Variability of Inverted Repeats in All Available Genomes of Bacteria

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dc.contributor.authorPorubiaková, Otíliacs
dc.contributor.authorHavlík, Jancs
dc.contributor.authorIndu, Michalcs
dc.contributor.authorŠedý, Michalcs
dc.contributor.authorPřepechalová, Veronikacs
dc.contributor.authorBartas, Martincs
dc.contributor.authorBidula, Stefancs
dc.contributor.authorŠťastný, Jiřícs
dc.contributor.authorFojta, Miroslavcs
dc.contributor.authorBrázda, Václavcs
dc.coverage.issue4cs
dc.coverage.volume11cs
dc.date.issued2023-06-26cs
dc.description.abstractNoncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions.IMPORTANCE Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation. Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation.en
dc.formattextcs
dc.format.extent1-11cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationMicrobiology spectrum. 2023, vol. 11, issue 4, p. 1-11.en
dc.identifier.doi10.1128/spectrum.01648-23cs
dc.identifier.issn2165-0497cs
dc.identifier.orcid0000-0001-9940-0941cs
dc.identifier.orcid0000-0003-3724-6357cs
dc.identifier.orcid0000-0003-2837-4226cs
dc.identifier.other184578cs
dc.identifier.researcheridF-8025-2012cs
dc.identifier.researcheridF-9582-2011cs
dc.identifier.scopus57191582635cs
dc.identifier.urihttp://hdl.handle.net/11012/244957
dc.language.isoencs
dc.publisherAmerican Society for Microbiologycs
dc.relation.ispartofMicrobiology spectrumcs
dc.relation.urihttps://journals.asm.org/doi/10.1128/spectrum.01648-23cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/2165-0497/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectinverted repeatsen
dc.subjectPalindrome analyseren
dc.subjectbacteria domainen
dc.subjectbacterial genome analysisen
dc.titleVariability of Inverted Repeats in All Available Genomes of Bacteriaen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-184578en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:38:43en
sync.item.modts2025.01.17 20:32:25en
thesis.grantorVysoké učení technické v Brně. Fakulta chemická. Ústav chemie potravin a biotechnologiícs
thesis.grantorVysoké učení technické v Brně. Fakulta strojního inženýrství. Ústav automatizace a informatikycs
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