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Advances on Bacterial Genomics II
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Advances on Bacterial Genomics II

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

Deadline for manuscript submissions: closed (15 January 2023) | Viewed by 5460

Special Issue Editor

Prof. Dr. Anne M. Alvarez

E-Mail Website1 Website2
Guest Editor
Department of Plant & Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
Interests: bacterial classification and genomics; population diversity; serological and molecular diagnostics; epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genome sequence-based investigations are emerging as a key area of research with respect to bacterial research. Bacterial interactions with the host—and infection severity—depend on genome constituents. There has been a tremendous increase in bacterial genome-wide analyses. In this Special Issue, we intend to highlight genome-wide analyses of pathogenicity determinants, CRISPR-Cas, type secretion systems, antimicrobial, EPS, and other important areas of genomics. Our aim is to provide a collection of manuscripts that describe the genomic biology and analyses of different bacterial pathogens. Research articles and reviews related to these areas are invited.

Submissions on—but not limited to—the following topics are invited:

  • Genome-wide comparative genomics;
  • Bacterial phylogenomics, evolution, and speciation;
  • Functional genomics;
  • Analyses of pathogenicity determinants and CRISPR cas;
  • Genome-informed molecular diagnostics.

Prof. Dr. Anne M. Alvarez
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. 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

  • comparative genomics
  • genomic evolution
  • phylogenomics
  • pathogenicity determinants
  • CRISPR cas
  • type secretion systems
  • bacterial speciation
  • functional genomics
  • genome-informed diagnostics

Published Papers (3 papers)

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Research

17 pages, 3414 KiB  
Article
Bipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes
by Cecilie Bækkedal Sonnenberg and Peik Haugen
Int. J. Mol. Sci. 2023, 24(5), 4292; https://doi.org/10.3390/ijms24054292 - 21 Feb 2023
Cited by 1 | Viewed by 1493
Abstract
Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is [...] Read more.
Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both which belong to the Enterobacterales order of Gammaproteobacteria, and compared the genomic openness with that of monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes. Full article
(This article belongs to the Special Issue Advances on Bacterial Genomics II)
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7 pages, 548 KiB  
Communication
Easy and Effective Method for Extracting and Purifying Wolbachia Genomic DNA
by Olga V. Andreenkova, Olga D. Shishkina, Alexandra I. Klimenko, Aleksandra E. Korenskaia, Margarita A. Bobrovskikh, Natalja V. Shatskaya, Gennady V. Vasiliev and Nataly E. Gruntenko
Int. J. Mol. Sci. 2022, 23(23), 15315; https://doi.org/10.3390/ijms232315315 - 5 Dec 2022
Cited by 1 | Viewed by 1582
Abstract
A number of methods for extracting the DNA of maternally inherited obligate intracellular bacteria Wolbachia from an insect host and its subsequent purification have been described in previous scholarship. As Wolbachia is present in the hosts’ organisms in rather low quantities, these techniques [...] Read more.
A number of methods for extracting the DNA of maternally inherited obligate intracellular bacteria Wolbachia from an insect host and its subsequent purification have been described in previous scholarship. As Wolbachia is present in the hosts’ organisms in rather low quantities, these techniques used to be quite labor-intensive. For this paper, we analyzed them in detail, searched for a possibility to simplify and accelerate the protocol, and proposed an easy and effective method for isolating Wolbachia DNA from Drosophila melanogaster with a purity sufficient for genomic sequencing. Our method involves the centrifugation of homogenized flies or just their ovaries, as the most Wolbachia-enriched tissue, followed by the filtration of homogenate and extraction of DNA using a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in the total DNA was quantified based on the results of sequencing with the use of the Illumina MiSeq platform and a pipeline of bioinformatic analysis. For the two analyzed D. melanogaster lines infected with two different Wolbachia strains, the proportion was at least 68 and 94%, respectively. Full article
(This article belongs to the Special Issue Advances on Bacterial Genomics II)
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18 pages, 1554 KiB  
Article
Effects of Global and Specific DNA-Binding Proteins on Transcriptional Regulation of the E. coli bgl Operon
by Dennis Tran, Zhongge Zhang, Katie Jing Kay Lam and Milton H. Saier, Jr.
Int. J. Mol. Sci. 2022, 23(18), 10343; https://doi.org/10.3390/ijms231810343 - 7 Sep 2022
Cited by 3 | Viewed by 1807
Abstract
Using reporter gene (lacZ) transcriptional fusions, we examined the transcriptional dependencies of the bgl promoter (Pbgl) and the entire operon regulatory region (Pbgl-bglG) on eight transcription factors as well as the inducer, salicin, and [...] Read more.
Using reporter gene (lacZ) transcriptional fusions, we examined the transcriptional dependencies of the bgl promoter (Pbgl) and the entire operon regulatory region (Pbgl-bglG) on eight transcription factors as well as the inducer, salicin, and an IS5 insertion upstream of Pbgl. Crp-cAMP is the primary activator of both Pbgl and the bgl operon, while H-NS is a strong dominant operon repressor but only a weak repressor of Pbgl. H-NS may exert its repressive effect by looping the DNA at two binding sites. StpA is a relatively weak repressor in the absence of H-NS, while Fis also has a weak repressive effect. Salicin has no effect on Pbgl activity but causes a 30-fold induction of bgl operon expression. Induction depends on the activity of the BglF transporter/kinase. IS5 insertion has only a moderate effect on Pbgl but causes a much greater activation of the bgl operon expression by preventing the full repressive effects of H-NS and StpA. While several other transcription factors (BglJ, RcsB, and LeuO) have been reported to influence bgl operon transcription when overexpressed, they had little or no effect when present at wild type levels. These results indicate the important transcriptional regulatory mechanisms operative on the bgl operon in E. coli. Full article
(This article belongs to the Special Issue Advances on Bacterial Genomics II)
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