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Microorganisms
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Advances in Bacterial Genetics
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Advances in Bacterial Genetics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: 15 February 2025 | Viewed by 12973

Special Issue Editors

Prof. Dr. Renato Fani

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Guest Editor
Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
Interests: antibiotic resistance; bacterial genetics; endophytes; environmental microbiology; gene and genome evolution; molecular evolution
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Marco Bazzicalupo

E-Mail Website
Guest Editor
Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
Interests: microbial genetics; plant-bacterial symbiosis; bacterial population genetics and evolution
Prof. Dr. Anna Maria Puglia

E-Mail Website
Guest Editor
Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
Interests: bacterial genetics; biology of actinomycetes; microbial biotechnologies
Dr. Sara Del Duca

E-Mail Website
Assistant Guest Editor
Department of Biology, University of Florence, 50019 Sesto Fiorentino, Florence, Italy
Interests: microbial genetics; gene evolution; histidine biosynthesis; bacterial communities
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

In recent years, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. There are approximately 2×1030 bacteria on Earth, forming a biomass that is only exceeded by plants. They were among the first life forms to appear on Earth and are present in most of its habitats where they may have very different ecological roles.

Because of their fast growth and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics, and biochemistry. Bacterial genetics has been the driving force of advancing modern genetics since the middle of the last century and is still at the forefront of genetic and microbiology research in several areas, which are the topics of this Special Issue:

  • Evolutionary mechanisms: indeed, bacteria are able to rapidly evolve and adapt to constantly changing environmental conditions, thanks to the constant fine tuning of their mutation rates and to the horizontal transfer of genetic information among different bacteria;
  • Regulatory mechanisms: thanks to the huge array of genetic tools that enable bacteria to control all levels of gene expression;
  • Growth and differentiation, including cell-cycle control and spore formation;
  • Pathogenicity mechanisms and spreading of antibiotic resistance;
  • Bacterial communication and interaction with each other and with the surrounding environment, through mechanisms such as quorum sensing and the production/detection of signal molecules including volatile organic compounds;
  • Symbiotic lifestyle, allowing bacteria to thrive inside plant and animal hosts;
  • Ecological roles: bacteria are vital in many stages of the nutrient cycle through recycling nutrients, such as the fixation of nitrogen from the atmosphere;
  • Systems biology and metabolic modelling: since most bacteria have not yet been characterized and there are many species that cannot be grown in the laboratory, these disciplines can allow studying and predicting those processes which could not be studied otherwise.

This Special Issue of Microorganisms aims to expand the current state of the art regarding all the areas of bacterial genetics, not limited to those mentioned above. Research articles, reviews, and short communications concerning the current challenges of bacterial genetics are of interest.

Prof. Dr. Renato Fani
Prof. Dr. Marco Bazzicalupo
Prof. Dr. Anna Maria Puglia
Dr. Sara Del Duca
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. 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

  • bacterial genetics
  • environmental adaptation
  • gene and genome evolution
  • regulatory networks
  • host microbiome
  • bacterial interactions
  • biotechnology
  • bioinformatics

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Published Papers (5 papers)

