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      Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance

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          Abstract

          The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.

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          Gene Ontology: tool for the unification of biology

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            Life in extreme environments.

            Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring 'extremophiles'. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe.
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              CDD: a curated Entrez database of conserved domain alignments.

              The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                21 March 2017
                2017
                : 8
                Affiliations
                [1] 1Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
                [2] 2Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello Santiago, Chile
                [3] 3Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte Antofagasta, Chile
                [4] 4Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta Antofagasta, Chile
                [5] 5Centre for Biotechnology and Bioengineering Antofagasta, Chile
                [6] 6Laboratorio de Ecofisiología Microbiana, Fundación Ciencia and Vida Santiago, Chile
                [7] 7Sys2Diag CNRS/Bio-Rad UMR3145 Montpellier, France
                [8] 8Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso Valparaíso, Chile
                Author notes

                Edited by: Martin G. Klotz, Queens College (CUNY), USA

                Reviewed by: Adrian Gustavo Turjanski, University of Buenos Aires, Argentina; Tatiana A. Vishnivetskaya, University of Tennessee, Knoxville, USA

                *Correspondence: Eduardo Castro-Nallar, eduardo.castro@ 123456unab.cl Claudia P. Saavedra, csaavedra@ 123456unab.cl

                These authors have contributed equally to this work.

                This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2017.00456
                5360010
                7cda28a8-5076-40cf-a9e8-bfe0f6540046
                Copyright © 2017 Castro-Severyn, Remonsellez, Valenzuela, Salinas, Fortt, Aguilar, Pardo-Esté, Dorador, Quatrini, Molina, Aguayo, Castro-Nallar and Saavedra.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 5, Tables: 2, Equations: 0, References: 112, Pages: 14, Words: 0
                Funding
                Funded by: Comisión Nacional de Investigación CientÃ-fica y Tecnológica 10.13039/501100002848
                Award ID: FONDECYT 1160315
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                exiguobacterium,polyextremophile,stress,comparative genomics,chilean altiplano

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