Multiple Losses of MSH1, Gain of mtMutS, and Other Changes in the MutS Family of DNA Repair Proteins in Animals

Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes

Mitochondrial DNA (mtDNA) mutagenesis remains poorly understood despite its crucial role in disease, aging, and evolutionary tracing. In this study, we reconstructed a comprehensive 192-component mtDNA mutational spectrum for chordates by analyzing 118,397 synonymous mutations in the CytB gene across 1,697 species and five classes. This analysis revealed three primary forces shaping mtDNA mutagenesis: (i) symmetrical, replication-driven errors by mitochondrial polymerase (POLG), resulting in C > T and A > G mutations that are highly conserved across classes; (ii) asymmetrical, damage-driven C > T mutations on the single-stranded heavy strand with clock-like dynamics; and (iii) asymmetrical A > G mutations on the heavy strand, with dynamics suggesting sensitivity to oxidative damage. The third component, sensitive to oxidative damage, positions mtDNA mutagenesis as a promising marker for metabolic and physiological processes across various classes, species, organisms, tissues, and cells. The deconvolution of the mutational spectra into mutational signatures uncovered deficiencies in both base excision repair (BER) and mismatch repair (MMR) pathways. Further analysis of mutation hotspots, abasic sites, and mutational asymmetries underscores the critical role of single-stranded DNA damage (components ii and iii), which, uncorrected due to BER and MMR deficiencies, contributes roughly as many mutations as POLG-induced errors (component i).

Flipping the switch on some of the slowest mutating genomes: Direct measurements of plant mitochondrial and plastid mutation rates in msh1 mutants

Plant mitochondrial and plastid genomes have exceptionally slow rates of sequence evolution, and recent work has identified an unusual member of the MutS gene family ("plant MSH1") as being instrumental in preventing point mutations in these genomes. However, the effects of disrupting MSH1-mediated DNA repair on "germline" mutation rates have not been quantified. Here, we used Arabidopsis thaliana mutation accumulation (MA) lines to measure mutation rates in msh1 mutants and matched wild type (WT) controls. We detected 124 single nucleotide variants (SNVs: 49 mitochondrial and 75 plastid) and 668 small insertions and deletions (indels: 258 mitochondrial and 410 plastid) in msh1 MA lines. In striking contrast, we did not find any organelle mutations in the WT MA lines, and reanalysis of data from a much larger WT MA experiment also failed to detect any variants. The observed number of SNVs in the msh1 MA lines corresponds to estimated mutation rates of 6.1×10-7 and 3.2 ×10-6 per bp per generation in mitochondrial and plastid genomes, respectively. These rates exceed those of species known to have very high mitochondrial mutation rates (e.g., nematodes and fruit flies) by an order of magnitude or more and are on par with estimated rates in humans despite the generation times of A. thaliana being nearly 100-fold shorter. Therefore, disruption of a single plant-specific genetic factor in A. thaliana is sufficient to erase or even reverse the enormous difference in organelle mutation rates between plants and animals.

The HNH endonuclease domain of the giant virus MutS7 specifically binds to branched DNA structures with single-stranded regions

Most giant viruses including Mimiviridae family build large viral factories within the host cytoplasms. These giant viruses are presumed to possess specific genes that enable the rapid and massive replication of their large double-stranded DNA genomes within viral factories. It has been revealed that a functionally uncharacterized protein, MutS7, is expressed during the operational phase of the viral factory. MutS7 contains an N-terminal mismatched DNA-binding domain, which is similar to the mismatched DNA-recognizing protein MutS1, and a unique C-terminal HNH endonuclease domain absent in other MutS family proteins. MutS7 gene of the genus Mimivirus of the family Mimiviridae is encoded in the locus that is responsible for resistance against infection of a virophage. In the present study, we characterized the MutS7 HNH domain of Mimivirus shirakomae. The HNH domain preferentially bound to branched DNA structures containing single-stranded regions, especially the displacement-loop structure, which is a primary intermediate in homologous/homeologous recombination, rather than to linear DNAs and branched DNAs lacking single-stranded regions. However, the HNH domain exhibited no endonuclease activity. The site-directed mutagenesis analysis revealed that the Cys4-type zinc finger of the HNH domain was not essential, but was important for the DNA binding. Given that giant virus MutS7 contains a mismatch-binding domain in addition to the HNH domain, we propose that giant virus MutS7 may suppress homeologous recombination in the viral factory.

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mitochondrial tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mitochondrial tRNAs with a uniform workflow. Here, we report our results on the complete reannotation of all mitogenomes available in the RefSeq database by September 2022 using mitos2. Based on the individual cases of mitochondrial tRNA variants reported throughout the literature, our data pinpoint the respective hotspots of change, i.e. Acanthocephala (Lophotrochozoa), Nematoda, Acariformes, and Araneae (Arthropoda). Less dramatic deviations of mitochondrial tRNAs from the norm are observed throughout many other clades. Loss of arms in animal mitochondrial tRNA clearly is a phenomenon that occurred independently many times, not limited to a small number of specific clades. The summary data here provide a starting point for systematic investigations into the detailed evolutionary processes of structural reduction and loss of mitochondrial tRNAs as well as a resource for further improvements of annotation workflows for mitochondrial tRNA annotation.

