Publication detail

Variability of Inverted Repeats in All Available Genomes of Bacteria

PORUBIAKOVÁ, O. HAVLÍK, J. INDU, M. ŠEDŸ, M. PŘEPECHALOVÁ, V. BARTAS, M. BIDULA, S. ŠŤASTNÝ, J. FOJTA, M. BRÁZDA, V.

Original Title

Variability of Inverted Repeats in All Available Genomes of Bacteria

Type

journal article in Web of Science

Language

English

Original Abstract

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. 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.

Keywords

inverted repeats; Palindrome analyser; bacteria domain; bacterial genome analysis

Authors

PORUBIAKOVÁ, O.; HAVLÍK, J.; INDU, M.; ŠEDŸ, M.; PŘEPECHALOVÁ, V.; BARTAS, M.; BIDULA, S.; ŠŤASTNÝ, J.; FOJTA, M.; BRÁZDA, V.

Released

26. 6. 2023

Publisher

American Society for Microbiology

Location

WASHINGTON

ISBN

2165-0497

Periodical

Microbiology spectrum

Year of study

11

Number

4

State

United States of America

Pages from

1

Pages to

11

Pages count

11

URL

https://journals.asm.org/doi/10.1128/spectrum.01648-23

Full text in the Digital Library

http://hdl.handle.net/11012/244957

BibTex

@article{BUT184578,
  author="Otília {Porubiaková} and Jan {Havlík} and Michal {Indu} and Michal {Šedý} and Veronika {Přepechalová} and Martin {Bartas} and Stefan {Bidula} and Jiří {Šťastný} and Miroslav {Fojta} and Václav {Brázda}",
  title="Variability of Inverted Repeats in All Available Genomes of Bacteria",
  journal="Microbiology spectrum",
  year="2023",
  volume="11",
  number="4",
  pages="11",
  doi="10.1128/spectrum.01648-23",
  issn="2165-0497",
  url="https://journals.asm.org/doi/10.1128/spectrum.01648-23"
}