Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4
Identifieur interne : 006426 ( Main/Exploration ); précédent : 006425; suivant : 006427Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4
Auteurs : Benjamin Janto [États-Unis] ; Azad Ahmed [États-Unis] ; Masahiro Ito [Japon] ; Jun Liu [États-Unis] ; David B. Hicks [États-Unis] ; Sarah Pagni [États-Unis] ; Oliver J. Fackelmayer [États-Unis] ; Terry-Ann Smith [États-Unis] ; Joshua Earl [États-Unis] ; Liam D. H. Elbourne [Australie] ; Karl Hassan [Australie] ; Ian T. Paulsen [Australie] ; Anne-Brit Kolst [Norvège] ; Nicolas J. Tourasse [France] ; Garth D. Ehrlich [États-Unis] ; Robert Boissy [États-Unis] ; D. Mack Ivey [États-Unis] ; Gang Li [République populaire de Chine] ; Yanfen Xue [République populaire de Chine] ; Yanhe Ma [République populaire de Chine] ; Fen Z. Hu [États-Unis] ; Terry A. Krulwich [États-Unis]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2011-12.
English descriptors
- KwdEn :
- Acidic, Alkaline, Alkaline conditions, Alkaliphile, Alkaliphiles, Alkaliphilic, Alkaliphilic bacillus, Alkaliphilic bacillus species, Alkaliphilic bacteria, Alkaliphily, Alkalophilic, Amino, Annotation, Antiporter, Antiporters, Atpe, Bacillus, Bacillus cellulosilyticus, Bacillus cereus group, Bacillus halodurans, Bacillus subtilis, Bacteriol, Bcr3, Bcr3 elements, Biochim biophys acta, Biol, Biol chem, Biophys, Blackwell, Blackwell publishing, Blastp, Blastp hits, Bpof4_, Bpr1, Bpr2, Catalytic site, Cell division, Cell wall, Cereus, Cereus group, Chaperone, Chem, Chemotaxis, Chromosomal, Chromosomal genes, Chromosome, Coli, Cytochrome, Cytoplasmic, Cytoplasmic proteins, Dehydrogenase, Dnaa, Dnaa boxes, Domain proteins, Encoding, Energy demands, Energy sources, Environmental microbiology, Epsx, Escherichia, Escherichia coli, Extremophiles, Ferric, Fujisawa, Gene, Gene cluster, Genome, Genome sequence, Genome sequences, Genomic, Gilmour, Guffanti, Halodurans, Helmann, Hick, Homeostasis, Horikoshi, Innermost intron, Intron, Janto, Kolst, Krulwich, Large number, Large plasmid, Locus, Metabolic, Microbiol, Microbiology, Mobile elements, Multiple sequence alignment, Mutant, Neutralophilic bacillus species, Nucleic, Nucleic acids, Operon, Orfs, Other stresses, Oxidase, Oxidative, Oxidative phosphorylation, Phosphorylation, Plasmid, Polyglutamate capsule, Proc natl acad, Proton, Rapid annotations, Replication, Resident plasmids, Rmus, Siderophore, Sigma, Sigma factors, Small plasmid, Sodium ions, Solute, Staphylococcus aureus, Stress responses, Subtilis, Synthase, Tmrna, Tourasse, Transporter, Uptake, Wang.
