Marco Alonzo Dueñas

Algae Rule the World!

Microalgae encompass a remarkably diverse group of photosynthetic microbes. Though they make up only about 0.2% of global photosynthetic biomass, these small but mighty cells are responsible for over 50% of photosynthesis on Earth. In other words, microalgae produce roughly half of the oxygen we breathe while capturing excess atmospheric CO₂. Some also naturally produce valuable compounds in the process. My research leverages microalgae as platforms for both fundamental discoveries that reshape how we understand biology and for engineering more sustainable biotechnologies. Below, I highlight several central topics of my research that advance this vision.

Auxenochlorella, the Real Green Yeast

When it comes to microalgae, the Auxenochlorella species are powerhouses for research and application. Like plants, they perform photosynthesis, but under stress conditions, the cells undergo a reversible trophic switch that drives the production of lipids valuable for biotechnology. Auxenochlorella is also distinctive for its genetic tractability, being readily amenable to targeted homologous recombination for precise and efficient gene editing. The Merchant Lab has assembled a high-quality, telomere-to-telomere genome for this organism, which, in tandem with its unique biology and ease of manipulation, makes Auxenochlorella a versatile platform for both discovery-based research and bioengineering. One of my ongoing goals is to expand its genetic toolkit, which includes the development of selectable markers, inducible promoters, quantifiable reporters, control strains for protein subcellular localization, and leveraging a natural trisomy to construct an artificial chromosome.

For more info, check out a Merchant lab publication I contributed to entitled Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella.

Textbook dogma holds that nucleus-encoded genes are monocistronic, producing transcripts with a single translated open reading frame (ORF) that encodes one protein. However, highly conserved bicistrons, in which two proteins are are encoded by a single mRNA, are widespread across the green algal lineage. Many of these bicistrons have been conserved over several hundred million years of evolution, speaking to their ancestral origins and importance within green algae. Through a combination of bioinformatic analyses and in vivo gene manipulation, I found that this phenomenon is most likely driven by episodic leaky scanning, a process in which the ribosome occasionally bypasses the first translation start site due to the presence of a weak sequence context (in contrast to the optimal consensus, known as the “Kozak Sequence”) around the start codon, allowing continued scanning for translation of a downstream ORF.

Although the underlying mechanism is increasingly clear, many questions remain: What is the evolutionary origin and regulatory purpose of this mode of protein translation? What are the functions of the many uncharacterized proteins encoded by these bicistronic loci? And could this mechanism be harnessed as a tool for synthetic biology applications? I aim to address these questions in my ongoing and future research.

For more info, check out the Merchant lab publication Widespread polycistronic gene expression in green algae and my very first first-author publication, Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae.

Lipid Droplets: Structure, Function, and Associated Proteins

Lipid droplets are the energy reservoirs of the cell, primarily storing triacylglycerols (TAGs). Although they sometimes get a bad rep as inert globs of fat, lipid droplets are actually dynamic hubs of metabolic activity, signaling, and protein interactions. In algae, lipid droplets are of particular interest due to their ability to accumulate gargantuan amounts of TAGs, which can be harnessed for biofuels, foods, cosmetics, specialty chemicals, and other biotechnological applications.

I’m currently investigating the most prominent protein in green algae associated with lipid droplets: Major Lipid Droplet Protein (MLDP). Using the naturally oleaginous Auxenochlorella, I am looking to explore several questions. What are the phenotypic consequences when Auxenochlorella cells lack MLDP? How does MLDP’s subcellular localization change across different stages of metabolism? What other proteins is does MLDP influence or interact with? Do MLDPs across different green algae function similarly? And could MLDP be used as a tool to enhance the production of rare oils?

Turning Waste into Designer Lipids

Growing algae in wastewater represents a sustainable and potentially economically viable strategy for the production of high-value bioproducts. With its ability to generate abundant triacylglycerols (TAGs) and its ease of genetic manipulation, Auxenochlorella is a promising system for engineering lipids with compositions that do not naturally occur in the organism, which I affectionately term “designer lipids.” One goal is to engineer Auxenochlorella to produce TAGs enriched in medium chain fatty acid (MCFAs), which are industrially relevant for lubricants, bioplastics, and pharmaceuticals. In addition to producing MCFAs, we are exploring ways to expand the substrates Auxenochlorella can utilize, enabling growth on waste sugars that the organism cannot normally metabolize. One such substrate is raffinose, a sugar abundant in soybean meal and other agricultural residues.

These questions guide our synthetic biology efforts: Can Auxenochlorella produce large amounts of TAGs when fed raffinose? Will these TAGs be enriched in MCFAs? And could the cells grow efficiently under mixotrophic conditions to reduce production costs?