Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
Mendel University in Brno, Brno, Czech Republic.
Microbiol Spectr. 2023 Aug 17;11(4):e0164823. doi: 10.1128/spectrum.01648-23. Epub 2023 Jun 26.
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 (61.89 IRs/kbp) and the lowest mean frequency was found in the (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. 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.
近年来，非规范的核酸二级结构受到了广泛关注。已经在包括人类在内的各种生物中证明了由反向重复（IR）形成的十字形结构的重要生物学作用。我们使用 Palindrome analyser 分析了所有可访问的细菌基因组序列中的 IR，以确定它们的频率、长度和定位。在所有物种中都发现了 IR 序列，但它们在不同进化群中的频率存在显著差异。我们在所有 1565 个细菌基因组中检测到 242373717 个 IR。在 （61.89 IRs/kbp）中检测到的平均 IR 频率最高，而在 （27.08 IRs/kbp）中检测到的平均频率最低。IR 在基因附近和调控、tRNA、转移信使 RNA（tmRNA）和 rRNA 区域周围丰富，这表明 IR 在基因组维护、DNA 复制和转录等基本细胞过程中非常重要。此外，我们发现 IR 频率较高的生物体更容易成为内共生体、产生抗生素或致病。另一方面，IR 频率较低的生物体更有可能是嗜热的。这是对所有可用细菌基因组中的 IR 进行的首次全面分析，证明了它们在基因组中的普遍性、非随机分布和在基因组调控区域的富集。我们的论文首次报道了对所有完全测序的细菌基因组中反向重复的完整分析。由于独特的计算资源的可用性，我们能够对这些重要调控序列在细菌基因组中的存在和定位进行统计评估。这项工作揭示了这些序列在调控区域中的丰富性，并为研究人员提供了一种有价值的工具来操纵它们。
