Research

Cell cycle and cell size control in Chlamydomonas

Eukaryotic cells encompass an astonishing amount of diversity in sizes, yet cells of each type maintain their size within a narrow range. The overarching goal of our cell size control project is to understand how eukaryotic cells sense and integrate size information to gate cell cycle progression. The multiple fission cell cycle of Chlamydomonas provides unique access to a cell “sizer” mechanism that works through the conserved retinoblastoma related (RBR) tumor suppressor pathway to control size-dependent cell cycle progression. Our work focuses on two areas, i) the retinoblastoma tumor suppressor complex (RBC) and upstream regulators of the RBC that play a role in governing cell size, ii) elucidating the stochastic and deterministic aspects of cell size control using modeling and empirical observations of single cells and populations. The long-term outcomes will be understanding the enigmatic role of RBC in human tumorigenesis and in plant development with possible targets for therapy and crop trait modifications.

Inositol polyphosphate signaling and its role in control of growth and metabolic homeostasis in Chlamydomonas

Algae have great potential as producers of lipids and high value products, but the ability to modulate tradeoffs between cell growth and product yield remains a hurdle for development of algal crops. Complex nutrient and environmental sensing mechanisms are used by algae to control metabolic flux, yet the way such mechanisms interact to produce specific metabolic states remains poorly understood. We investigate the interaction of conserved signaling systems found in nearly all eukaryotes, Target of Rapamycin (TOR) and inositol polyphosphates (InsPs). Our finding that imbalances in InsP production influence TOR signaling, phosphate homeostasis and storage lipids accumulation suggest a central role for InsPs in coordinating metabolic flux and energy metabolism. Current research focuses on the role of InsPs in governing polyphosphate storage and adenylate charge balance, and how these connect to mitochondrial function and flux through storage lipid pathways.

Evolution of cell types and sexual dimorphism in Volvox and volvocine algae

Multicellularity has arisen dozens of times in eukaryotic evolution, yet little is known about the early steps in evolution that allowed single cells to form cooperative groups and eventually become integrated multicellular individuals. Volvox and volvocine green algae form a snapshot of these steps captured within a set of genera and species that form a graded path from single celled Chlamydomonas representing the ancestral state through Volvox carteri which has thousands of cells and complete germ-soma division of labor. Our current work in Volvocine multicellularity focuses on the genetic programming that evolved to control cell type differentiation, and the relationship of this programming to that in simpler relatives like Chlamydomonas which lacks differentiated cell types. We also study a master regulator of somatic cell differentiation, regA, a transcription factor whose targets and upstream regulatory controls remain unknown.

Ancestral unicellular eukaryotes had isogamous mating types, yet nearly every multicellular lineage has evolved anisogamy or oogamy with male and female sexes. What drives the evolution of sexual dimorphism and how does it evolve along with sex chromosomes? Volvocine algae are a model for answering these questions. Chlamydomonas and simple volvocine genera have mating types called plus and minus that control differentiation into morphologically indistinguishable iso-gametes; but larger volvocine genera display a progression towards anisogamy and oogamy as found in Volvox which has also evolved differentiated sex chromosomes. Current projects involve investigating two conserved sex regulators, the RWP-RK family transcription factors MID and VSR1. While the regulatory logic of plus/minus or male/female differentiation appears conserved across volvocine genera, the downstream targets and interactions of VSR1 and MID appear to have expanded in Volvox to control sexually dimorphic embryogenesis and sperm-egg differentiation.

By Dianyi Liu

Conserved uncharacterized green lineage proteins (Deep Green proteins) and their function in Chlamydomonas

The number of sequenced plant and algal genomes continues to grow exponentially, but the capacity for annotation and functional studies on genes remains far behind. Between at least 30% of genes in any newly sequenced green lineage species have no annotation or functional data. We are leveraging Chlamydomonas as a microbial model for green eukaryotes to investigate conserved genes of unknown function shared between Chlamydomonas and land plants. Their conservation and lack of conserved domains and functional data make these genes high-value targets for reverse genetics. A collection of around 500 Deep Green mutants are being screened for abiotic stress phenotypes and subcellular localization in Chlamydomonas where high throughput screening assays can be implemented rapidly. The information from phenotypic screening and structural predictions in Chlamydomonas will provide a roadmap for predicting phenotype and functions in the land plant homologs of Deep Green genes and will help define and expand the genetic architecture of important plant abiotic stress traits such as heat, cold, salt and high light tolerance.

Harnessing algal centromeres to make artificial chromosomes

An ambitious goal of plant and algal synthetic biology is to encode complex multigene traits on a single heritable genetic unit—an artificial chromosome. A major hurdle in this field is to insert functional synthetic centromeres into artificial chromosomes so they can be faithfully maintained and inherited. One way to bypass the epigenetic nature of centromeres is to tether centromeric proteins to specific sequence arrays on artificial chromosomes that will nucleate new centromere formation. Our project involves adapting the established approach of tethering CenH3 to an artificial sequence array to form new centromeres in Chlamydomonas. Having identified and validated the Chlamydomonas CenH3 paralogs we are now developing the tools needed to create tethered artificial centromeres and methods to introduce artificial chromosomes into Chlamydomonas cells for functional testing.