- Teeft :
- Acidic, Alkaline, Alkaline conditions, Alkaliphile, Alkaliphiles, Alkaliphilic, Alkaliphilic bacillus, Alkaliphilic bacillus species, Alkaliphilic bacteria, Alkaliphily, Alkalophilic, Amino, Annotation, Antiporter, Antiporters, Atpe, Bacillus, Bacillus cellulosilyticus, Bacillus cereus group, Bacillus halodurans, Bacillus subtilis, Bacteriol, Bcr3, Bcr3 elements, Biochim biophys acta, Biol, Biol chem, Biophys, Blackwell, Blackwell publishing, Blastp, Blastp hits, Bpof4_, Bpr1, Bpr2, Catalytic site, Cell division, Cell wall, Cereus, Cereus group, Chaperone, Chem, Chemotaxis, Chromosomal, Chromosomal genes, Chromosome, Coli, Cytochrome, Cytoplasmic, Cytoplasmic proteins, Dehydrogenase, Dnaa, Dnaa boxes, Domain proteins, Encoding, Energy demands, Energy sources, Environmental microbiology, Epsx, Escherichia, Escherichia coli, Extremophiles, Ferric, Fujisawa, Gene, Gene cluster, Genome, Genome sequence, Genome sequences, Genomic, Gilmour, Guffanti, Halodurans, Helmann, Hick, Homeostasis, Horikoshi, Innermost intron, Intron, Janto, Kolst, Krulwich, Large number, Large plasmid, Locus, Metabolic, Microbiol, Microbiology, Mobile elements, Multiple sequence alignment, Mutant, Neutralophilic bacillus species, Nucleic, Nucleic acids, Operon, Orfs, Other stresses, Oxidase, Oxidative, Oxidative phosphorylation, Phosphorylation, Plasmid, Polyglutamate capsule, Proc natl acad, Proton, Rapid annotations, Replication, Resident plasmids, Rmus, Siderophore, Sigma, Sigma factors, Small plasmid, Sodium ions, Solute, Staphylococcus aureus, Stress responses, Subtilis, Synthase, Tmrna, Tourasse, Transporter, Uptake, Wang.
Abstract
Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non‐fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions.
Url:
- https://api.istex.fr/document/82444BFFA797091E8E9001E2CA108A9C035CAB8E/fulltext/pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228905
DOI: 10.1111/j.1462-2920.2011.02591.x
Affiliations:
- Australie, France, Japon, Norvège, République populaire de Chine, États-Unis
- Arkansas, Nouvelle-Galles du Sud, Pennsylvanie, État de New York, Île-de-France
- Paris, Pékin, Sydney
- Université Pierre-et-Marie-Curie
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 001863
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- to stream Istex, to step Checkpoint: 000846
- to stream Pmc, to step Corpus: 001534
- to stream Pmc, to step Curation: 001394
- to stream Pmc, to step Checkpoint: 002141
- to stream Ncbi, to step Merge: 000B81
- to stream Ncbi, to step Curation: 000B81
- to stream Ncbi, to step Checkpoint: 000B81
- to stream Main, to step Merge: 006803
- to stream Main, to step Curation: 006426
Le document en format XML
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<term>Alkaline</term>
<term>Alkaline conditions</term>
<term>Alkaliphile</term>
<term>Alkaliphiles</term>
<term>Alkaliphilic</term>
<term>Alkaliphilic bacillus</term>
<term>Alkaliphilic bacillus species</term>
<term>Alkaliphilic bacteria</term>
<term>Alkaliphily</term>
<term>Alkalophilic</term>
<term>Amino</term>
<term>Annotation</term>
<term>Antiporter</term>
<term>Antiporters</term>
<term>Atpe</term>
<term>Bacillus</term>
