Abstract
SummaryTo explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence‐like transposons, (iv) integrative‐conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly‐roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I‐B CRISPR‐Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.
Highlights
Similar to bacteria and eukaryotes, archaea are associated with diverse classes of mobile genetic elements (MGE), collectively referred to as the mobilome
Based on genomic features and the mode of interaction with the host cells, the archaeal mobilome can be divided into five large classes: (i) viruses (Pietilä et al, 2014; Snyder et al, 2015; Prangishvili et al, 2017; Krupovic et al, 2018; Munson-McGee et al, 2018), (ii) conjugative elements (Prangishvili et al, 1998; Greve et al, 2004), (iii) small cryptic plasmids (Forterre et al, 2014; Wang et al, 2015), (iv) transposable elements closely related to bacterial insertion sequences (IS) (Filée et al, 2007) and (v) the more recently discovered self-synthesizing transposon-like elements called casposons which employ a homologue of the CRISPR-associated Cas1 protein as their integrase (Krupovic et al, 2014; Krupovic et al, 2017)
The genomes of 21 species representative of the taxonomic diversity and environmental distribution of the phylum Thaumarchaeota were analysed for the presence of Integrated MGE (iMGE) (Supporting Information Table S1)
Summary
Similar to bacteria and eukaryotes, archaea are associated with diverse classes of mobile genetic elements (MGE), collectively referred to as the mobilome. The cosmopolitan fraction of the archaeal virosphere consist of viruses that display common architectural and genomic features with viruses of bacteria and eukaryotes, and for many genes, homologues in bacterial viruses are readily detectable (Iranzo et al, 2016b) These include tailed dsDNA viruses representing all three major families of the order Caudovirales (Myoviridae, Siphoviridae and Podoviridae), the dominant supergroup of bacterial viruses, as well as icosahedral viruses with the double jelly-roll (DJR) and single jelly-roll (SJR) major capsid proteins (MCP) classified in the families Turriviridae and Sphaerolipoviridae, respectively (Pietilä et al, 2014; Prangishvili et al, 2017)
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