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The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria

M. Bartas, M. Čutová, V. Brázda, P. Kaura, J. Šťastný, J. Kolomazník, J. Coufal, P. Goswami, J. Červeň, P. Pečinka,

. 2019 ; 24 (9) : . [pub] 20190502

Language English Country Switzerland

Document type Journal Article

Persistent link   https://www.medvik.cz/link/bmc19034593

Grant support
18-15548S Grant Agency of the Czech Republic
LO1208 TEWEP Ministry of Education, Youth and Sports of the Czech Republic in the "National Feasibility Program I"
CZ.1.05/2.1.00/19.0388 EU structural funding Operational Programme Research and Development for innovation
SGS/09/PrF/2019 University of Ostrava

The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.

References provided by Crossref.org

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$a Bartas, Martin $u Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic. dutartas@gmail.com.
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$a The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
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$a Čutová, Michaela $u Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic. xcfricova@fch.vut.cz.
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$a Brázda, Václav $u Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic. vaclav@ibp.cz. Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic. vaclav@ibp.cz.
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$a Kaura, Patrik $u Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic. 160702@vutbr.cz.
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$a Šťastný, Jiří $u Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic. stastny@fme.vutbr.cz. Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic. stastny@fme.vutbr.cz.
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$a Kolomazník, Jan $u Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic. jan.kolomaznik@gmail.com.
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$a Coufal, Jan $u Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic. jac@ibp.cz.
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$a Goswami, Pratik $u Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic. pratikgoswami@ibp.cz.
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$a Červeň, Jiří $u Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic. jiri.cerven@osu.cz.
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$a Pečinka, Petr $u Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic. petr.pecinka@osu.cz.
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