Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes

Abstract

Genomes provide a platform for storage of chemical information that must be stable under the context in which an organism thrives. The 2‘-deoxyguanosine (G) nucleotide has the potential to provide additional chemical information beyond its Watson-Crick base-pairing capacity. Sequences with four or more runs of three G nucleotides each are potential G-quadruplex forming sequences (PQSs) that can adopt G-quadruplex folds. Herein, we analyzed sequenced genomes from the NCBI database to determine the PQS densities of the genome sequences. First, we found organisms with large genomes, including humans, alligators, and maize, have similar densities of PQSs (~300 PQSs/Mbp), and the genomes are significantly enriched in PQSs with more than four G tracks. Analysis of microorganism genomes found a greater diversity of PQS densities. In general, PQS densities positively tracked with the GC% of the genome. Exceptions to this observation were the genomes from thermophiles that had many more PQSs than expected by random chance. Analysis of the location of these PQSs in annotated genomes from the order Thermales showed these G-rich sequences to be randomly distributed; in contrast, in the order Deinococcales the PQSs were enriched and biased around transcription start sites of genes. Four representative PQSs, two each from the Thermales and Deinococcales, were studied by biophysical methods to establish the ability of them to fold to G-quadruplexes. The experiments found the two PQSs in the Thermales did not adopt G-quadruplex folds, while the two most common in the Deinococcales adopted stable parallel-stranded G-quadruplexes. The findings lead to a hypothesis that thermophilic organisms are enriched with PQSs as an unavoidable consequence to stabilize thermally their genomes to live at high temperature; in contrast, the genomes from stress-resistant bacteria found in the Deinococcales may utilize PQSs for gene regulatory purposes.

G-Quadruplexes in the Archaea Domain

“…We therefore cannot anticipate a higher density of G4-prone motifs in thermophiles, due to a GC-bias. A comparison with Extremophiles in bacteria is interesting [ 35 ]. Ding et al hypothesized that stress-resistant bacteria found in the Deinococcales may utilize putative quadruplex sequences (PQS) for gene regulatory purposes.…”

“…In contrast, little is currently known regarding the abundancy and location of PQS in the archaeal domain. Ding et al performed an initial search on bacterial and archaeal genomes using a modified Quadparser algorithm with relaxed parameters allowing long loops (up to 12 nucleotides) [ 35 ]. They found that thermophilic microorganisms (both archaea and bacteria) appear to favor PQS in their genomes.…”

Conserved G-Quadruplex Motifs in Gene Promoter Region Reveals a Novel Therapeutic Approach to Target Multi-Drug Resistance Klebsiella pneumoniae

“…Recent analysis of genome mining in bacterial domains revealed non-random distribution of G4 motifs in their genome, with the highest frequency in the harsh environment-resistant Deinococcus-Thermus phylum, while the lowest was in Thermotogae ( Bartas et al, 2019 ). The presence of G4 motifs in the extremophiles like Deinococcus radiodurans and Thermus aquaticus might help in surviving the extreme environment ( Kota et al, 2015 ; Ding et al, 2018 ). Various other studies have shown the presence of evolutionarily conserved G4 motifs in the crucial genomic locations in several bacteria and protozoans, including Escherichia coli ( Kaplan et al, 2016 ), Neisseria gonorrhea ( Cahoon and Seifert, 2009 ), M. tuberculosis ( Perrone et al, 2017 ; Mishra et al, 2019b ), S. pneumoniae ( Mishra et al, 2019a ), and Plasmodium falciparum ( Harris et al, 2018 ).…”

Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2

“…They have been found to be regulatory elements in the human genome implicated in key functions such as telomere maintenance and genome transcription regulation, replication and repair (17). G4 structures have also been identified in fungi (18)(19)(20)(21), bacteria (22)(23)(24)(25)(26) and parasites (27)(28)(29)(30)(31)(32). Their occurrence are known in many viruses that afflict humans as well.…”