Variability of Inverted Repeats in All Available Genomes of
Bacteria

J 2023

Variability of Inverted Repeats in All Available Genomes of Bacteria

PORUBIAKOVÁ, Otília, Jan HAVLÍK, Indu ., Michal ŠEDÝ, Veronika PŘEPECHALOVÁ et. al.

Basic information

Original name

Variability of Inverted Repeats in All Available Genomes of Bacteria

Authors

PORUBIAKOVÁ, Otília (703 Slovakia), Jan HAVLÍK, Indu . (356 India, belonging to the institution), Michal ŠEDÝ, Veronika PŘEPECHALOVÁ, Martin BARTAS, Stefan BIDULA, Jiří ŠŤASTNÝ, Miroslav FOJTA (203 Czech Republic) and Václav BRÁZDA (203 Czech Republic, guarantor)

Edition

Microbiology Spectrum, American Society for Microbiology, 2023, 2165-0497

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.700 in 2022

RIV identification code

RIV/00216224:14310/23:00131464

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1128/spectrum.01648-23

UT WoS

001016285500001

Keywords in English

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

Abstract

V originále

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.

Citovat

PORUBIAKOVÁ, Otília, Jan HAVLÍK, Indu ., Michal ŠEDÝ, Veronika PŘEPECHALOVÁ, Martin BARTAS, Stefan BIDULA, Jiří ŠŤASTNÝ, Miroslav FOJTA and Václav BRÁZDA. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiology Spectrum. American Society for Microbiology, 2023, vol. 11, No 4, p. 1-11. ISSN 2165-0497. Available from: https://dx.doi.org/10.1128/spectrum.01648-23.

@article{2303486,
   author = {Porubiaková, Otília and Havlík, Jan and ., Indu and Šedý, Michal and Přepechalová, Veronika and Bartas, Martin and Bidula, Stefan and Šťastný, Jiří and Fojta, Miroslav and Brázda, Václav},
   article_number = {4},
   doi = {http://dx.doi.org/10.1128/spectrum.01648-23},
   keywords = {inverted repeats; Palindrome analyser; bacteria domain; bacterial genome analysis},
   language = {eng},
   issn = {2165-0497},
   journal = {Microbiology Spectrum},
   title = {Variability of Inverted Repeats in All Available Genomes of Bacteria},
   url = {https://doi.org/10.1128/spectrum.01648-23},
   volume = {11},
   year = {2023}
}

TY  - JOUR
ID  - 2303486
AU  - Porubiaková, Otília - Havlík, Jan - ., Indu - Šedý, Michal - Přepechalová, Veronika - Bartas, Martin - Bidula, Stefan - Šťastný, Jiří - Fojta, Miroslav - Brázda, Václav
PY  - 2023
TI  - Variability of Inverted Repeats in All Available Genomes of Bacteria
JF  - Microbiology Spectrum
VL  - 11
IS  - 4
SP  - 1-11
EP  - 1-11
PB  - American Society for Microbiology
SN  - 21650497
KW  - inverted repeats
KW  - Palindrome analyser
KW  - bacteria domain
KW  - bacterial genome analysis
UR  - https://doi.org/10.1128/spectrum.01648-23
N2  - 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.
ER  -

PORUBIAKOVÁ, Otília, Jan HAVLÍK, Indu ., Michal ŠEDÝ, Veronika PŘEPECHALOVÁ, Martin BARTAS, Stefan BIDULA, Jiří ŠŤASTNÝ, Miroslav FOJTA and Václav BRÁZDA. Variability of Inverted Repeats in All Available Genomes of Bacteria. \textit{Microbiology Spectrum}. American Society for Microbiology, 2023, vol.~11, No~4, p.~1-11. ISSN~2165-0497. Available from: https://dx.doi.org/10.1128/spectrum.01648-23.

Detailed Information on Publication Record