Genome Copy Numbers and Gene Conversion in Methanogenic Archaea

Abstract

Previous studies revealed that one species of methanogenic archaea, Methanocaldococcus jannaschii, is polyploid, while a second species, Methanothermobacter thermoautotrophicus, is diploid. To further investigate the distribution of ploidy in methanogenic archaea, species of two additional genera-Methanosarcina acetivorans and Methanococcus maripaludis-were investigated. M. acetivorans was found to be polyploid during fast growth (t D ‫؍‬ 6 h; 17 genome copies) and oligoploid during slow growth (doubling time ‫؍‬ 49 h; 3 genome copies). M. maripaludis has the highest ploidy level found for any archaeal species, with up to 55 genome copies in exponential phase and ca. 30 in stationary phase. A compilation of archaeal species with quantified ploidy levels reveals a clear dichotomy between Euryarchaeota and Crenarchaeota: none of seven euryarchaeal species of six genera is monoploid (haploid), while, in contrast, all six crenarchaeal species of four genera are monoploid, indicating significant genetic differences between these two kingdoms. Polyploidy in asexual species should lead to accumulation of inactivating mutations until the number of intact chromosomes per cell drops to zero (called "Muller's ratchet"). A mechanism to equalize the genome copies, such as gene conversion, would counteract this phenomenon. Making use of a previously constructed heterozygous mutant strain of the polyploid M. maripaludis we could show that in the absence of selection very fast equalization of genomes in M. maripaludis took place probably via a gene conversion mechanism. In addition, it was shown that the velocity of this phenomenon is inversely correlated to the strength of selection.

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

“…M. maripaludis cells show a broad distribution of DNA content and cell size, with no distinct genome peaks visible during exponential growth, in contrast to the distinct genome peaks observed for Archaeoglobus fulgidus, Methanothermobacter thermautotrophicus and Sulfolobus solfataricus [32,40,41]. This observation supports the previous observation [42], that M. maripaludis cells are highly polyploid under normal growth conditions, as is the case for exponentially growing bacteria [43] and halophilic archaea [44].…”

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

“…maripaludis is polyploid and contains 30-55 genomes per cell, depending upon the growth phase (6). To prevent accumulation of heterologous genes, gene conversion rapidly homogenizes the genomes following insertions (6). Therefore, in our experimental design, insertions in nonessential genes are expected to rapidly replace the wild-type alleles during growth with puromycin selection (Fig.…”

“…maripaludis is polyploid and contains 30-55 genomes per cell, depending upon the growth phase (6). To prevent accumulation of heterologous genes, gene conversion rapidly homogenizes the genomes following insertions (6).…”

“…Because the full replacement of the wild-type allele is lethal for essential genes, cells are expected to maintain both the wild-type and mutant genes during puromycin selection. When the puromycin selection is removed, the mutant alleles are expected to be lost rapidly, and wild-type alleles are expected to dominate (6). To test this model, the fraction of genomes with insertions was determined by real-time PCR for library 1.…”

Chemical markers for rumen methanogens and methanogenesis

“…This lack of consistent relationship may reflect the problems with sampling methods and choice of primers mentioned previously, as well as underlying problems with the qPCR technique. These problems include differences in the rrs gene copy number within a genome (Hook et al, 2009) and differences in genome copy number within a cell (Hildenbrand et al, 2011). There is increasing concern about bias in the PCR reaction (Tymensen and McAllister, 2012), and the small number of sequences related to known methanogens (Firkins and Yu, 2006) may also cause problems.…”