RECG Maintains Plastid and Mitochondrial Genome Stability by Suppressing Extensive Recombination between Short Dispersed Repeats

Abstract

Maintenance of plastid and mitochondrial genome stability is crucial for photosynthesis and respiration, respectively. Recently, we have reported that RECA1 maintains mitochondrial genome stability by suppressing gross rearrangements induced by aberrant recombination between short dispersed repeats in the moss Physcomitrella patens. In this study, we studied a newly identified P. patens homolog of bacterial RecG helicase, RECG, some of which is localized in both plastid and mitochondrial nucleoids. RECG partially complements recG deficiency in Escherichia coli cells. A knockout (KO) mutation of RECG caused characteristic phenotypes including growth delay and developmental and mitochondrial defects, which are similar to those of the RECA1 KO mutant. The RECG KO cells showed heterogeneity in these phenotypes. Analyses of RECG KO plants showed that mitochondrial genome was destabilized due to a recombination between 8–79 bp repeats and the pattern of the recombination partly differed from that observed in the RECA1 KO mutants. The mitochondrial DNA (mtDNA) instability was greater in severe phenotypic RECG KO cells than that in mild phenotypic ones. This result suggests that mitochondrial genomic instability is responsible for the defective phenotypes of RECG KO plants. Some of the induced recombination caused efficient genomic rearrangements in RECG KO mitochondria. Such loci were sometimes associated with a decrease in the levels of normal mtDNA and significant decrease in the number of transcripts derived from the loci. In addition, the RECG KO mutation caused remarkable plastid abnormalities and induced recombination between short repeats (12–63 bp) in the plastid DNA. These results suggest that RECG plays a role in the maintenance of both plastid and mitochondrial genome stability by suppressing aberrant recombination between dispersed short repeats; this role is crucial for plastid and mitochondrial functions.

The RECG1 DNA Translocase Is a Key Factor in Recombination Surveillance, Repair, and Segregation of the Mitochondrial DNA in Arabidopsis

“…However, in recG1 knockdown and knockout plants, we have not seen any significant effects on the copy number of the cpDNA, on the stoichiometry of the cpDNA regions, or on the surveillance of recombination mobilizing repeated sequences. These observations contrast with recently published results on the P. patens ortholog of RECG1, which is also dually targeted to both organelles and whose deletion caused an increase in recombination mobilizing mtDNA IRs of 47 to 79 bp, but also cpDNA IRs of 48 to 63 bp (Odahara et al, 2015). There are several possible explanations for these functional differences.…”

“…In Arabidopsis mitochondria, efficient mobilization of such small repeats for recombination has not been observed (Davila et al, 2011). On the contrary, mitochondrial and chloroplastic repeated sequences that are active in ectopic HR in P. patens are essentially small (Odahara et al, 2009(Odahara et al, , 2015, definitely reflecting differences between the organellar recombination machineries of the two species. In this context, it might be noted that recombinational activities that reshuffle mtDNA gene arrangements only came with the onset of spermatophytes (Knoop, 2013).…”

“…Subcellular localization of the fusion protein was analyzed both in transfected Nicotiana benthamiana leaf cells and in stable Arabidopsis transformants, and in both systems the protein was found in chloroplasts and in mitochondria ( Figure 1C), implying that RECG1 is an additional example of a dually targeted organellar protein. Recently, the Physcomitrella patens ortholog of Arabidopsis RECG1 was described and shown as well to be targeted to both mitochondria and chloroplasts (Odahara et al, 2015).…”

RecG controls DNA amplification at double‐strand breaks and arrested replication forks

“…However, recently several candidates have been proposed. These include the mitochondrial helicase Irc3 of Saccharomyces cerevisiae , the plastid and mitochondrial helicase RECG of Physcomitrella patens , the mitochondrial helicase RECG1 of Arabidopsis thaliana and the human nuclear helicase SMARCAL1 . All of these genes are implicated in the maintenance of DNA stability and all the plastid and mitochondrial genes show partial cross‐complementation with recG .…”

The Plastid Genome of Polytoma uvella Is the Largest Known among Colorless Algae and Plants and Reflects Contrasting Evolutionary Paths to Nonphotosynthetic Lifestyles

“…Perhaps the efficiency of the plastid recombinationbased DNA-repair mechanisms potentially contributing to genomic rearrangements and expansion took over the molecular systems that counteract repeatmediated recombination events (e.g. RECA-like proteins, RECG helicases, MutS homologs, and DNAbinding proteins of the Whirly family; Inouye et al, 2008;Cappadocia et al, 2010;Xu et al, 2011;Odahara et al, 2015), compromising the stability of the oganelle genome. These mechanisms limiting the impact of repeat-mediated DNA repair probably became relatively inefficient in the P. uvella plastid after facing relaxed pressures following the loss of photosynthesis.…”