Scholarly Interests: 

Chromatin; Histone Modifications; Top Down Mass Spectrometry; Biosequestration

The industrialized world currently satisfies its energy needs by relying heavily on combustion of hydrocarbons, resulting in elevated levels of the greenhouse gas carbon dioxide. Over the last 70 years, the atmospheric levels of carbon dioxide have increased by nearly 100 parts-per-million and is widely suspected as the main culprit in the increase of ocean and air temperature. In order to avoid irreversible harm to the planet, scientists have investigated means to generate power from renewable, emissionless sources (e.g., solar, wind, etc.) and also ways to sequester carbon dioxide from sources that generate it (e.g., coal-burning power plants). One such efficient and cost-effective way to sequester carbon dioxide is through the utilization of microalgae. Microalgae are single-celled organisms that have the ability to grow photoautotrophically, using carbon dioxide as the sole source of organic carbon. In addition to sequestering carbon dioxide, microalgae hold promise as a source of lipids and carbohydrates that can be processed into biofuels and biogas. Not surprisingly, there exists a natural correlation between the highly efficient biosequestering algae and their ability to create biomass, the precursor for biofuels.

While several species of microalgae have been investigated for their intrinsic ability to produce biofuels, no one species has been found that can produce the quantity of biofuel needed to satisfy our current energy needs at an economical level. With this in mind, scientists are focusing more on genetic manipulation of microalgae to make them produce higher amounts of lipids, carbohydrates and other bio-products. To date, the microalga most amenable to genetic manipulation is the model organism Chlamydomonas, as its genome has been sequenced and a significant number of genetic tools are available for this organism, including RNAi gene silencing and implementation of the CRISPR/Cas9 system for genome editing. Indeed, some of these tools have already been used to determine key enzymes responsible for the generation of triacylglycerols, a key storage lipid precursor for biofuels.

In addition to genetic manipulation, the engineering of microalgae to produce economically viable biofuel requires a deep understanding at the genetic and epigenetic level. Surprisingly, there are few researchers studying epigenetic changes in microalgae and thus our collective knowledge on this subject is rather limited. Chromatin organization, which, among other things, affects gene expression and genome stability, arises from intimate interactions between DNA and a class of small proteins called histones (histone H2A, H2B, H3 and H4). Histones may alter DNA structure directly through protein:DNA electrostatic interactions or indirectly by serving as a binding platform for other chromatin-modifying proteins. In either case, the histone proteins carry out their intended functions by presenting a specific set of chemical modifications (e.g., acetylation, methylation, phosphorylation, etc.) located at specific amino acids (e.g. Lysine 9 of histone H3) within the termini of the protein. Thus, there may be a “histone code” governing many genetic functions including turning on/off gene expression, compacting DNA into higher order structures, or even flagging a damaged region of DNA for repair. Post-translational modifications of histone proteins across different organisms do not always lead to the same gene expression outcomes, making species-specific investigations essential for truly understanding histone-based epigenetic influences on chromatin structure and gene regulation.

While histone H3 post-translational modifications and their corresponding biological responses have been the primary focus in microalgae and plants (especially A. thaliana), the same cannot be said for histone H4, leaving a large gap in our knowledge regarding its role in epigenetic regulation. Indeed, only two papers have reported on Chlamydomonas histone H4 (CrH4) PTMs, both of which focused on the dynamics of H4 acetylation and its role in transcriptional activation. Methylation of histone H4 has also been reported. Recent work on animal histone H4 showed discrete patterns of modifications (e.g., progressive methylation at Lysine-20) during the cell cycle in human tissue culture cells. Work is now underway to investigate the significance of H4K20 methylation in the context of the cell cycle, but initial studies suggest this modification is a hallmark of cellular quiescence. Interestingly, H4K20 methylation is present in some organisms (e.g., S. pombe, H. sapiens, D. melanogaster) and absent in others (e.g., S. cerevisiae, A. thaliana, C. reinhardtii), suggesting that it is not a critical feature necessary for chromatin maintenance in all eukaryotic (or multicellular) organisms. Thus, methylation of CrH4 was assumed absent until my research group uncovered, by using intact protein mass spectrometry, that histone H4 is nearly completely monomethylated at Lys 79. The novelty and ubiquitousness of H4K79me1 in Chlamydomonas brings up several questions: Why is H4K79me1 absent in animals and fungi yet present in microalgae? Does its high abundance make it a mark for nucleosomal age? Does the environment and ‘life style’ of green algae require methylation at that residue to ensure some type of structural stability between DNA and histones? Do other photosynthetic organisms have it? Is it specific to Chlamydomonas or is it found in other Chlorophyte algal relatives, including the closely related, multicellular alga Volvox carteri? These questions and many others can only begin to be answered if the function of H4K79me1 and the enzyme ‘writing’ this epigenetic mark are determined.