Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA
Identifieur interne : 000340 ( Main/Exploration ); précédent : 000339; suivant : 000341Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA
Auteurs : Clara Jegousse [France, Australie] ; Yuedong Yang [Australie] ; Jian Zhan [Australie] ; Jihua Wang [République populaire de Chine] ; Yaoqi Zhou [Australie, République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Bactéries.
- pharmacologie : Solvants.
- ARN bactérien, ARN de transfert, ARN messager, ARN ribosomique, Bases de données génétiques, Conformation d'acide nucléique, Modèles moléculaires, Pliage de l'ARN, Température.
English descriptors
- KwdEn :
- Bacteria (genetics), Databases, Genetic, Models, Molecular, Nucleic Acid Conformation, RNA Folding (drug effects), RNA, Bacterial (chemistry), RNA, Bacterial (drug effects), RNA, Messenger (chemistry), RNA, Messenger (drug effects), RNA, Ribosomal (chemistry), RNA, Ribosomal (drug effects), RNA, Transfer (chemistry), RNA, Transfer (drug effects), Solvents (pharmacology), Temperature.
- MESH :
- chemical , chemistry : RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, RNA, Transfer.
- drug effects : RNA Folding, RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, RNA, Transfer.
- genetics : Bacteria.
- chemical , pharmacology : Solvents.
- Databases, Genetic, Models, Molecular, Nucleic Acid Conformation, Temperature.
Abstract
Temperature adaptation of bacterial RNAs is a subject of both fundamental and practical interest because it will allow a better understanding of molecular mechanism of RNA folding with potential industrial application of functional thermophilic or psychrophilic RNAs. Here, we performed a comprehensive study of rRNA, tRNA, and mRNA of more than 200 bacterial species with optimal growth temperatures (OGT) ranging from 4°C to 95°C. We investigated temperature adaptation at primary, secondary and tertiary structure levels. We showed that unlike mRNA, tRNA and rRNA were optimized for their structures at compositional levels with significant tertiary structural features even for their corresponding randomly permutated sequences. tRNA and rRNA are more exposed to solvent but remain structured for hyperthermophiles with nearly OGT-independent fluctuation of solvent accessible surface area within a single RNA chain. mRNA in hyperthermophiles is essentially the same as random sequences without tertiary structures although many mRNA in mesophiles and psychrophiles have well-defined tertiary structures based on their low overall solvent exposure with clear separation of deeply buried from partly exposed bases as in tRNA and rRNA. These results provide new insight into temperature adaptation of different RNAs.
Url:
DOI: 10.1371/journal.pone.0184722
PubMed: 28910383
PubMed Central: 5598986
Affiliations:
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Le document en format XML
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last="Jegousse">Clara Jegousse</name><affiliation wicri:level="4"><nlm:aff id="aff001"><addr-line>UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, Nantes, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Institute for Glycomics and School of Information and Communication Technology, 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moléculaires</term><term>Pliage de l'ARN ()</term><term>Solvants (pharmacologie)</term><term>Température</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Bacterial</term><term>RNA, Messenger</term><term>RNA, Ribosomal</term><term>RNA, Transfer</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>RNA Folding</term><term>RNA, Bacterial</term><term>RNA, Messenger</term><term>RNA, Ribosomal</term><term>RNA, Transfer</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Solvants</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Solvents</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN bactérien</term><term>ARN de transfert</term><term>ARN messager</term><term>ARN ribosomique</term><term>Bases de données génétiques</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Pliage de l'ARN</term><term>Température</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Temperature adaptation of bacterial RNAs is a subject of both