Special Issue "Genetics and Genomics of Extremophiles"

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

Deadline for manuscript submissions: 31 December 2017

Special Issue Editors

Guest Editor
Prof. Dr. Antonio Ventosa

Dept. Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Calle Prof. Garcia González, 2, 41012 Sevilla, Spain
Website | E-Mail
Phone: +34-954556765
Fax: +34-954628162
Interests: halophiles; halophilic archaea; halophilic bacteria; hypersaline habitats; comparative genomics; phylogenomics; molecular systematics
Guest Editor
Dr. Ken Stedman

Center for Life in Extreme Environments, Department of Biology, Portland State University, Room 466, SRTC, 1719 SW 10th Avenue - P.O. Box 751, Portland, OR 97207-0751, USA
Website | E-Mail
Phone: 503-725-3253
Fax: 503-725-3888
Interests: extremophile viruses; virus evolution; vaccine formulation
Guest Editor
Prof. Dr. Thane Papke

Dept of Molecular & Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Biology/Physics Building 402, Storrs, CT 06269-3125, USA
Website | E-Mail
Phone: 860-486-7963
Fax: 860-486-4331
Interests: Halophiles, Haloarchaea, Haloferax volcanii, Microbial Evolution, Microbial Genomics, Microbial Genetics, Microbial Ecology

Special Issue Information

Dear Colleagues,

Life in extreme environments is limited to a few groups of organisms that are adapted to environmental conditions, such as excesses of temperature, pH, or salt concentrations; thus, extremophiles include thermophiles or hyperthermophiles, psychrophiles, alkaliphiles, acidophiles, halophiles, and piezophiles, among others. Many of them live in habitats in which more than a single environmental factor may limit or prevent the growth of other organisms, and they are categorized as polyextremophiles. Extremophiles belong to all domains of life, Archaea, Bacteria and Eukarya, and also include their viruses. Extensive studies on their diversity and mechanisms of adaptation to these extreme habitats have been carried out during the recent years. However, the genetic basis of these adaptation responses and other basic genetic mechanisms have not been addressed in detail.

This research topic is focused on studies related to the genetics and genomics of extremophiles, from the mechanisms of genetic exchange to the adaptations resulting from horizontal gene transfer, as well as their genomic organization and comparative genomics, including any extremophilic organism, as well as their viruses.

We cordially invite to researchers working actively in these fields to submit their original research or review manuscripts to this research topic on the genetics and genomics of extremophilic microorganisms.

Prof. Dr. Antonio Ventosa
Prof. Dr. Ken Stedman
Prof. Dr. Thane Papke
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 papers will be 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 1200 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

  • extremophiles
  • thermophiles
  • hyperthermophiles
  • prychrophiles
  • alkaliphiles
  • acidophiles
  • halophiles
  • piezophiles
  • archaea
  • bacteria
  • eukaryotes
  • viruses

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Working title: Proteomic analysis of Methanonatronarchaeum thermophilum, a representative of a new archaeal lineage Methanonatronarchaeia

Authors: Manuel Ferrer1, Dmitry Sorokin2, Yuri Wolf3, Sergio Ciordia4, María C. Mena4, Kira Makarova3, Eugene Koonin3.

Affiliations: 1 Institute of Catalysis, CSIC, Madrid, Spain. 2 Winogradsky Institute of Microbiology, Centre for Biotechnology, Russian Academy of Sciences, Moscow, Russia. 2 Department of Biotechnology, Delft University of Technology, Delft, The Netherlands. 3 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. 4 Proteomics Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain. Institute of Catalysis, CSIC, Madrid, Spain. 