Evolution and maintenance of mtDNA gene content across eukaryotes

Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.

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.

UV damage induces production of mitochondrial DNA fragments with specific length profiles

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.

Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.

Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease

MutS HOMOLOG 1 (MSH1) is an organellar-targeted protein that obstructs ectopic recombination and the accumulation of mutations in plant organellar genomes. MSH1 also modulates the epigenetic status of nuclear DNA, and its absence induces a variety of phenotypic responses. MSH1 is a member of the MutS family of DNA mismatch repair proteins but harbors an additional GIY-YIG nuclease domain that distinguishes it from the rest of this family. How MSH1 hampers recombination and promotes fidelity in organellar DNA inheritance is unknown. Here, we elucidate its enzymatic activities by recombinantly expressing and purifying full-length MSH1 from Arabidopsis thaliana (AtMSH1). AtMSH1 is a metalloenzyme that shows a strong binding affinity for displacement loops (D-loops). The DNA-binding abilities of AtMSH1 reside in its MutS domain and not in its GIY-YIG domain, which is the ancillary nickase of AtMSH1. In the presence of divalent metal ions, AtMSH1 selectively executes multiple incisions at D-loops, but not other DNA structures including Holliday junctions or dsDNA, regardless of the presence or absence of mismatches. The selectivity of AtMSH1 to dismantle D-loops supports the role of this enzyme in preventing recombination between short repeats. Our results suggest that plant organelles have evolved novel DNA repair routes centered around the anti-recombinogenic activity of MSH1.

Complete mitochondrial genome of the abyssal coral Abyssoprimnoagemina Cairns, 2015 (Octocorallia, Primnoidae) from the Clarion-Clipperton Zone, Pacific Ocean

The Clarion-Clipperton Zone (CCZ) in the tropical East Pacific is a region of interest for deep-sea mining due to its underwater deposits of polymetallic nodules containing economically important metals such as nickel, copper, and cobalt. It is also a region of extensive baseline studies aiming to describe the state of the environment, including the biodiversity of the benthic fauna. An abundant component of the abyssal plain ecosystem consists of sessile fauna which encrusts polymetallic nodules and are vulnerable to potential impacts arising from exploitation activities, particularly removal of substrate. Therefore, this fauna is often considered to have key species whose genetic connectivity should be studied to assess their ecological resilience. One such species is Abyssoprimnoagemina Cairns, 2015, a deep-sea coral from the CCZ whose presence in the Interoceanmetal Joint Organization (IOM) claim area has been confirmed during samplings. In this study, we used next-generation sequencing (NGS) to obtain the 18S nuclear rRNA gene and the complete mitochondrial genome of A.gemina from IOM exploration area. The mitogenome is 18,825 bp long and encodes for 14 protein coding genes, 2 rRNAs, and a single tRNA. The two phylogeny reconstructions derived from these data confirm previous studies and display A.gemina within a highly supported cluster of seven species whose mitogenomes are all colinear and of comparable size. This study also demonstrates the suitability of NGS for DNA barcoding of the benthic megafauna of the CCZ, which could become part of the IOM protocol for the assessment of population diversity and genetic connectivity in its claim area.

Origin of minicircular mitochondrial genomes in red algae

Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.

Mitochondrial genome comparison reveals the evolution of cnidarians

Cnidarians are the most primitive metazoans, but their evolutionary relationships are poorly understood, although recent studies present several phylogenetic hypotheses. Here, we collected 266 complete cnidarian mitochondrial genomes and re-evaluated the phylogenetic relationships between the major lineages. We described the gene rearrangement patterns of Cnidaria. Anthozoans had significantly greater mitochondrial genome size and lower A + T content than medusozoans. Most of the protein-coding genes in anthozoans such as COX 13, ATP6, and CYTB displayed a faster rate of evolution based on selection analysis. There were 19 distinct patterns of mitochondrial gene order, including 16 unique gene orders in anthozoans and 3 mtDNA gene orders pattern in medusozoans, were identified among cnidarians. The gene order arrangement suggested that a linearized mtDNA structure may be more conducive to Medusozoan mtDNA stability. Based on phylogenetic analyses, the monophyly of the Anthozoa was strongly supported compared to previous mitochondrial genome-based analyses rather than octocorals forming a sister group relationship with medusozoans. In addition, Staurozoa were more closely related to Anthozoa than to Medusozoa. In conclusion, these results largely support the traditional phylogenetic view of the relationships of cnidarians and provide new insights into the evolutionary processes for studying the most ancient animal radiations.

Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes

In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.