<term>Bacillus cellulosilyticus</term>
<term>Bacillus cereus group</term>
<term>Bacillus halodurans</term>
<term>Bacillus subtilis</term>
<term>Bacteriol</term>
<term>Bcr3</term>
<term>Bcr3 elements</term>
<term>Biochim biophys acta</term>
<term>Biol</term>
<term>Biol chem</term>
<term>Biophys</term>
<term>Blackwell</term>
<term>Blackwell publishing</term>
<term>Blastp</term>
<term>Blastp hits</term>
<term>Bpof4_</term>
<term>Bpr1</term>
<term>Bpr2</term>
<term>Catalytic site</term>
<term>Cell division</term>
<term>Cell wall</term>
<term>Cereus</term>
<term>Cereus group</term>
<term>Chaperone</term>
<term>Chem</term>
<term>Chemotaxis</term>
<term>Chromosomal</term>
<term>Chromosomal genes</term>
<term>Chromosome</term>
<term>Coli</term>
<term>Cytochrome</term>
<term>Cytoplasmic</term>
<term>Cytoplasmic proteins</term>
<term>Dehydrogenase</term>
<term>Dnaa</term>
<term>Dnaa boxes</term>
<term>Domain proteins</term>
<term>Encoding</term>
<term>Energy demands</term>
<term>Energy sources</term>
<term>Environmental microbiology</term>
<term>Epsx</term>
<term>Escherichia</term>
<term>Escherichia coli</term>
<term>Extremophiles</term>
<term>Ferric</term>
<term>Fujisawa</term>
<term>Gene</term>
<term>Gene cluster</term>
<term>Genome</term>
<term>Genome sequence</term>
<term>Genome sequences</term>
<term>Genomic</term>
<term>Gilmour</term>
<term>Guffanti</term>
<term>Halodurans</term>
<term>Helmann</term>
<term>Hick</term>
<term>Homeostasis</term>
<term>Horikoshi</term>
<term>Innermost intron</term>
<term>Intron</term>
<term>Janto</term>
<term>Kolst</term>
<term>Krulwich</term>
<term>Large number</term>
<term>Large plasmid</term>
<term>Locus</term>
<term>Metabolic</term>
<term>Microbiol</term>
<term>Microbiology</term>
<term>Mobile elements</term>
<term>Multiple sequence alignment</term>
<term>Mutant</term>
<term>Neutralophilic bacillus species</term>
<term>Nucleic</term>
<term>Nucleic acids</term>
<term>Operon</term>
<term>Orfs</term>
<term>Other stresses</term>
<term>Oxidase</term>
<term>Oxidative</term>
<term>Oxidative phosphorylation</term>
<term>Phosphorylation</term>
<term>Plasmid</term>
<term>Polyglutamate capsule</term>
<term>Proc natl acad</term>
<term>Proton</term>
<term>Rapid annotations</term>
<term>Replication</term>
<term>Resident plasmids</term>
<term>Rmus</term>
<term>Siderophore</term>
<term>Sigma</term>
<term>Sigma factors</term>
<term>Small plasmid</term>
<term>Sodium ions</term>
<term>Solute</term>
<term>Staphylococcus aureus</term>
<term>Stress responses</term>
<term>Subtilis</term>
<term>Synthase</term>
<term>Tmrna</term>
<term>Tourasse</term>
<term>Transporter</term>
<term>Uptake</term>
<term>Wang</term>
</keywords>
<keywords scheme="Teeft" xml:lang="en"><term>Acidic</term>
<term>Alkaline</term>
<term>Alkaline conditions</term>
<term>Alkaliphile</term>
<term>Alkaliphiles</term>
<term>Alkaliphilic</term>
<term>Alkaliphilic bacillus</term>
<term>Alkaliphilic bacillus species</term>
<term>Alkaliphilic bacteria</term>
<term>Alkaliphily</term>
<term>Alkalophilic</term>
<term>Amino</term>
<term>Annotation</term>
<term>Antiporter</term>
<term>Antiporters</term>
<term>Atpe</term>
<term>Bacillus</term>
