Dr. Matthew Andrusiak
Biological Sciences, University of California, San Diego

The genetic mutation and de-regulation of prion-like domain (PrLD) containing proteins is over-represented in human disease. Despite their role in human disease, little is known about how PrLD’s regulate protein function. PrLD-containing proteins are often capable of liquid-liquid phase separation (LLPS) resulting in the formation of non-membrane bound cellular compartments. The in vivo function and cellular mechanisms regulated by LLPS remain unknown. My work identified the PrLD coding gene tiar-2, a C. elegans member of the TIA1 family, as an intrinsic inhibitor of axon regeneration. TIAR-2 forms granules and inhibits axon regeneration in a dose-dependent manner. TIAR-2 undergoes LLPS in vitro and granules have liquid-features in vivo. Following axon injury, TIAR-2 granule number increases, and their liquid-like features are significantly reduced. Importantly, the PrLD of TIAR-2 is necessary and sufficient for its ability to inhibit regeneration and form granules. Post-translational modifications, such as phosphorylation, have been shown to act as molecular switches regulating LLPS. TIAR-2 is serine phosphorylated and this modification is required for TIAR-2 granule formation and function in axon regeneration. This work identified axonal injury as an acute cue that modulates the formation of LLPS granules and the function of the PrLD containing protein TIAR-2. Future research efforts will focus on understanding the role of prion-like domains in the regulation of biological outputs during nervous system and organismal development, as well as following neuronal injury.

Transcription is essential for life and in eukaryotes it is performed by one of several RNA polymerases (RNAP). Of these, RNAPII is responsible for the synthesis of all mRNAs and many non-coding transcripts, an activity that requires the integration of general and gene-specific signals. However, how these activities are coordinated and contribute to the response to environmental contexts remains poorly understood, despite a clear significance in the adaptation, health and survival of all organisms. Furthermore, the extent to which genetic variability affects transcription and thus modulates individual differences in the response to challenge remains largely unknown. Using yeast, I have identified new players in the response to oxidative stress, a challenge that affects all organisms and that can have grave consequences for cellular integrity. I also showed that the transcriptional response to oxidant involved alterations in both mRNA synthesis and mRNA decay, effects that must be teased apart in order to fully understand how organisms respond to environmental contexts. Furthermore, my work in fruit flies identified sex-specific differences in gene expression under normal and stress conditions, thus underscoring the importance of considering sex when studying the molecular underpinnings of the biological embedding of experience.

Over the last thirty years, several molecular events operating on the products of the central dogma processes of DNA replication, transcription and translation have been found to play an important role in controlling gene regulation in a rapid and adaptive manner in response to various external stimuli. Here, I will present unpublished work investigating the role of three such “post-genetic” phenomena: extrachromosomal circular DNA (eccDNA) production, RNA splicing, and protein phosphorylation in the model plant Arabidopsis thaliana. First, I will discuss on-going work studying the role of eccDNA molecules in plant responses to heat-stress through the invention of a new DNA sequencing method called CIDER-Seq. CIDER-Seq leverages the power of long-read PacBio sequencing technology to produce accurate sequences of eccDNA (and other circular DNA such as viruses) without computational sequence assembly. Using CIDER-Seq we have generated the first comprehensive sequence dataset of eccDNA in plants, gaining insights into eccDNA composition and function that have implications in stress and evolutionary biology. I will also discuss recent work using quantitative proteomics and phosphoproteomics that has uncovered new regulatory roles for protein phosphorylation during phosphate starvation. Collectively, these proteomics and genomics-technology driven experiments point towards an important role for genome plasticity and post-genetic regulation in plant responses to future challenges in agriculture such as rising temperatures and declining nutrient supply. Next I will describe future projects employing genomics, proteomics, genome editing, and chemical genetics approaches to investigate eccDNA and RNA splicing regulation in plants. Finally, I will briefly touch upon my work outside the lab: in science communication, research culture, and equity in science publishing with the premier open-access life science journal eLife. 

Muscles are made up of muscle fibers, each containing thousands of cylindrical segments called sarcomeres, which are the smallest contractile unit of muscles. When animals move, proteins in the sarcomere move past each other, shortening the muscles. In the relaxed state, all sarcomeres have the same length and diameter. To study muscle biology I use the fruit fly Drosophila. Their flight muscles are extremely regular, because they have to mediate 200 small contractions per second, and are therefore ideally suited to detect phenotypic variations. Sarcomeres are composed of antiparallel actin and myosin filaments that slide past each other. Both filaments are anchored to big protein complexes that provide structural stability. The Z-discs anchor actin filaments and the M-lines myosin filaments. This fascinating structural arrangement provides the basis of muscle contraction. The general sarcomere structure is well known but the mechanisms that assemble sarcomeres from unorganized components and maintain sarcomeres during muscle contractions are not well understood. The Z-disc anchors actin filaments and thus coordinates sarcomere assembly and function. Accordingly, most mutations linked to myopathies are components of the Z-disc.

To study sarcomere assembly and function, I combine the power of Drosophila genetics with quantitative microscopy and a novel bioinformatics method for inferring protein-protein interactions.  First, I will talk about how the scaffolding protein Zasp mediates sarcomere growth through a finely tuned protein oligomerization mechanism. Oligomerization is induced by long Zasp isoforms and terminated upon upregulation of shorter Zasp isoforms, which lack multivalent LIM domains. The balance between these two isoforms sets the stereotyped size of sarcomeres. Second, I will describe how elastic proteins help maintain sarcomere stability during muscle contraction. In this model, two elastic proteins filamin and titin function together as an elastic bridge between thin filaments of opposing sarcomeres. Both filamin and titin have protein regions than unfold upon pulling forces and then refold, essentially working as springs. Their function is required for compensating for the contractile forces and maintaining the sarcomere structure. Finally, I will discuss future directions and approaches.