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.
Highlights
The Archaea domain was classified separately from Bacteria by Carl Woese and George Fox in 1977 [1]
A schematic phylogenic tree for the Archaea domain is proposed in Figure 1; this phylogeny is rapidly evolving with many new phyla recently identified via the accumulation of metagenome associated genomes (MAGs) and various new proposals for phylum definition and nomenclature [9,10]
We suggested in parallel the term Eury superphylum because Euryarchaeota includes very diverse groups of cultivated and uncultivated Archaea which are difficult to the group in a single phylum, especially considering that phyla, such as Verstratearchaeota Marsarchaeota, or Nezaarchaeota only contain few uncultivated species only defined by a few metagenome associated genomes (MAGs)
Summary
The Archaea domain was classified separately from Bacteria by Carl Woese and George Fox in 1977 [1]. It was found that all major molecular machinery, such as DNA replication, transcription, and translation, of archaea are much more similar to those of eukaryotes than to those of bacteria [2,3]. This is true for some important membrane proteins, such as ATP synthases and proteins of the Sec transport system [4,5], or for some proteins involved in cell division and vesicle trafficking [6]. Methanogenesis, the production of greenhouse methane gas as a metabolic by-product, occurs only in the archaeal domain [15,16]
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