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Variability of Inverted Repeats in All Available Genomes of Bacteria
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SYSNO ASEP 0583620 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Variability of Inverted Repeats in All Available Genomes of Bacteria Author(s) Porubiakova, Otilia (BFU-R)
Havlík, J. (CZ)
Indu, Indu (BFU-R)
Sedy, M. (CZ)
Přepechalová, Veronika (BFU-R)
Bartas, M. (CZ)
Bidula, S. (GB)
Šťastný, J. (CZ)
Fojta, Miroslav (BFU-R) RID, ORCID
Brázda, Václav (BFU-R) RID, ORCIDNumber of authors 10 Source Title Microbiology Spectrum. - : American Society for Microbiology - ISSN 2165-0497
Roč. 11, č. 4 (2023)Number of pages 11 s. Publication form Online - E Language eng - English Country US - United States Keywords dna-structure ; sticky dna ; sp-nov. ; evolution ; stability ; binding ; server ; gene ; rnas Subject RIV EE - Microbiology, Virology OECD category Microbiology R&D Projects GA22-21903S GA ČR - Czech Science Foundation (CSF) EF15_003/0000477 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Open access Institutional support BFU-R - RVO:68081707 UT WOS 001016285500001 EID SCOPUS 85171994866 DOI 10.1128/spectrum.01648-23 Annotation Noncanonical 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. Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2024 Electronic address https://journals.asm.org/doi/epub/10.1128/spectrum.01648-23
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