Abstract: Methanonatronarchaeia are methanogenic archaea from Euryarchaeota phylum which are extremely halophilic and moderately thermophilic. This combination of phenotypic features is so far unique among archaea. We here offer a detailed analysis of 1D-nano liquid chromatography–electrospray ionization tandem mass spectrometry data obtained for Methanonatronarchaeum thermophilum grown in different physiological conditions, including variation of the growth temperature. Compared to the variation of the nutrient source, changes in temperature have stronger effect on the distribution of the protein abundances with more genes up- and down-regulated relative to the basal conditions. This analysis allows us to refine our understanding of the key biosynthetic pathways typical for the organism and identify proteins that are involved in response to variation of the growth temperature.

 

Working title: Differential gene expression in response to salinity and temperature in a Haloarcula strain from Great Salt Lake, Utah

Putative authors: Swati Almeida-Dalmet 1 , Carol D Litchfield 1 , Patrick Gillevet1 and Bonnie K. Baxter2 *

Affiliation: 1 Department of Environmental Science and Policy, George Mason University, 10900 University Blvd, Manassas, Virginia, 20110, USA. 2 Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, Utah, 84105, USA

Abstract: Great Salt Lake (GSL) is a thalassohaline, terminal lake, which responds to the fluctuating climate conditions of the elevated desert of Utah. It is a dynamic ecosystem with shifting salinity gradients, lake levels, and variable temperatures over the seasons. Identified as a stable member of the GSL microbial community, /Haloarcula/ sp. strain NA6*-*27, an isolate from the hypersaline north arm of the lake, optimally grows at 42^o C in 20% (w/v) total salts. We investigated how environmental factors, specifically salinity and temperature, affected gene expression in this representative GSL haloarchaeon. In this study, RNA arbitrarily primed PCR (RAP-PCR) was used to determine the transcriptional responses of NA6-27 grown under suboptimal salinity and temperature conditions. We noted expression of genes related to signal transduction, respiration, transport, transcription, and translation of stress proteins responded to the test conditions. Ten genes were expressed differentially at different salinities and eight genes were expressed differentially at different temperatures. Eight of the total ten genes responded in both conditions. Taken together, these data indicate that /Haloarcula/ sp. str. NA6-27 responds similarly to either salinity or temperature stress, and this suggests a mechanistic model for homeostasis, allowing haloarchaea to maintain a stable presence in the community as environmental conditions shift.

 

Working title: Are small RNAs involved in the regulation of nitrogen metabolism in haloarchaea?

Putative authors: Gloria Payá, Vanesa Bautista, Mónica Camacho, María-José Bonete, Julia Esclapez

Affiliation: Departamento de Agroquimica y Bioquimica, Division de Bioquimica y Biologia Molecular, Facultad Ciencias, Universidad Alicante, Ap99, E-03080 Alicante, Spain

Abstract: Since the small RNAs (sRNA) were discovered in Bacteria Domain, the number of papers related to this topic has significantly increased in recent years. Although the sRNAs have been studied in detail in Bacteria and Eukarya Domain, in the case of Archaea Domain the knowledge is scarce. Thanks to RNomics and in silico analysis, it has been identified different putative sRNA sequences in Methanosarcina mazei, Sulfolobus solfataricus, Haloferax volcanii, Halobacterium salinarum, Nanoarchaeum equitans, Methanopyrus kandleri, Pyrococcus abyssi, Thermococcus kodakarensis and Methanolobus psycrophilus. However, the physiological function of the majority is still uncertain because of there is not experimental data to support it.

In order to extend the understanding of sRNAs in Archaea Domain and analyse its possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. Bioinformatic approach has been used to predict sRNAs genes in the genome of H. mediterranei. The bioinformatic analysis results in a significant number of putative sRNA sequences, some of which are common with sRNAs identified in H. volcanii. Analysis of RNA-seq has been carried out with RNA samples from cultures of H. mediterranei grown with different nitrogen sources to identify sRNAs with potential regulatory functions under these conditions. Candidates sRNAs have been identified manually using IGV as small (<200 pb) transcripts expressed from intergenic regions or antisense to characterized ORFs. Moreover, it has been found out putative sRNAs which show differences in their expression pattern according to the nitrogen source. 

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