fundamental and practical interest because it will allow a better understanding of molecular mechanism of RNA folding with potential industrial application of functional thermophilic or psychrophilic RNAs. Here, we performed a comprehensive study of rRNA, tRNA, and mRNA of more than 200 bacterial species with optimal growth temperatures (OGT) ranging from 4°C to 95°C. We investigated temperature adaptation at primary, secondary and tertiary structure levels. We showed that unlike mRNA, tRNA and rRNA were optimized for their structures at compositional levels with significant tertiary structural features even for their corresponding randomly permutated sequences. tRNA and rRNA are more exposed to solvent but remain structured for hyperthermophiles with nearly OGT-independent fluctuation of solvent accessible surface area within a single RNA chain. mRNA in hyperthermophiles is essentially the same as random sequences without tertiary structures although many mRNA in mesophiles and psychrophiles have well-defined tertiary structures based on their low overall solvent exposure with clear separation of deeply buried from partly exposed bases as in tRNA and rRNA. These results provide new insight into temperature adaptation of different RNAs.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Koonin, Ev" uniqKey="Koonin E">EV Koonin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Turner, P" uniqKey="Turner P">P Turner</name></author><author><name sortKey="Mamo, G" uniqKey="Mamo G">G Mamo</name></author><author><name sortKey="Karlsson, En" uniqKey="Karlsson E">EN Karlsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bouzas, Td" uniqKey="Bouzas T">TD Bouzas</name></author><author><name sortKey="Barros Velazquez, J" uniqKey="Barros Velazquez J">J Barros-Velazquez</name></author><author><name sortKey="Villa, Tg" uniqKey="Villa T">TG Villa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Siddiqui, Ks" uniqKey="Siddiqui K">KS 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sortKey="Russell, Rjm" uniqKey="Russell R">RJM Russell</name></author><author><name sortKey="Ferguson, Jmc" uniqKey="Ferguson J">JMC Ferguson</name></author><author><name sortKey="Hough, Dw" uniqKey="Hough D">DW Hough</name></author><author><name sortKey="Danson, Mj" uniqKey="Danson M">MJ Danson</name></author><author><name sortKey="Taylor, Gl" uniqKey="Taylor G">GL Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, Mj" uniqKey="Thompson M">MJ Thompson</name></author><author><name sortKey="Eisenberg, D" uniqKey="Eisenberg D">D Eisenberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hurley, Td" uniqKey="Hurley T">TD Hurley</name></author><author><name sortKey="Weiner, H" uniqKey="Weiner H">H Weiner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gromiha, Mm" uniqKey="Gromiha M">MM Gromiha</name></author><author><name sortKey="Oobatake, M" uniqKey="Oobatake M">M 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Lineweaver</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>France</li><li>République populaire de Chine</li></country><region><li>Pays de la Loire</li></region><settlement><li>Nantes</li></settlement><orgName><li>Université de Nantes</li></orgName></list><tree><country name="France"><region name="Pays de la Loire"><name sortKey="Jegousse, Clara" sort="Jegousse, Clara" uniqKey="Jegousse C" first="Clara" last="Jegousse">Clara Jegousse</name></region></country><country name="Australie"><noRegion><name sortKey="Jegousse, Clara" sort="Jegousse, Clara" uniqKey="Jegousse C" first="Clara" last="Jegousse">Clara Jegousse</name></noRegion><name sortKey="Yang, Yuedong" sort="Yang, Yuedong" uniqKey="Yang Y" first="Yuedong" last="Yang">Yuedong Yang</name><name sortKey="Zhan, Jian" sort="Zhan, Jian" uniqKey="Zhan J" first="Jian" last="Zhan">Jian Zhan</name><name sortKey="Zhou, Yaoqi" sort="Zhou, Yaoqi" uniqKey="Zhou Y" first="Yaoqi" last="Zhou">Yaoqi Zhou</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Jihua" sort="Wang, Jihua" uniqKey="Wang J" first="Jihua" last="Wang">Jihua Wang</name></noRegion><name sortKey="Zhou, Yaoqi" sort="Zhou, Yaoqi" uniqKey="Zhou Y" first="Yaoqi" last="Zhou">Yaoqi Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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