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Advances in Gene Research in Nuclear-Free Organisms and Entities: Prokaryotes and Organelles

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 2308

Special Issue Editors

Prof. Dr. Maria S. Muntyan

E-Mail Website
Guest Editor
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
Interests: biochemistry; bioenergetics; mitochondria; proteorhodopsins; efflux pumps; ion pumps; extremophiles; structural biology; molecular microbiology; genomics
Prof. Dr. Margarita Grabovich

E-Mail Website
Guest Editor
Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
Interests: taxonomy; phylogeny; ecology and metabolism of prokaryotes; sulfur metabolism; carbon metabolism; nitrogen metabolism

Special Issue Information

Dear Colleagues,

This Special Issue will cover research on bacteria and archaea, mitochondria, and plastids. At present, without genetic studies, it would be impossible to imagine research on unculturable microorganisms, the relationship and taxonomic position of microbes, and the identification of genetically determined diseases at the mitochondrial level, and much more. The applications of genomics are closely intertwined with advances in other areas of biology. One example is the process of describing new prokaryotic taxa, for which molecular biologists, biochemists, and microbiologists combine phenotypic and biochemical studies with genomic sequence analysis.

This issue welcomes articles on the study of the genetic structures of the above organisms, the development of new methods in this direction, and the discovery of new systems and functions in organisms that are important for their life activity. In addition, many protein structures have become of interest due to advances in the study of genomes and individual genomic clusters. Therefore, reports on the discovery of new proteins in this way with both known and new functions are welcome.

Overall, we strongly believe that advances in genomic studies of the listed entities will lead to reports of new gene discovery, new knowledge about the products of these genes, and new capabilities of the organisms possessing these genes.

This Special Issue aims to provide an overview of recent advances in genetic research on cellular organelles and one of the simplest life forms, prokaryotes, as well as the impact of these advances on adjacent problems.

Prof. Dr. Maria S. Muntyan
Prof. Dr. Margarita Grabovich
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • bacteria
  • archaea
  • mitochondria
  • plastids
  • genes
  • genome
  • mitochondrial diseases
  • plastid genes
  • proteins
  • new taxa

Published Papers (2 papers)

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Research

23 pages, 9070 KiB  
Article
Neuromodulators as Interdomain Signaling Molecules Capable of Occupying Effector Binding Sites in Bacterial Transcription Factors
by Yuri A. Purtov and Olga N. Ozoline
Int. J. Mol. Sci. 2023, 24(21), 15863; https://doi.org/10.3390/ijms242115863 - 01 Nov 2023
Viewed by 667
Abstract
Hormones and neurotransmitters are important components of inter-kingdom signaling systems that ensure the coexistence of eukaryotes with their microbial community. Their ability to affect bacterial physiology, metabolism, and gene expression was evidenced by various experimental approaches, but direct penetration into bacteria has only [...] Read more.
Hormones and neurotransmitters are important components of inter-kingdom signaling systems that ensure the coexistence of eukaryotes with their microbial community. Their ability to affect bacterial physiology, metabolism, and gene expression was evidenced by various experimental approaches, but direct penetration into bacteria has only recently been reported. This opened the possibility of considering neuromodulators as potential effectors of bacterial ligand-dependent regulatory proteins. Here, we assessed the validity of this assumption for the neurotransmitters epinephrine, dopamine, and norepinephrine and two hormones (melatonin and serotonin). Using flexible molecular docking for transcription factors with ligand-dependent activity, we assessed the ability of neuromodulators to occupy their effector binding sites. For many transcription factors, including the global regulator of carbohydrate metabolism, CRP, and the key regulator of lactose assimilation, LacI, this ability was predicted based on the analysis of several 3D models. By occupying the ligand binding site, neuromodulators can sterically hinder the interaction of the target proteins with the natural effectors or even replace them. The data obtained suggest that the direct modulation of the activity of at least some bacterial transcriptional factors by neuromodulators is possible. Therefore, the natural hormonal background may be a factor that preadapts bacteria to the habitat through direct perception of host signaling molecules. Full article
(This article belongs to the Special Issue Advances in Gene Research in Nuclear-Free Organisms and Entities: Prokaryotes and Organelles)
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19 pages, 10381 KiB  
Article
Metagenomics Revealed a New Genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. and a New Species ‘Candidatus Thiothrix putei’ sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na+- and H+-Motive Energetics
by Nikolai V. Ravin, Maria S. Muntyan, Dmitry D. Smolyakov, Tatyana S. Rudenko, Alexey V. Beletsky, Andrey V. Mardanov and Margarita Yu. Grabovich
Int. J. Mol. Sci. 2023, 24(18), 14199; https://doi.org/10.3390/ijms241814199 - 17 Sep 2023
Cited by 1 | Viewed by 1121
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG [...] Read more.
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%). We proposed to assign GKL-01 to a new species and genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name ‘Candidatus Thiothrix putei’ sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically. Full article
(This article belongs to the Special Issue Advances in Gene Research in Nuclear-Free Organisms and Entities: Prokaryotes and Organelles)
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