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Microorganisms
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Metabolism in the Bacillus subtilis
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Metabolism in the Bacillus subtilis

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 3908

Special Issue Editor

Prof. Dr. Christoph Mayer

E-Mail Website
Guest Editor
Faculty of Science, Universität Tübingen, Tubingen, Germany
Interests: metabolism; catabolism; B. subtilis; E. coli

Special Issue Information

Dear Colleagues,

Bacillus subtilis is one of the best-studied living organisms; much research has been devoted to many aspects of this bacterium. B. subtilis is endowed with sophisticated regulatory networks; therefore, it can adapt its metabolism to a variety of growth conditions. Moreover, the ability of B. subtilis to differentiate and coexist in different cell forms such as exploring motile and non-motile cells as well as spores increases its probability of survival under harsh growth conditions. Due to these diverse properties of B. subtilis, the bacterium is particularly well suited for the investigation of a wide range of issues in basic microbiological research. This Special Issue is intended to provide a platform for publications about recent findings related to topics such as gene regulation and the physiology of the model bacterium, B. subtilis.

Prof. Dr. Christoph Mayer
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Bacillus subtilis
  • metabolism
  • gene regulation

Published Papers (3 papers)

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20 pages, 4456 KiB  
Article
Molecular Cloning, In Silico Analysis, and Characterization of a Novel Cellulose Microfibril Swelling Gene Isolated from Bacillus sp. Strain AY8
by Md. Azizul Haque, Dhirendra Nath Barman, Aminur Rahman, Md. Shohorab Hossain, Sibdas Ghosh, Most. Aynun Nahar, Mst. Nur-E-Nazmun Nahar, Joyanta K. Saha, Kye Man Cho and Han Dae Yun
Microorganisms 2023, 11(12), 2857; https://doi.org/10.3390/microorganisms11122857 - 24 Nov 2023
Viewed by 906
Abstract
A novel cellulose microfibril swelling (Cms) gene of Bacillus sp. AY8 was successfully cloned and sequenced using a set of primers designed based on the conserved region of the gene from the genomic database. The molecular cloning of the Cms gene revealed that [...] Read more.
A novel cellulose microfibril swelling (Cms) gene of Bacillus sp. AY8 was successfully cloned and sequenced using a set of primers designed based on the conserved region of the gene from the genomic database. The molecular cloning of the Cms gene revealed that the gene consisted of 679 bp sequences encoding 225 amino acids. Further in silico analysis unveiled that the Cms gene contained the NlpC/P60 conserved region that exhibited a homology of 98% with the NlpC/P60 family proteins found in both the strains, Burkholderialata sp. and Burkholderia vietnamiensis. The recombinant Cms enzyme had a significant impact on the reduction of crystallinity indices (CrI) of various substrates including a 3%, a 3.97%, a 4.66%, and a substantial 14.07% for filter paper, defatted cotton fiber, avicel, and alpha cellulose, respectively. Additionally, notable changes in the spectral features were observed among the substrates treated with recombinant Cms enzymes compared to the untreated control. Specifically, there was a decrease in band intensities within the spectral regions of 3000–3450 cm−1, 2900 cm−1, 1429 cm−1, and 1371 cm−1 for the treated filter paper, cotton fiber, avicel, and alpha cellulose, respectively. Furthermore, the recombinant Cms enzyme exhibited a maximum cellulose swelling activity at a pH of 7.0 along with a temperature of 40 °C. The molecular docking data revealed that ligand molecules, such as cellobiose, dextrin, maltose 1-phosphate, and feruloyated xyloglucan, effectively bonded to the active site of the Cms enzyme. The molecular dynamics simulations of the Cms enzyme displayed stable interactions with cellobiose and dextrin molecules up to 100 ns. It is noteworthy to mention that the conserved region of the Cms enzyme did not match with those of the bioadditives like expansins and swollenin proteins. This study is the initial report of a bacterial cellulose microfibril swellase enzyme, which could potentially serve as an additive to enhance biofuel production by releasing fermentable sugars from cellulose. Full article
(This article belongs to the Special Issue Metabolism in the Bacillus subtilis)
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13 pages, 8244 KiB  
Article
The Multiomics Response of Bacillus subtilis to Simultaneous Genetic and Environmental Perturbations
by Li Liu, Gaoyang Li and Huansheng Cao
Microorganisms 2023, 11(8), 1949; https://doi.org/10.3390/microorganisms11081949 - 30 Jul 2023
