Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis

Abstract

A comprehensive whole-genome analysis of gene function by transposon mutagenesis and deep sequencing methodology has been implemented successfully in a representative of the Archaea domain. Libraries of transposon mutants were generated for the hydrogenotrophic, methanogenic archaeon Methanococcus maripaludis S2 using a derivative of the Tn5 transposon. About 89,000 unique insertions were mapped to the genome, which allowed for the classification of 526 genes or about 30% of the genome as possibly essential or strongly advantageous for growth in rich medium. Many of these genes were homologous to eukaryotic genes that encode fundamental processes in replication, transcription, and translation, providing direct evidence for their importance in Archaea. Some genes classified as possibly essential were unique to the archaeal or methanococcal lineages, such as that encoding DNA polymerase PolD. In contrast, the archaeal homolog to the gene encoding DNA polymerase B was not essential for growth, a conclusion confirmed by construction of an independent deletion mutation. Thus PolD, and not PolB, likely plays a fundamental role in DNA replication in methanococci. Similarly, 121 hypothetical ORFs were classified as possibly essential and likely play fundamental roles in methanococcal information processing or metabolism that are not established outside this group of prokaryotes.Tn-seq | polyploidy | methanogenesis

Non-essential MCM-related proteins mediate a response to DNA damage in the archaeon Methanococcus maripaludis

“…This situation is similar to that described for the eukaryotic MCMs where a complex of MCMs 4, 6 and 7 is sufficient for in vitro helicase activity (probably as a dimer of trimers), but the active complex in vivo is additionally modulated by the presence of other MCM subunits [46]. M. maripaludis encodes multiple RecJ homologues, several of which have been shown to be nonessential, and a single GINS protein, which is probably essential [39]. We have previously reported the recovery of a complex containing all four recombinant M. maripaludis Mcm proteins, supporting the notion that a heteromeric complex may be formed in vivo [28].…”

“…3a). This observation is supported by a recent genome-wide transposon mutagenesis study in M. maripaludis that classified McmA as 'possibly essential' [39].…”

Coevolution of RtcB and Archease created a multiple-turnover RNA ligase

“…Indeed, E. coli with a deletion in the rtcB gene has no apparent growth defects in rich media (Baba et al 2006). In contrast, rtcB in the archaeon Methanococcus maripaludis has been annotated as possibly essential for growth in rich media based on a whole-genome transposon mutagenesis study (Sarmiento et al 2013). Likewise, RtcB is required for tRNA splicing in humans (Popow et al 2011).…”

“…RtcB is an essential enzyme for the ligation of tRNAs in metazoa (Popow et al 2011), and possibly archaea Sarmiento et al 2013), upon intron removal by the tRNA splicing endonuclease (Abelson et al 1998;Popow et al 2012). RtcB is also essential for the ligation of XBP1 exons in metazoa upon intron removal by IRE1, which initiates the unfolded protein response during endoplasmic reticulum stress Kosmaczewski et al 2014;Lu et al 2014).…”

Molecular Mechanisms of Transcription Initiation—Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation

“…In Sso the gene coding for TFEβ is essential while deletion of the gene coding for TFEα has not been attempted [11]. In the euryarchaeon Methanococcus maripaludis the gene coding for monomeric TFEα is essential [48]. TFEα interacts with the RNAP in a bidentate fashion:…”