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.

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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.

Tentative title: Making the extremolytes ectoine and hydroxyectoine: insights from biochemistry, structural analysis, and phlyogenomics

Putative authors: Laura Czech1, Alexandra Richter1, Sander H.J. Smits2, Johann Heider1,3 and

Erhard Bremer1,3*

Affiliations: 1Philipps-University Marburg, Department of Biology, Laboratory for Microbiology, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany, 2Heinrich Heine University Düsseldorf, Institute of Biochemistry, Universitäts Str. 1,D-402325 Düsseldorf, Germany, 3Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6

Abstract: Fluctuations in the environmental osmolarity are one of the most ubiquitously occurring stress factors in natural habitats of most free-living Bacteria and Archaea since they will inevitably trigger influx (at low osmolarity) or efflux (at high osmolarity) of water from the cell. Under hyper-osmotic conditions, many microorganisms fend-off the detrimental effects of the dehydration of the cytoplasm and drop in turgor to physiologically non-sustainable values through the accumulation of a selected class of organic osmolytes, the compatible solutes. The physico-chemical attributes of compatible solutes make them highly compliant with cellular biochemistry and functionality of macromolecular complexes. Hence, compatible solutes can be accumulated to exceedingly high concentrations, and the degree of the osmotic stress imposed onto the microbial cell determines their pool size. The tetrahydropyrimidine ectoine and its derivative hydroxyectoine are prominent members of the compatible solutes and are synthesized widely by members of the Bacteria, and more restricted in Archaea, in response to increases in the external salinity/osmolarity and extremes in growth temperature. We will review here the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and explore the phylogenomics of the corresponding structural and regulatory genes to provide an overview on their distribution in the microbial world.

D-35043 Marburg, Germany

 

Tentative title: : Approaches and advancements in understanding archaeal virus gene function(s)

Putative authors: Jacob Munson-McGee, Jamie Snyder2, Martin Lawrence3, Mark Young1

Dept. of Microbiology and Immunology, Montana State University, Bozeman, MT, USA

Biological Sciences Department, California State Polytechnic University, Pomona, CA, USA

3 Dept. of Chemistry and Biochemistry, Montana State University, Bozeman, MT

Abstract: A major challenge in archaeal virology is determining the function of genes encoded by archaeal viruses. While the sequencing of new archaeal viral genomes has become more routine, determining gene function(s) has remained elusive. This is due in part to the difficulty in establishing viable host-virus culture systems, creating genetic systems for archaeal hosts and their viruses, a general lack of knowledge of archaeal biochemistry, and the low homology between archaeal viral genes to other genes in the databases.  However, a combination of approaches, including structural analysis, culture independent systems for probing host-virus associations (e.g. single cell genomics, in situ host-virus FISH), along with improved bioinformatics and genetic tools are beginning to make advancements in our understanding of archaeal virus gene function. We discuss these advances, with examples, in this work.  We also provide a perspective on how these advances will impact our understanding of the role of archaeal viruses in the ecology and evolution of microbial communities found in extreme environments.

 

Tentative title: Hierarchical of control of nitrite respiration cluster upon integration into a new Thermus thermophilus host 

Putative authors: Laura Alvarez, Nieves García-Quintans, Carlos Bricio, Ignacio Baquedano, Alba Blesa, Mario Mencía  and José Berenguer

Abstract: The strain Thermus thermophilus HB27 is strictly aerobic. However, derivatives capable of growth under anaerobic conditions in the presence of nitrate or/and nitrite can be easily obtained by natural competence or conjugation from a denitrificant isolate.  The expression of the nitrite respiration genes in this new denitrificant derivative of the formerly aerobic strain has been studied. By using a combination of promoter reporters in different mutants of this strain we show how regulatory elements encoded by the nitrate respiration cluster are required for the expression of all the promoters of the nitrite respiration cluster, including those for the nitrite and the nitric oxide reductases. We also analyse the role in this expression of an additional regulator protein of the Nsr family encoded by the nitrite respiration cluster.

 

Tentative title: Small non-coding RNAs in Archaea: regulatory roles and functional implications 

Putative authors: Diego Gelsinger and Jocelyne DiRuggiero

Affiliation: Department of Biology, Biology Department, The Johns Hopkins University, Baltimore, MD, USA

Abstract: Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing, and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and target many genes and pathways, suggesting extensive roles in gene regulation. These Antisense sRNAs can be further classified based on their binding patterns towards mRNAs (3’ UTR, 5’ UTR, CDS-binding). Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Future work is needed to elucidate sRNA-RNA binding mechanisms, the precise regulatory mechanisms involved in sRNA-mediated regulation, and the discovery of whether protein components are involved in sRNA-mediated regulation as seen in Bacteria and Eukarya.

 

Putative authors: Gygli, P.E., J. Evans, J. McCaskill and L.C. DeVeaux

Tentative title: Divergent roles of RPA homologs of the model archaeon Halobacterium salinarum in survival of DNAdamage

Abstract: The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or RPA) found in all three domains of life.  Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the megaplasmids, and one is uniquely euryarchaeal.  Radiation resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes.   Here, we have created deletions of four of the five genes.  In Haloferax volcanii, the euryarchaeal homolog is essential, whereas in Halobacterium salinarum, this homolog is not.  These deletion mutants were exposed to DNA damaging conditions:  ionizing radiation, UV radiation, hydrogen peroxide, and mitomycin C.  Deletion of the euryarchaeal homolog, although not lethal, causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered.

 

Working title: Development of a 6-Methylpurine (6-MP) stringent counterselection marker for genetic manipulation studies of the hyperthermophilic piezophilic archaeon Thermococcus barophilus

Putative authors: Tiphaine Birien1,2,3, Axel Thiel1,2,3, Ghislaine Henneke1,2,3, Didier Flament1,2,3, Yann Moalic1,2,3 and Mohamed Jebbar1,2,3, *.

Affiliation:  1Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) – UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d’Urville, F-29280 Plouzané, France. 2CNRS, IUEM – UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d’Urville, F-29280 Plouzané, France. 3Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.

Abstract: A gene disruption system for T. barophilus was developed using simvastatin( HMG-CoA reductase encoding gene) for positive selection and 5-FOA (5-Fluoroorotic acid ) (pyrF gene) for negative selection. This method leads to the construction of multiple gene mutants and give the possibility of complementation in Trans but resulting in a high rate of false positive (up to 80%).

In order to reduce drastically the false-positive ratio, we improved our genetic tools by using another counter-selective marker  6-methylpurine (6-MP) a toxic analog of adenine developed in T. kodakarensis, which is consistently correlated to TK0664 gene encoding a hypoxanthine-guanine phosphoribosyl-transferase. Thus, in this study, we replaced pyrF by TK0664 on our suicide vector and we tested the susceptibility of T. barophilus strains to 6-MP before and after transformation. T. barophilus WT is less sensitive to 6-MP than T. kodakarensis WT and an increase of cell sensitivity is even achieved after deletion of T. barophilus TERMP_00517 gene homologous to T. kodakarensis TK0664 gene. The results obtained confirm the natural resistance of T. barophilus to 6-MP and show that sensitivity can be brought by TK0664. This new counter-selection system strongly improves genetic manipulations in T. barophilus MP with a strong decrease of false-positive rate under 15%. By using the genetic tools developed for T. barophilus, we already started to investigate the functions of several genes involved in high pressure adaptation and in genomic maintenance.

 

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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