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2 results on '"Pratik Goswami"'

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

Author

Martin Bartas, Michaela Čutová, Václav Brázda, Patrik Kaura, Jiří Šťastný, Jan Kolomazník, Jan Coufal, Pratik Goswami, Jiří Červeň, and Petr Pečinka

Subjects
G-quadruplex, bacteria, bioinformatics, deinococcus, G4Hunter, Organic chemistry, QD241-441
Abstract

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.

Published
2019
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2. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria

Author

Jan Coufal, Václav Brázda, Jan Kolomazník, Jiří Šťastný, Petr Pečinka, Jiří Červeň, Pratik Goswami, Martin Bartas, Michaela Čutová, and Patrik Kaura

Subjects
DNA, Bacterial, Pharmaceutical Science, Bacterial genome size, Computational biology, G-quadruplex, Genome, Article, Analytical Chemistry, lcsh:QD241-441, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, lcsh:Organic chemistry, Drug Discovery, Humans, heterocyclic compounds, Deinococcus, Physical and Theoretical Chemistry, bacteria, G4Hunter, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, Organic Chemistry, bioinformatics, deinococcus, biology.organism_classification, G-Quadruplexes, chemistry, Chemistry (miscellaneous), Regulatory sequence, 030220 oncology & carcinogenesis, Transfer RNA, Thermotogae, Nucleic Acid Conformation, Molecular Medicine, Genome, Bacterial, DNA
Abstract

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.

Published
2019

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