Research

RESEARCH PROJECTS

Evolution of Cytonuclear Interactions

The basic functionality of the eukaryotic cell depends on coordinated interactions between two or more genomes. In the case of plants, three distinct genomic compartments—the nucleus, mitochondria, and plastids—all coexist within cells but experience very distinct conditions with respect to DNA replication, recombination, damage, repair, and inheritance. What effects do these contrasting genetic environments have on co-evolution between the genomic compartments? Because of the striking differences in mutation rates between mitochondrial and nuclear DNA in animals, it has long been hypothesized that differential mutation pressure may shape the interactions between organelle genomes. For example, high mutation rates in animal mitochondrial genes may create selection for compensatory mutations in the nuclear genome because mitochondrially encoded gene products experience direct protein-protein interactions with nuclear-encoded gene products. Theory suggests that frequent mutations and lack of recombination in mtDNA create selection for transfer of genes from the mitochondria to the nucleus to avoid the deleterious consequences of mutation accumulation. The natural mitochondrial mutation rate variation found in the angiosperm genus Silene (see below) presents an opportunity for us to test these hypotheses and better understand key mechanisms of cellular function (and dysfunction), using a combination of comparative genomic analysis and manipulative experiments that employ genome-editing techniques. We are also investigating the evolutionary dynamics associated with interactions between tRNAs and the aminoacyl-tRNA synthetase enzymes that are responsible for charging them with the correct amino acid. We have ongoing projects in Silene and in parasitic plants to investigate how these systems respond when the relationships between organelle-encoded tRNAs and nuclear-encoded enzymes are perturbed.

Mechanisms of Mitochondrial Mutation and DNA Damage

Although we typically think of mitochondrial genomes as enduring a much higher rate of point mutations than the nucleus, it is not clear how general this pattern is outside of animals, and it is most certainly not the case in plants, in which the rates of nucleotide substitution in mtDNA are exceptionally slow. The high mutation rates in human mitochondrial genomes are of great biomedical importance, making it valuable to understand how some other eukaryotic lineages like plants have evolved such low rates. Using special modifications to high throughput DNA sequencing techniques, we are detecting de novo mutations and DNA damage at low frequencies within plant tissues. Applying these approaches in mutant backgrounds of the model angiosperm Arabidopsis thaliana with disruptions in some key components of mitochondrial DNA replication and recombination is helping us elucidate the mechanisms the determine rates of mutation and DNA damage. Our work has identified the gene MSH1 as a key player in suppressing mitochondrial and plastid mutation rates and shaping the dynamics of heteroplasmic sorting -- the process by which a new mutation either proliferates or is eliminated among the many cytoplasmic genome copies that exist within the cell. Ongoing efforts are aimed at better understanding the mechanisms by which MSH1 affects these processes.

The Evolution of  Plant Organelle Genome Architecture

We and others have identified  a number of flowering plant groups with dramatically elevated mitochondrial mutation rates. Mutation rates in these atypical plant lineages appear to be as fast or even faster than those normally seen in animals. We work on one of these groups, the genus Silene (Caryophyllaceae), in which accelerations in mutation rate appear to have occurred in just the past few million years, making it an excellent system to investigate the consequences of mitochondrial mutation rate variation.

By sequencing complete mitochondrial genomes from a number of species, we found that increases in mitochondrial mutation rates in Silene have been associated with extreme changes in genome size and structure as well as reductions in the frequency of RNA editing. Remarkably, the fast-evolving Silene mtDNAs include the largest organelle genomes ever identified (up to 11.3 Mb in size) and have been fragmented into dozens of circular-mapping chromosomes. However, in many cases, the observed changes in these species run counter to existing theories about the relationship between mutation rates and genome architecture. Our current efforts are aimed at understanding the origins of this mitochondrial genomic diversity and identifying the mechanisms by which the enormous, multichromosomal genomes in Silene are replicated and inherited.