Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid Haloarchaeon Haloferax volcanii

Abstract

Gene conversion is defined as the non-reciprocal transfer of genetic information from one site to a homologous, but not identical site of the genome. In prokaryotes, gene conversion can increase the variance of sequences, like in antigenic variation, but can also lead to a homogenization of sequences, like in the concerted evolution of multigene families. In contrast to these intramolecular mechanisms, the intermolecular gene conversion in polyploid prokaryotes, which leads to the equalization of the multiple genome copies, has hardly been studied. We have previously shown the intermolecular gene conversion in halophilic and methanogenic archaea is so efficient that it can be studied without selecting for conversion events. Here, we have established an approach to characterize unselected intermolecular gene conversion in Haloferax volcanii making use of two genes that encode enzymes involved in carotenoid biosynthesis. Heterozygous strains were generated by protoplast fusion, and gene conversion was quantified by phenotype analysis or/and PCR. It was verified that unselected gene conversion is extremely efficient and it was shown that gene conversion tracts are much longer than in antigenic variation or concerted evolution in bacteria. Two sites were nearly always co-converted when they were 600 bp apart, and more than 30% co-conversion even occurred when two sites were 5 kbp apart. The gene conversion frequency was independent from the extent of genome differences, and even a one nucleotide difference triggered conversion.

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages

“…The observation that anchor genes in the syntenic blocks linked to rho were mapped to both the MRCA of Poaceae and subsequent backbone nodes of the grass phylogeny suggested that, following the rho event, the sequences of the paralogues of an ingroup (such as the core Poaceae) became more similar to each other, relative to sequences of earlier divergent lineage(s) (such as Anomochlooideae). This could be due to gene conversion (also referred to as nonreciprocal exchange), which copies the sequence of one homologue to replace the sequence of another during meiosis (and, to a lesser extent, during the mitotic cell cycle) and can lead to equalization of different gene copies 49 . Indeed, analyses of diploid and allopolyploid cottons ( Gossypium ) supported gene conversion between homologous sequences from past WGD 50 .…”

“…30 ). The mapping of some GDs to a later node could be due to gene conversion, which can lead to equalization of different gene copies 49 . Gene conversions occur frequently in meiosis and has been hypothesized to play a key role in promoting polyploidy-dependent establishment of mutational robustness in plants 92 .…”

One Advantage of Being Polyploid: Prokaryotes of Various Phylogenetic Groups Can Grow in the Absence of an Environmental Phosphate Source at the Expense of Their High Genome Copy Numbers

“…The latter opinion was obtained with genetic approaches, e.g., the generation of homozygous mutants or the way mutations segregated were taken as genetic proof for monoploidy [ 37 , 39 ]. However, since then, it has become clear that at least two polyploid prokaryotes, the methanogenic archaeon Methanococcus maripaludis and the haloarchaeon H. volcani , exhibit highly efficient gene conversion [ 8 , 65 , 66 ]. Gene conversion equalizes homologous, but nonidentical gene copies [ 67 ].…”

The nitrogenase cofactor biogenesis enzyme NifB is essential for the viability of methanogens

“…In the absence of sexual reproduction, gene conversion can help offset the accumulation of deleterious mutations in asexual organisms (Muller’s Ratchet) (38). Gene conversion has been observed in other polyploid archaea, including M. maripaludis (55 genome copies) and Haloferix volcanii (20 genome copies) (28, 39, 40). M. acetivorans contains up to 17 genome copies when growing with methanol (28), the condition used in this study.…”