Viral Targeting of Host Hubs: Interactions between the Rabies Virus and LC8

As obligate intracellular parasites, viruses rely on host machinery for their own reproduction. Viruses are therefore required to interact with a wide variety of host proteins, despite limitations in viral genome size. The most parsimonious method of success is to hijack central and essential proteins, known as hub proteins. LC8 is a notable example of a hub protein, and has been shown to interact with more than 100 eukaryotic partners in various unrelated pathways. An increasing number of studies have noted interactions between LC8 and viruses, including the Ebola, rabies, and rotaviruses; however, LC8’s role within these systems is unclear. This thesis examines the structural and functional properties of hub proteins, with a particular focus on LC8 and its interactions with the rabies virus. Three chapters of original work include two primary research reports and one review/opinion piece. The first research report, Chapter 2, structurally characterizes the interaction between LC8 and the rabies virus phosphoprotein (RavP). We use insights gleaned from our structural studies to predict and test potential roles for LC8 in the rabies virus infection cycle, and demonstrate that LC8 is important for efficient viral polymerase activity. Chapter 3 is an in-depth study of the LC8 recognition motif, where we examine both the structural and functional plasticity of LC8, and identify and validate many new LC8 interactions. We also develop a tool that can be used to predict LC8 binding motifs in proteins of interest, which will greatly improve the ability of those outside of the LC8 field to recognize, test, and validate partner proteins. In Chapter 4 we present a variety of new ideas about what qualities describe a linear motif-binding hub protein. This work provides ideological and linguistic suggestions for important structural and functional features of hubs that underlie their plasticity. It then further describes how viruses take advantage of these features to more efficiently hijack host pathways. Finally, Chapter 5 discusses the impacts of my thesis work, and outlines some potential future projects. Each individual chapter builds on the previous one to create an expanding view of the importance of linear motif-binding hubs for infectious viruses

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Systematic identification of recognition motifs for the hub protein LC8

Hub proteins participate in cellular regulation by dynamic binding of multiple proteins within interaction networks. The hub protein LC8 reversibly interacts with more than 100 partners through a flexible pocket at its dimer interface. To explore the diversity of the LC8 partner pool, we screened for LC8 binding partners using a proteomic phage display library composed of peptides from the human proteome, which had no bias toward a known LC8 motif. Of the identified hits, we validated binding of 29 peptides using isothermal titration calorimetry. Of the 29 peptides, 19 were entirely novel, and all had the canonical TQT motif anchor. A striking observation is that numerous peptides containing the TQT anchor do not bind LC8, indicating that residues outside of the anchor facilitate LC8 interactions. Using both LC8-binding and nonbinding peptides containing the motif anchor, we developed the "LC8Pred" algorithm that identifies critical residues flanking the anchor and parses random sequences to predict LC8-binding motifs with similar to 78% accuracy. Our findings significantly expand the scope of the LC8 hub interactome

TRY plant trait database - enhanced coverage and open access

10.1111/gcb.14904GLOBAL CHANGE BIOLOGY261119-18