Mechanism of the Potential Therapeutic Candidate Bacillus subtilis BSXE-1601 Against Shrimp Pathogenic Vibrios and Multifunctional Metabolites Biosynthetic Capability of the Strain as Predicted by Genome Analysis

ABSTRACT The Bacillus subtilis competence transcription factor ComK is required for establishment of competence for genetic transformation. In an attempt to study the ComK factor further, we explored the genes regulated by ComK using the DNA microarray technique. In addition to the genes known to be dependent on ComK for expression, we found many genes or operons whose ComK dependence was not known previously. Among these genes, we confirmed the ComK dependence of 16 genes by using lacZ fusions, and three genes were partially dependent on ComK. Transformation efficiency was significantly reduced in an smf disruption mutant, although disruption of the other ComK-dependent genes did not result in significant decreases in transformation efficiency. Nucleotide sequences similar to that of the ComK box were found for most of the newly discovered genes regulated by ComK.

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In Vitro Evaluation and Genome Mining of Bacillus subtilis Strain RS10 Reveals Its Biocontrol and Plant Growth-Promoting Potential

Agriculture ◽

10.3390/agriculture11121273 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1273

Author(s):

Sajid Iqbal ◽

Nimat Ullah ◽

Hussnain Ahmed Janjua

Keyword(s):

Bacillus Subtilis ◽

Plant Growth ◽

Genome Analysis ◽

Growth Promotion ◽

Gene Clusters ◽

Subtilis Strain ◽

Antifungal Metabolites ◽

Plant Growth Promoting ◽

Growth Promoting

Recently, crop management has involved excessive use of chemical fertilizers and pesticides, compromising public health and environmental integrity. Rhizobacteria, which can enhance plant growth and protect plants from phytopathogen, are eco-friendly and have been attracting increasing attention. In the current study, Bacillus subtilis RS10 isolated from the rhizosphere region of Cynodon dactylon, inhibited the growth of indicator strains and exhibited in vitro plant growth-promoting traits. A whole-genome analysis identified numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites including bacillibactin, bogorol A, fengycin, bacteriocin, type III polyketides (PKs), and bacilysin. The plant growth-promoting conferring genes involved in nitrogen metabolism, phosphate solubilization, hydrogen sulfide, phytohormones, siderophore biosynthesis, chemotaxis and motility, plant root colonization, lytic enzymes, and biofilm formation were determined. Furthermore, genes associated with abiotic stresses such as high salinity and osmotic stress were identified. A comparative genome analysis indicated open pan-genome and the strain was identified as a novel sequence type (ST-176). In addition, several horizontal gene transfer events were found which putatively play a vital role in the evolution and new functionalities of a strain. In conclusion, the current study demonstrates the potential of RS10 antagonism against important pathogens and plant growth promotion, highlighting its application in sustainable agriculture.

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Whole-genome analysis of the chromosome partitioning and sporulation protein Spo0J (ParB) reveals spreading and origin-distal sites on the Bacillus subtilis chromosome

Molecular Microbiology ◽

10.1111/j.1365-2958.2007.05690.x ◽

2007 ◽

Vol 64 (3) ◽

pp. 703-718 ◽

Cited By ~ 114

Author(s):

Adam M. Breier ◽

Alan D. Grossman

Keyword(s):

Bacillus Subtilis ◽

Genome Analysis ◽

Whole Genome ◽

Whole Genome Analysis ◽

Chromosome Partitioning ◽

Subtilis Chromosome ◽

Bacillus Subtilis Chromosome

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Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains

Briefings in Bioinformatics ◽

10.1093/bib/bbaa013 ◽

2020 ◽

Cited By ~ 2

Author(s):

Hao Wu ◽

Dan Wang ◽

Feng Gao

Keyword(s):

Bacillus Subtilis ◽

Genome Analysis ◽

High Quality ◽

Pan Genome ◽

Output Quality ◽

Reduction Strategies ◽

Control Step ◽

Important Quality ◽

Genome Analyses ◽

The Impact

Abstract Pan-genome analysis is widely used to study the evolution and genetic diversity of species, particularly in bacteria. However, the impact of strain selection on the outcome of pan-genome analysis is poorly understood. Furthermore, a standard protocol to ensure high-quality pan-genome results is lacking. In this study, we carried out a series of pan-genome analyses of different strain sets of Bacillus subtilis to understand the impact of various strains on the performance and output quality of pan-genome analyses. Consequently, we found that the results obtained by pan-genome analyses of B. subtilis can be influenced by the inclusion of incorrectly classified Bacillus subspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains. Since the presence of these confounding strains can seriously affect the quality and true landscape of the pan-genome, we should remove these deviations in the process of pan-genome analyses. Our study provides new insights into the removal of biases from confounding strains in pan-genome analyses at the beginning of data processing, which enables the achievement of a closer representation of a high-quality pan-genome landscape of B. subtilis that better reflects the performance and credibility of the B. subtilis pan-genome. This procedure could be added as an important quality control step in pan-genome analyses for improving the efficiency of analyses, and ultimately contributing to a better understanding of genome function, evolution and genome-reduction strategies for B. subtilis in the future.

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