title: Genome-wide identification of SF1 and SF2 helicases from archaea.
abstract: Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions.
authors.affiliation: Faculty of Science, Department of Biology, Lebanese University, Tripoli, Lebanon; Centre AZM pour la Recherche en Biotechnologie et ses Applications, Laboratoire de Biotechnologie Appliquée, Ecole Doctorale Sciences et Technologies, Mitein Street, Tripoli, Lebanon. Electronic address: hala.chamieh@ul.edu.lb.
authors.forename: Hala
authors.initials: H
authors.lastname: Chamieh
authors.affiliation: Faculty of Science, Department of Environmental and Biological Science, Beirut Arab University, Tripoli, Lebanon.
authors.forename: Hiba
authors.initials: H
authors.lastname: Ibrahim
authors.affiliation: Faculty of Science, Université Saint Esprit de Kaslik, Jounieh, Lebanon.
authors.forename: Juliana
authors.initials: J
authors.lastname: Kozah
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D017124:Conserved Sequence; D004265:DNA Helicases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004260:DNA Repair / Q000502:physiology; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D020745:Genome, Archaeal; D006801:Humans; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D000072260:RNA Splicing Factors; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D000072260:RNA Splicing Factors; C107467:SF1 protein, human; D014157:Transcription Factors; D004265:DNA Helicases
keywords: Archaea; Genomics; Superfamily helicase I; Superfamily helicase II