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Research

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13 pages, 2821 KiB  
Article
The Restriction Activity Investigation of Rv2528c, an Mrr-like Modification-Dependent Restriction Endonuclease from Mycobacterium tuberculosis
by Tong Liu, Wei Wei, Mingyan Xu, Qi Ren, Meikun Liu, Xuemei Pan, Fumin Feng, Tiesheng Han and Lixia Gou
Microorganisms 2024, 12(7), 1456; https://doi.org/10.3390/microorganisms12071456 - 18 Jul 2024
Viewed by 836
Abstract
Mycobacterium tuberculosis (Mtb), as a typical intracellular pathogen, possesses several putative restriction–modification (R-M) systems, which restrict exogenous DNA’s entry, such as bacterial phage infection. Here, we investigate Rv2528c, a putative Mrr-like type IV restriction endonuclease (REase) from Mtb H37Rv, which is [...] Read more.
Mycobacterium tuberculosis (Mtb), as a typical intracellular pathogen, possesses several putative restriction–modification (R-M) systems, which restrict exogenous DNA’s entry, such as bacterial phage infection. Here, we investigate Rv2528c, a putative Mrr-like type IV restriction endonuclease (REase) from Mtb H37Rv, which is predicted to degrade methylated DNA that contains m6A, m5C, etc. Rv2528c shows significant cytotoxicity after being expressed in Escherichia coli BL21(DE3)pLysS strain. The Terminal deoxynucleotidyl transferase dUTP Nick-End Labeling (TUNEL) assay indicates that Rv2528c cleaves genomic DNA in vivo. The plasmid transformation efficiency of BL21(DE3)pLysS strain harboring Rv2528c gene was obviously decreased after plasmids were in vitro methylated by commercial DNA methyltransferases such as M.EcoGII, M.HhaI, etc. These results are consistent with the characteristics of type IV REases. The in vitro DNA cleavage condition and the consensus cleavage/recognition site of Rv2528c still remain unclear, similar to that of most Mrr-family proteins. The possible reasons mentioned above and the potential role of Rv2528c for Mtb were discussed. Full article
(This article belongs to the Special Issue Advances in Bacterial Genetics)
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20 pages, 2499 KiB  
Article
Genomic Characterization of Arcobacter butzleri Strains Isolated from Various Sources in Lithuania
by Dainius Uljanovas, Greta Gölz, Susanne Fleischmann, Egle Kudirkiene, Neringa Kasetiene, Audrone Grineviciene, Egle Tamuleviciene, Jurgita Aksomaitiene, Thomas Alter and Mindaugas Malakauskas
Microorganisms 2023, 11(6), 1425; https://doi.org/10.3390/microorganisms11061425 - 28 May 2023
Cited by 1 | Viewed by 2102
Abstract
Arcobacter (A.) butzleri, the most widespread species within the genus Arcobacter, is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 A. butzleri strains from Lithuania to determine the genetic relationship, pangenome [...] Read more.
Arcobacter (A.) butzleri, the most widespread species within the genus Arcobacter, is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 A. butzleri strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential antimicrobial- and heavy-metal-resistance genes. Core genome single nucleotide polymorphism (cgSNP) analysis revealed low within-group variability (≤4 SNPs) between three milk strains (RCM42, RCM65, RCM80) and one human strain (H19). Regardless of the type of input (i.e., cgSNPs, accessory genome, virulome, resistome), these strains showed a recurrent phylogenetic and hierarchical grouping pattern. A. butzleri demonstrated a relatively large and highly variable accessory genome (comprising of 6284 genes with around 50% of them identified as singletons) that only partially correlated to the isolation source. Downstream analysis of the genomes resulted in the detection of 115 putative antimicrobial- and heavy-metal-resistance genes and 136 potential virulence factors that are associated with the induction of infection in host (e.g., cadF, degP, iamA), survival and environmental adaptation (e.g., flagellar genes, CheA-CheY chemotaxis system, urease cluster). This study provides additional knowledge for a better A. butzleri-related risk assessment and highlights the need for further genomic epidemiology studies in Lithuania and other countries. Full article
(This article belongs to the Special Issue Advances in Bacterial Genetics)
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15 pages, 1920 KiB  
Article
Characterization of Bacterial Transcriptional Regulatory Networks in Escherichia coli through Genome-Wide In Vitro Run-Off Transcription/RNA-seq (ROSE)
by Pascal Schmidt, David Brandt, Tobias Busche and Jörn Kalinowski
Microorganisms 2023, 11(6), 1388; https://doi.org/10.3390/microorganisms11061388 - 25 May 2023
