Biology subjects

Penafiel-Ayala, A.

Publications and source records attributed to Penafiel-Ayala, A..

3 recordsLinked to original sources

bioRxiv2026

Uracil/guanine mismatches trigger MutS HOMOLOG1-dependent mitochondrial DNA double-strand breaks in Arabidopsis

Angiosperm mitochondrial genomes exhibit exceptionally low nucleotide substitution rates, likely supported by active homologous recombination-mediated repair, while maintaining genome integrity by suppressing illegitimate recombination between imperfectly matched sequences that could otherwise cause deleterious structural rearrangements. The nuclear-encoded MutS HOMOLOG1 (MSH1) protein has been proposed to help resolve this paradox by recognizing mismatches and promoting DNA double-strand break-associated repair responses that suppress both point mutations and illegitimate recombination. However, direct experimental evidence for this proposed activity of MSH1 has been lacking. Here, we demonstrate that targeted base editing using a mitochondrial TALE-cytidine deaminase fusion (mitoTALECD) in Arabidopsis mitochondria induces deletions at the redundant gene atp6-2. These deletions phenocopy those generated by mitochondria-targeted TALEN (mitoTALEN) cleavage at the same locus. Notably, deletion events that encompass the base-editing target site were markedly reduced in msh1 mutant backgrounds, indicating that functional MSH1 promotes their formation. In vitro assays further demonstrated that recombinantly expressed MSH1 efficiently recognizes U:G mismatches derived from deoxycytidine-to-deoxyuridine deamination events and performs coordinated double incisions, thereby generating staggered dsDNA breaks with short 3' overhangs. Together, these findings provide direct experimental support for the long-postulated role of MSH1: the induction of mismatch-triggered DNA double-strand breaks. This MSH1 activity likely promotes the repair of mismatched bases and prevents illegitimate recombination by rejecting annealing between imperfect repeat sequences, thereby helping maintain the characteristic mutational stasis and recombinational dynamics of angiosperm mitochondrial genomes.

Plant Biology↗

bioRxiv2026

Plant MutS Homolog 1 is a mismatch-directed nuclease required for organelle genome maintenance

The exceptionally low mutation rates of plant organellar genomes imply the existence of DNA surveillance mechanisms that counteract replication errors and DNA damage. Genetic evidence implicates MutS HOMOLOG 1 (MSH1) as a central component of this pathway, as loss of MSH1 results in the accumulation of point mutations. MSH1 is a unique protein that combines an N-terminal MutS-like mismatch-recognition module with a Cterminal GIYYIG nuclease domain. Here, we show that Arabidopsis thaliana MSH1 (AtMsh1) recognizes mismatches, insertion/deletion loops, and damaged bases within double-stranded DNA and introduces staggered DNA breaks at positions flanking the mismatch or lesion. Given the presence of an active homologous recombination machinery in plant organelles, we hypothesize that these DNA ends may be processed by exonucleases to remove the mismatched or damaged DNA while generating 3' single-stranded DNA substrates suitable for homologous recombination-mediated repair and gene conversion. Together, our findings support a model in which AtMsh1 functions as a minimal mismatch repair system that couples mismatch recognition to DNA incision, providing a potential mechanism for suppressing mutation accumulation and maintaining the remarkable stability of plant organellar genomes

biochemistry↗

bioRxiv2024

Expansion of the MutS gene family in plants

The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics. One-Sentence SummaryPlants are distinguished from other eukaryotes by a functionally diverse complement of MutS proteins gained via a combination of gene duplication, endosymbiotic gene transfer, and horizontal gene transfer.

evolutionary biology↗