<term>Bacillus cellulosilyticus</term>
<term>Bacillus cereus group</term>
<term>Bacillus halodurans</term>
<term>Bacillus subtilis</term>
<term>Bacteriol</term>
<term>Bcr3</term>
<term>Bcr3 elements</term>
<term>Biochim biophys acta</term>
<term>Biol</term>
<term>Biol chem</term>
<term>Biophys</term>
<term>Blackwell</term>
<term>Blackwell publishing</term>
<term>Blastp</term>
<term>Blastp hits</term>
<term>Bpof4_</term>
<term>Bpr1</term>
<term>Bpr2</term>
<term>Catalytic site</term>
<term>Cell division</term>
<term>Cell wall</term>
<term>Cereus</term>
<term>Cereus group</term>
<term>Chaperone</term>
<term>Chem</term>
<term>Chemotaxis</term>
<term>Chromosomal</term>
<term>Chromosomal genes</term>
<term>Chromosome</term>
<term>Coli</term>
<term>Cytochrome</term>
<term>Cytoplasmic</term>
<term>Cytoplasmic proteins</term>
<term>Dehydrogenase</term>
<term>Dnaa</term>
<term>Dnaa boxes</term>
<term>Domain proteins</term>
<term>Encoding</term>
<term>Energy demands</term>
<term>Energy sources</term>
<term>Environmental microbiology</term>
<term>Epsx</term>
<term>Escherichia</term>
<term>Escherichia coli</term>
<term>Extremophiles</term>
<term>Ferric</term>
<term>Fujisawa</term>
<term>Gene</term>
<term>Gene cluster</term>
<term>Genome</term>
<term>Genome sequence</term>
<term>Genome sequences</term>
<term>Genomic</term>
<term>Gilmour</term>
<term>Guffanti</term>
<term>Halodurans</term>
<term>Helmann</term>
<term>Hick</term>
<term>Homeostasis</term>
<term>Horikoshi</term>
<term>Innermost intron</term>
<term>Intron</term>
<term>Janto</term>
<term>Kolst</term>
<term>Krulwich</term>
<term>Large number</term>
<term>Large plasmid</term>
<term>Locus</term>
<term>Metabolic</term>
<term>Microbiol</term>
<term>Microbiology</term>
<term>Mobile elements</term>
<term>Multiple sequence alignment</term>
<term>Mutant</term>
<term>Neutralophilic bacillus species</term>
<term>Nucleic</term>
<term>Nucleic acids</term>
<term>Operon</term>
<term>Orfs</term>
<term>Other stresses</term>
<term>Oxidase</term>
<term>Oxidative</term>
<term>Oxidative phosphorylation</term>
<term>Phosphorylation</term>
<term>Plasmid</term>
<term>Polyglutamate capsule</term>
<term>Proc natl acad</term>
<term>Proton</term>
<term>Rapid annotations</term>
<term>Replication</term>
<term>Resident plasmids</term>
<term>Rmus</term>
<term>Siderophore</term>
<term>Sigma</term>
<term>Sigma factors</term>
<term>Small plasmid</term>
<term>Sodium ions</term>
<term>Solute</term>
<term>Staphylococcus aureus</term>
<term>Stress responses</term>
<term>Subtilis</term>
<term>Synthase</term>
<term>Tmrna</term>
<term>Tourasse</term>
<term>Transporter</term>
<term>Uptake</term>
<term>Wang</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non‐fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions.</div>
</front>
</TEI>
<affiliations><list><country><li>Australie</li>
<li>France</li>
<li>Japon</li>
<li>Norvège</li>
<li>République populaire de Chine</li>
<li>États-Unis</li>
</country>
<region><li>Arkansas</li>
<li>Nouvelle-Galles du Sud</li>
<li>Pennsylvanie</li>
<li>État de New York</li>
<li>Île-de-France</li>
</region>
<settlement><li>Paris</li>
<li>Pékin</li>
<li>Sydney</li>
</settlement>
