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Regulation of Microbial Biosynthetic Genes and Biodegradation Genes
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Regulation of Microbial Biosynthetic Genes and Biodegradation Genes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 January 2022) | Viewed by 12662

Special Issue Editors

Dr. Manuel Carmona

E-Mail Website
Guest Editor
Environmental Microbiology Group, Department of Microbial & Plant Biotechnology, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
Interests: environmental microbiology; gene regulation; biotechnology; metal resistance; metallic nanoparticle bioproduction; synthetic biology
Special Issues, Collections and Topics in MDPI journals
Dr. Gonzalo Durante-Rodríguez

E-Mail Website
Guest Editor
Environmental Microbiology Group, Department of Microbial & Plant Biotechnology, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
Interests: environmental microbiology; synthetic biology; biotechnology; CO2 fixation and energization in bacteria; metabolic engineering; genetic circuits; transcriptional regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

The expression of metabolic pathways involved in catabolism or anabolism is energetically expensive. Hence, evolution has raised complex regulatory circuits that control the expression of the genes involved in metabolism. Since the control of metabolic pathways is mandatory to achieve the optimal function of bacterial cells, the high diversity of the prokaryotic world has evolved a varied number of mechanisms that control gene expression. This Special Issue is devoted to the description of regulatory mechanisms of biosynthetic and degradative pathways attending all levels of control: from transcriptional to post-transcriptional, translational, or post-translational levels, and also from specific to overimposed mechanisms of regulation. Description of regulation factors focusing on global or specific regulators, the analysis of mechanisms underlying the behavior of promoters, or the analysis of regulation networks using omics techniques are welcome. Understanding metabolic regulation is also an important facet to engineer metabolic pathways. The description of metabolic flux variations and synthetic metabolic pathways promoted by the use of genetic engineering and synthetic biology also fits in the scope of this Special Issue.

Dr. Manuel Carmona
Dr. Gonzalo Durante-Rodríguez
Guest Editors

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. Genes 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 2600 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

  • Transcriptional regulation
  • Genetic circuits
  • Bacterial regulation
  • Regulation of metabolism
  • Metabolic engineering
  • Biotechnology
  • Synthetic biology
  • Molecular microbiology

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Published Papers (3 papers)

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Research

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20 pages, 4727 KiB  
Article
Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor
by Juan Ibero, Beatriz Galán and José L. García
Genes 2021, 12(12), 1846; https://doi.org/10.3390/genes12121846 - 23 Nov 2021
Cited by 3 | Viewed by 3114
Abstract
In this work, Caenibius tardaugens NBRC 16725 (strain ARI-1) (formerly Novosphingobium tardaugens) was isolated due to its capacity to mineralize estrogenic endocrine disruptors. Its genome encodes the edc genes cluster responsible for the degradation of 17β-estradiol, consisting of two putative operons (OpA and [...] Read more.
In this work, Caenibius tardaugens NBRC 16725 (strain ARI-1) (formerly Novosphingobium tardaugens) was isolated due to its capacity to mineralize estrogenic endocrine disruptors. Its genome encodes the edc genes cluster responsible for the degradation of 17β-estradiol, consisting of two putative operons (OpA and OpB) encoding the enzymes of the upper degradation pathway. Inside the edc cluster, we identified the edcR gene encoding a TetR-like protein. Genetic studies carried out with C. tardaugens mutants demonstrated that EdcR represses the promoters that control the expression of the two operons. These genetic analyses have also shown that 17β-estradiol and estrone, the second intermediate of the degradation pathway, are the true effectors of EdcR. This regulatory system has been heterologously expressed in Escherichia coli, foreseeing its use to detect estrogens in environmental samples. Genome comparisons have identified a similar regulatory system in the edc cluster of Altererythrobacter estronivorus MHB5, suggesting that this regulatory arrangement has been horizontally transferred to other bacteria. Full article
(This article belongs to the Special Issue Regulation of Microbial Biosynthetic Genes and Biodegradation Genes)
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18 pages, 2812 KiB  
Article
Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories
by Chinenyenwa Fortune Chukwuneme, Ayansina Segun Ayangbenro and Olubukola Oluranti Babalola
Genes 2021, 12(9), 1431; https://doi.org/10.3390/genes12091431 - 17 Sep 2021
Cited by 13 | Viewed by 5178
Abstract
Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes [...] Read more.
Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils. Full article
(This article belongs to the Special Issue Regulation of Microbial Biosynthetic Genes and Biodegradation Genes)
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Review

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30 pages, 2321 KiB  
Review
The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions
by Elizabet Monteagudo-Cascales, Eduardo Santero and Inés Canosa
Genes 2022, 13(2), 375; https://doi.org/10.3390/genes13020375 - 18 Feb 2022
Cited by 15 | Viewed by 3402
Abstract
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great [...] Read more.
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA–CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage. Full article
(This article belongs to the Special Issue Regulation of Microbial Biosynthetic Genes and Biodegradation Genes)
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