Cited by 3 | Viewed by 2057
Abstract
The global characterization of transcriptional regulatory networks almost exclusively uses in vivo conditions, thereby providing a snapshot on multiple regulatory interactions at the same time. To complement these approaches, we developed and applied a method for characterizing bacterial promoters genome-wide by in vitro [...] Read more.
The global characterization of transcriptional regulatory networks almost exclusively uses in vivo conditions, thereby providing a snapshot on multiple regulatory interactions at the same time. To complement these approaches, we developed and applied a method for characterizing bacterial promoters genome-wide by in vitro transcription coupled to transcriptome sequencing specific for native 5′-ends of transcripts. This method, called ROSE (run-off transcription/RNA-sequencing), only requires chromosomal DNA, ribonucleotides, RNA polymerase (RNAP) core enzyme, and a specific sigma factor, recognizing the corresponding promoters, which have to be analyzed. ROSE was performed on E. coli K-12 MG1655 genomic DNA using Escherichia coli RNAP holoenzyme (including σ70) and yielded 3226 transcription start sites, 2167 of which were also identified in in vivo studies, and 598 were new. Many new promoters not yet identified by in vivo experiments might be repressed under the tested conditions. Complementary in vivo experiments with E. coli K-12 strain BW25113 and isogenic transcription factor gene knockout mutants of fis, fur, and hns were used to test this hypothesis. Comparative transcriptome analysis demonstrated that ROSE could identify bona fide promoters that were apparently repressed in vivo. In this sense, ROSE is well-suited as a bottom-up approach for characterizing transcriptional networks in bacteria and ideally complementary to top-down in vivo transcriptome studies. Full article
(This article belongs to the Special Issue Advances in Bacterial Genetics)
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22 pages, 2905 KiB  
Article
Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria
by Anthony J. Farlow, Darshani B. Rupasinghe, Khalid M. Naji, Robert J. Capon and Dieter Spiteller
Microorganisms 2023, 11(4), 1005; https://doi.org/10.3390/microorganisms11041005 - 12 Apr 2023
Viewed by 2573
Abstract
Rosenbergiella bacteria have been previously isolated predominantly from floral nectar and identified in metagenomic screenings as associated with bees. Here, we isolated three Rosenbergiella strains from the robust Australian stingless bee Tetragonula carbonaria sharing over 99.4% sequence similarity with Rosenbergiella strains isolated from [...] Read more.
Rosenbergiella bacteria have been previously isolated predominantly from floral nectar and identified in metagenomic screenings as associated with bees. Here, we isolated three Rosenbergiella strains from the robust Australian stingless bee Tetragonula carbonaria sharing over 99.4% sequence similarity with Rosenbergiella strains isolated from floral nectar. The three Rosenbergiella strains (D21B, D08K, D15G) from T. carbonaria exhibited near-identical 16S rDNA. The genome of strain D21B was sequenced; its draft genome contains 3,294,717 bp, with a GC content of 47.38%. Genome annotation revealed 3236 protein-coding genes. The genome of D21B differs sufficiently from the closest related strain, Rosenbergiella epipactidis 2.1A, to constitute a new species. In contrast to R. epipactidis 2.1A, strain D21B produces the volatile 2-phenylethanol. The D21B genome contains a polyketide/non-ribosomal peptide gene cluster not present in any other Rosenbergiella draft genomes. Moreover, the Rosenbergiella strains isolated from T. carbonaria grew in a minimal medium without thiamine, but R. epipactidis 2.1A was thiamine-dependent. Strain D21B was named R. meliponini D21B, reflecting its origin from stingless bees. Rosenbergiella strains may contribute to the fitness of T. carbonaria. Full article
(This article belongs to the Special Issue Advances in Bacterial Genetics)
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Review

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16 pages, 470 KiB  
Review
Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation
by Jun Hirose
Microorganisms 2023, 11(2), 438; https://doi.org/10.3390/microorganisms11020438 - 9 Feb 2023
Cited by 8 | Viewed by 2242
Abstract
Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest [...] Read more.
Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed. Full article
(This article belongs to the Special Issue Advances in Bacterial Genetics)
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