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. 2019 May 2;24(9):1711.
doi: 10.3390/molecules24091711.

The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria

Martin Bartas  1 , Michaela Čutová  2 , Václav Brázda  3   4 , Patrik Kaura  5 , Jiří Šťastný  6   7 , Jan Kolomazník  8 , Jan Coufal  9 , Pratik Goswami  10 , Jiří Červeň  11 , Petr Pečinka  12
Affiliations

The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria

Martin Bartas et al. Molecules. .

Abstract

The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.

Keywords: G-quadruplex; G4Hunter; bacteria; bioinformatics; deinococcus.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
G-quadruplexes: (A) guanine tetrad stabilized by Hoogsten base pairing and positively charged central ion; (B) schematic drawing of intramolecular G4 structure arising from double stranded DNA; (C) G4Hunter, a new user-friendly web server for high throughput analyses of G4-forming sequences in DNA; and (D) 3D model of intramolecular antiparallel G4 formed from the sequence (5′-GGGGTGTGGGGTGT GGGGTGTGGGGTGT-3′) found in Microcystis aeruginosa built using 3D-NuS webserver [23].
Figure 2
Figure 2
Phylogenetic tree of inspected Bacterial Groups and Subgroups.
Figure 3
Figure 3
Frequencies of PQS in subgroups of the analyzed bacterial genomes. Data within boxes span the interquartile range and whiskers show the lowest and highest values within 1.5 interquartile range. Black diamonds denote outliers.
Figure 4
Figure 4
Relationship between observed frequency of PQS per 1000 bp and GC content in all analyzed prokaryotic sequences in various G4 Hunter score intervals. In each G4Hunter score interval miniplot, frequencies were normalized according to the highest observed frequency of PQS. Organisms with max. frequency per 1000 bp greater than 50% are described and highlighted in color.
Figure 5
Figure 5
Differences in PQS frequency by DNA locus. The chart shows PQS frequencies according to “gene” annotation and other annotated locations from the NCBI database. We analyzed the frequencies of all PQS within (inside), before (100 bp) and after (100 bp) annotated locations.
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