HOXA4 differential methylation in Malaysian CRC. The new knowledge from this study can be utilized to further increase our understanding of CRC methylomics, particularly on the homeobox A genes. The prognostic and diagnostic roles of the differentially methylated HOXA genes warrant future investigations.

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