Irrespective of species, plant roots have remarkably similar patterning, and thus, many cell types are considered functionally homologous across species.  Despite these similarities, there is also diversity in root cell types, such as the exodermis, which is present in a reported 89% of angiosperms, but absent in the intensely studied model species Arabidopsis (Perumalla, Peterson, and Enstone 1990).  Additionally,  multiple cortical cell types exist in species like tomato and rice (Henry et al. 2015), but only a single cortical cell type exists in Arabidopsis.  To understand this diversity we profiled tomato root cell type translatomes and chromatin accessibility.  Using xylem differentiation in tomato, relative to Arabidopsis, examples of functional innovation, repurposing and conservation of transcription factors are described.  Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function.  Finally, we extend these comparisons between Arabidopsis and tomato, to rice, and explore the question of homology between cell types across diverse species. 

Carmen Gonzalez-Ferrer 
MSc Candidate, Monaghan Lab 

Initial characterization of a subgroup of Arabidopsis group VIII receptor-like cytoplasmic kinases in immune and flowering time pathways

In order to defend against disease, plants have evolved a tightly coordinated signaling
network to rapidly prevent the spread of infection. Given the severity of yearly crop loss to pathogen threats, further understanding how plants defend against pathogens is vital to the improvement of current agricultural strategies. Receptor protein kinases on the plant cell surface recognize microbes and trigger phosphorylation-dependent signaling events, ultimately leading to genetic reprogramming. Receptor-like cytoplasmic kinases are key mediators of immune signal transduction, but many remain largely understudied. This thesis focuses on the group VIII RLCKs in Arabidopsis thaliana, also known as the AtPTI1-like kinases, for which an immune function has not been shown. Using a functional genomics approach, I demonstrate that a subgroup of the group VIII RLCKs regulate flowering time and may additionally function as negative regulators of immunity by mediating the oxidative burst. Additionally, I found that one of these RLCKs, PTI1-1, interacts with the negative regulator of defense CALCIUM -DEPENDENT PROTEIN KINASE 28 (CPK28) and the positive immune regulator BOTRYTIS INDUCED KINASE 1 (BIK1), further suggesting the involvement of these RLCKs in immune signal transduction. Broadly, this work has shown two novel functions for the AtPTI1-like kinase family in both defense and development, and primes future research for this previously uncharacterized group.
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We are going virtual! Please mark your calendars and get in touch if you want to present your work. The format is flexible but will typically be 20-30 min seminar followed by 20-30 min Q&A/discussion. 

We are looking forward to it! 

Joseph Quagraine
Masters Candidate, Regan Lab
Queen's University

Anthropogenic activities have led to widespread heavy metal contaminants such cadmium and arsenic. When left untreated, they pose risk to both human and ecosystem health as well as further reduce arable lands. Phytoremediation, which is the use of plants and their associated microorganisms to clean up such contaminants, is environmentally friendly, cost effective and fast-growing trees such as Populus sp. are good candidates for phytoremediation because of their tolerance of heavy metals, high biomass and their distribution across much of the northern hemisphere. However, the molecular mechanisms underlying poplar’s phytoremediation are poorly understood. Although Populus is a model tree species, with a sequenced genome and many genetic and genomic resources, the identification of genes for important tree traits is still slower than in other model plants such as Arabidopsis. This study uses a functional genomics approach to identify genes related to bioremediation by taking advantage of a large collection of activation tagged poplars (Populus tremula x P. alba hybrid 717-1B4) created by Dr. Sharon Regan’s  Lab. After screening over 1700 independent transgenic lines for characteristics that could affect phytoremediation, seven mutants had altered root biomass whereas 15 mutants had altered response to heavy metals. Of the seven root phenotypes identified, two previously studied mutants, called rippled leaf and adventitious root were further investigated. RT-qPCR analysis showed an up-regulation of CYCLIND1;2 and E3 ubiquitin-protein ligase XBAT32/33 in the roots of rippled leaf and adventitious root mutants respectively. The upregulation of CYCLIND1;2 is suspected to increase root biomass through accelerated cell cycle division. XBAT32/33 on the other hand is suspected to promote the production of lateral roots through the regulation of ethylene biosynthesis. Altogether, this study provides a starting point in the quest to discover key genes responsible for phytoremediation and could lead ultimately to the development of biomarkers for selection of superior trees from natural population for clean-up purposes.

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.