<orgName><li>Université Pierre-et-Marie-Curie</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Janto, Benjamin" sort="Janto, Benjamin" uniqKey="Janto B" first="Benjamin" last="Janto">Benjamin Janto</name>
</region>
<name sortKey="Ahmed, Azad" sort="Ahmed, Azad" uniqKey="Ahmed A" first="Azad" last="Ahmed">Azad Ahmed</name>
<name sortKey="Boissy, Robert" sort="Boissy, Robert" uniqKey="Boissy R" first="Robert" last="Boissy">Robert Boissy</name>
<name sortKey="Earl, Joshua" sort="Earl, Joshua" uniqKey="Earl J" first="Joshua" last="Earl">Joshua Earl</name>
<name sortKey="Ehrlich, Garth D" sort="Ehrlich, Garth D" uniqKey="Ehrlich G" first="Garth D." last="Ehrlich">Garth D. Ehrlich</name>
<name sortKey="Fackelmayer, Oliver J" sort="Fackelmayer, Oliver J" uniqKey="Fackelmayer O" first="Oliver J." last="Fackelmayer">Oliver J. Fackelmayer</name>
<name sortKey="Hicks, David B" sort="Hicks, David B" uniqKey="Hicks D" first="David B." last="Hicks">David B. Hicks</name>
<name sortKey="Hu, Fen Z" sort="Hu, Fen Z" uniqKey="Hu F" first="Fen Z." last="Hu">Fen Z. Hu</name>
<name sortKey="Ivey, D Mack" sort="Ivey, D Mack" uniqKey="Ivey D" first="D. Mack" last="Ivey">D. Mack Ivey</name>
<name sortKey="Krulwich, Terry A" sort="Krulwich, Terry A" uniqKey="Krulwich T" first="Terry A." last="Krulwich">Terry A. Krulwich</name>
<name sortKey="Liu, Jun" sort="Liu, Jun" uniqKey="Liu J" first="Jun" last="Liu">Jun Liu</name>
<name sortKey="Pagni, Sarah" sort="Pagni, Sarah" uniqKey="Pagni S" first="Sarah" last="Pagni">Sarah Pagni</name>
<name sortKey="Smith, Terry Nn" sort="Smith, Terry Nn" uniqKey="Smith T" first="Terry-Ann" last="Smith">Terry-Ann Smith</name>
</country>
<country name="Japon"><noRegion><name sortKey="Ito, Masahiro" sort="Ito, Masahiro" uniqKey="Ito M" first="Masahiro" last="Ito">Masahiro Ito</name>
</noRegion>
</country>
<country name="Australie"><region name="Nouvelle-Galles du Sud"><name sortKey="Elbourne, Liam D H" sort="Elbourne, Liam D H" uniqKey="Elbourne L" first="Liam D. H." last="Elbourne">Liam D. H. Elbourne</name>
</region>
<name sortKey="Hassan, Karl" sort="Hassan, Karl" uniqKey="Hassan K" first="Karl" last="Hassan">Karl Hassan</name>
<name sortKey="Paulsen, Ian T" sort="Paulsen, Ian T" uniqKey="Paulsen I" first="Ian T." last="Paulsen">Ian T. Paulsen</name>
</country>
<country name="Norvège"><noRegion><name sortKey="Kolst, Anne Rit" sort="Kolst, Anne Rit" uniqKey="Kolst A" first="Anne-Brit" last="Kolst">Anne-Brit Kolst</name>
</noRegion>
</country>
<country name="France"><region name="Île-de-France"><name sortKey="Tourasse, Nicolas J" sort="Tourasse, Nicolas J" uniqKey="Tourasse N" first="Nicolas J." last="Tourasse">Nicolas J. Tourasse</name>
</region>
</country>
<country name="République populaire de Chine"><noRegion><name sortKey="Li, Gang" sort="Li, Gang" uniqKey="Li G" first="Gang" last="Li">Gang Li</name>
</noRegion>
<name sortKey="Ma, Yanhe" sort="Ma, Yanhe" uniqKey="Ma Y" first="Yanhe" last="Ma">Yanhe Ma</name>
<name sortKey="Xue, Yanfen" sort="Xue, Yanfen" uniqKey="Xue Y" first="Yanfen" last="Xue">Yanfen Xue</name>
</country>
</tree>
</affiliations>
</record>
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