G-Quadruplexes in the Archaea Domain

Abstract

The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.

CNBP Binds and Unfolds In Vitro G-Quadruplexes Formed in the SARS-CoV-2 Positive and Negative Genome Strands

“…Besides in human beings, G4s are widespread across nucleic acids of all the taxonomic phyla [ 22 ] including Bacteria [ 23 ], Archaea [ 24 ], and viruses [ 25 , 26 ]. Critical roles for viral G4s have been described in human viruses, including immunodeficiency virus (HIV), herpes simplex virus (HSV), Epstein-Barr virus (EBV), human papillomavirus (HPV), hepatitis B virus (HBV), Nipah virus, hepatitis C virus (HCV), Zika virus, and Ebola virus [ 27 , 28 , 29 ], and some G4-specific compounds have shown powerful antiviral activity by targeting G4 structures [ 28 , 29 ].…”

Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

“…There is a growing interest in so-called noncanonical nucleic acid structures and proteins that preferentially bind them [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. Noncanonical nucleic acid structures are DNA and RNA structures different from their basic form, i.e., double-stranded right-handed DNA or single-stranded RNA, and are often formed by simple nucleotide repeats [ 25 , 26 , 27 , 28 ]. Physiologically, they are represented mainly by G-quadruplexes [ 29 ], i-motifs [ 30 ], triplexes [ 31 ], R-loops [ 32 ], slipped hairpins [ 33 ], DNA cruciforms [ 34 ], RNA hairpins [ 35 ], and Z-DNA [ 36 ].…”

Tracing dsDNA Virus–Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences

“…Next, to evaluate the relationship between PQS frequencies of the virus and the host, we analyzed selected genomes of host organisms for PQS presence. For hosts from archaea and bacteria, we utilized the previously published results of our group on PQS occurrence in all accessible archaeal and bacterial genomes [ 19 , 42 ]. In all analyses, we used the same workflow and same parameters for G4Hunter and data processing.…”

“…A full list of NCBI IDs and host assignments are presented in Supplementary Materials S1 . For hosts from archaea and bacteria, we utilized the previously published results of our group on PQS occurrence in all accessible archaeal and bacterial genomes [ 19 , 42 ]. For eukaryote groups, we selected the 10 most frequented hosts for each viral group, and these are also listed in Supplementary Materials S1 .…”