Viewed by 833
Abstract
How bacteria respond at the systems level to both genetic and environmental perturbations imposed at the same time is one fundamental yet open question in biology. Bioengineering or synthetic biology provides an ideal system for studying such responses, as engineered strains always have [...] Read more.
How bacteria respond at the systems level to both genetic and environmental perturbations imposed at the same time is one fundamental yet open question in biology. Bioengineering or synthetic biology provides an ideal system for studying such responses, as engineered strains always have genetic changes as opposed to wildtypes and are grown in conditions which often change during growth for maximal yield of desired products. So, engineered strains were used to address the outstanding question. Two Bacillus subtilis strains (MT1 and MT2) were created previously for the overproduction of N-acetylglucosamine (GlcNAc), which were grown in an environment with a carbon shift from glucose to glucose and xylose in the same culture system. We had four groups: (1) a wildtype (WT) grown with glucose at t1; (2) a WT with glucose and xylose at t2; (3) a mutant (MT1) grown with glucose at t1; and (4) MT1 with glucose and xylose at t2. By measuring transcriptomes and metabolomes, we found that GlcNAc-producing mutants, particularly MT2, had a higher yield of N-acetylglucosamine than WT but displayed a smaller maximum growth rate than the wildtype, despite MT1 reaching higher carrying capacity. Underlying the observed growth, the engineered pathways leading to N-acetylglucosamine had both higher gene expression and associated metabolite concentrations in MT1 than WT at both t1 and t2; in bioenergetics, there was higher energy supply in terms of ATP and GTP, with the energy state metric higher in MT1 than WT at both timepoints. Additionally, most top key precursor metabolites were equally abundant in MT1 and WT at either timepoints. Besides that, one prominent feature was the high consistency between transcriptomics and metabolomics in revealing the response. First, both metabolomes and transcriptomes revealed the same PCA clusters of the four groups. Second, we found that the important functions enriched both by metabolomes and transcriptomes overlapped, such as amino acid metabolism and ABC transport. Strikingly, these functions overlapped those enriched by the genes showing a high (positive or negative) correlation with metabolites. Furthermore, these functions also overlapped the enriched KEGG pathways identified using weighted gene coexpression network analysis. All these findings suggest that the responses to simultaneous genetic and environmental perturbations are well coordinated at the metabolic and transcriptional levels: they rely heavily on bioenergetics, but core metabolism does not differ much, while amino acid metabolism and ABC transport are important. This serves as a design guide for bioengineering, synthetic biology, and systems biology. Full article
(This article belongs to the Special Issue Metabolism in the Bacillus subtilis)
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17 pages, 3810 KiB  
Article
Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production
by Freddy Castillo-Alfonso, Alejandro Quintana-Menéndez, Gabriel Vigueras-Ramírez, Alfonso Mauricio Sales-Cruz, Luis Manuel Rosales-Colunga and Roberto Olivares-Hernández
Microorganisms 2022, 10(12), 2352; https://doi.org/10.3390/microorganisms10122352 - 28 Nov 2022
Cited by 1 | Viewed by 1828
Abstract
The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary [...] Read more.
The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary metabolism. In this work, Bacillus subtilis was cultivated in a bioreactor to produce IAA using propionate and glucose as carbon sources in an M9-modified media; in both cases, tryptophan was added as a co-substrate. The yield of IAA using propionate is 17% higher compared to glucose. After 48 h of cultivation, the final concentration was 310 mg IAA/L using propionate and 230 mg IAA/L using glucose, with a concentration of 500 mg Trp/L. To gain more insight into propionate metabolism and its advantages, the genome-scale metabolic model of B. subtilis (iBSU 1147) and computational analysis were used to calculate flux distribution and evaluate the metabolic capabilities to produce IAA using propionate. The metabolic fluxes demonstrate that propionate uptake favors the production of precursors needed for the synthesis of the hormone, and the sensitivity analysis shows that the control of a specific growth rate has a positive impact on the production of IAA. Full article
(This article belongs to the Special Issue Metabolism in the Bacillus subtilis)
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