Currently the lab has two main research themes:

Phaseolus Genomics
Phaseolus Genomics for Improved Bio-Product Development:
Relatively few genome sequences are available for Phaseolus vulgaris (dry beans) in public databases like GenBank. The lack of genomic information for the dry bean is a major anomaly for such important crop species in the world and it represents an important opportunity for a Ontario genomics effort to have a major international impact. The long-term objectives of the work are to accelerate the rate of genetic improvement in dry beans by developing genomics resources and tools for genomics-assisted improvement of Phaseolus for bio-product development. In the current study we are to focusing the genomics research in bean around five themes, namely: Read More

Elucidation and characterization of introgression mechanisms via the OAC-Rex P. vulgaris model:
OAC-Rex has a unique pedigree, that of a P. vulgaris cultivar (G-19833) introgressed with a distant relative P. acutifolius (PI440795). This known crossing event, called an introgression, provides a unique chance for insight into the mechanisms by which plants cope with the inherent associated genomic reorganizations. By assembling and analyzing the genomes of OAC-Rex, G-19833, and PI4401795, some light may be shed on this little understood, though widely used, process.

SCF ligase Regualtion
Systematic profiling of SCF E3 ligase regulatory attributes at play in cell cycle control and cancer:
Proteins act as the building blocks of the cellular machinery thus playing an essential role in a wide array of the cellular processes including regulation of cellular division as an important feature of human cancers. Functional regulation of these proteins over time is vital to ensure the proper functioning of cells. This regulation is governed in part by the regulated but competing processes of protein production and destruction. Since the destruction of proteins in cells is strongly directed via the ubiquitin-proteasome system (UPS) machinery, it is no surprise that defects in genes encoding the UPS machinery components haven been widely implicated in the development of several human cancers including breast, cervical, colon, renal, and prostate, as well as other developmental defects.

As components of the cellular UPS machinery, SCF complexes are responsible for targeting about about 20% of all proteins destined for controlled degradation, including onco-proteins and tumor suppressors. Aberrant regulation of SCF complexes is associated with the development of human cancers and other diseases, and as such, have become an established therapeutic target for treatment of cancer. In order to identify drug candidates with enhanced efficacy and reduced cytotoxicity, we need a better understanding of the regulatory mechanisms governing the activity of the UPS machinery in general, and SCF complexes in particular, as it relates to human cancer.

In collaboration with labs at Harvard University and the University of Toronto, we have recently discovered that one of the main components of the SCF complex, Skp1, is heavily modified in human cells. We have shown that Skp1 modification plays a significant role in the regulation of SCF assembly and activity and the interplay between SCF and other UPS members. As a key regulator of the UPS, Skp1 not only governs accumulation and degradation of cell cycle regulators, but may also serve structural roles during in the regulation of chromosome instability – an important cellular feature of cancerous cells. We are investigating this novel functional role of Skp1 and its contribution to tumorigenesis. We anticipate that this study will shed new light on how protein abundance is ultimately regulated, thus offering novel therapeutic targets and approaches for the regulation of cell division and DNA repair as key processes in the development of human malignancies.
Read More

Historical lab research themes:

Global Protein Profiling
High-throughput methods for identifying ubiquitinated proteins in Arabidopsis:
More than 5% of the Arabidopsis thaliana genome encodes for a wide variety of proteins involved in the ubiquitin-proteasome system (UPS); most notably, the Arabidopsis genome encodes for over 700 known or predicted F-box proteins, the substrate-specifying subunit of SCF complexes. Despite the breadth of known UPS components, very little is known about the number of proteins that are subject to regulation by the UPS. Thus far, the catalogue of candidate ubiquitinated proteins in Arabidopsis only comprises a few thousand proteins. Given the large number of UPS components, we anticipate that the actual number of ubiquitinated proteins vastly outnumbers the size of the current catalogue.

With a view towards expanding this catalogue, our group has adapted and employed the diglycine-scanning-based approach for the high-throughput identification of ubiquitinated proteins in Arabidopsis seedlings. Our preliminary studies have identified over 600 novel candidate proteins.

Castor Genomics
Castor as a Next-Generation Crop for the Biorenewable Chemical and Energy Sectors:
A combination of market pressures have resulted in significant increases in consumption and associated cost of petroleum-based energy. These forces have co-emerged with improvements in fuel production technology, such that fuels derived from biorenewable plant-based chemical feedstocks are now a viable opportunity within the global energy sector. The global biorenewable fuels industry, while expanding rapidly in both size and value, is nevertheless confronted with significant obstacles to future growth. Chief among these is the limited availability and cost of input agricultural feedstocks - particularly those based on food crops (e.g. corn starch, Canola oil and soybean oil). For ethanol or biodiesel production, Castor meets all these criteria, and is particularly attractive as a novel source of biorenewable oil feedstocks for the liquid fuel transportation sector. In this project we propose to develop and use advanced genomics tools to develop the Castor plant (Ricinus communis L.) as a non-food source of biorenewable energy. The specific project objectives include completion of the Castor genome sequence to a high quality, developing expression arrays, whole genome tiling arrays, and reverse-genetic resources, that will accelerate development of the crop into the Ontario regional and national sectors.

SCF ligase Regualtion
Functional Analysis of SKP1 orthologs in Arabidopsis thaliana:
Protein degradation is an important post-transcriptional gene regulatory process that allows cells to respond rapidly to changing environmental conditions by adjusting the steady state abundance of key proteins that regulate environmental responses, patterning, and development. One major process for targeted proteolysis in eukaryotes involves the Ubiquitin (Ub)/26S proteasome pathway. In which, proteins destined for degradation become modified by the covalent attachment of multiple Ub molecules under the action of E3 ligase complexes, followed by degradation via the 26S proteosome. SCF ligase, a well charcterized subclass of E3 Ligases, exhibits a quaternary structure that includes Cullin1/Cdc53, Rbx1/Roc1/Hrt1, Skp1, and F-box protein subunits. Structural analysis of a human SCF complex has shown that the Skp1 component acts as an adapter that associates Cullin to the F-box protein in the functional complex. The Arabidopsis genome contains 21 known or predicted Skp1-like (ASK) genes compared to only a single gene in both Baker's Yeast (S. cerevisiae) and Humans. The large number of ASK genes may reflect the unique adaptive strategy of plants versus animals, where plants are well-adapted to rapidly adjust their metabolic and developmental profiles in response to changing environmental conditions. All known or predicted products of the ASK gene family are believed to be part of SCF complexes (E3 ligases) but this has been directly demonstrated for only two of the genes in Arabidopsis - ASK1 and ASK2. Functional studies of a subset of the predicted ASK family of genes are being carried out initially using a reverse genetic approach. Artificial miRNA (amiRNA) constructs will be used to simultaneously interfere with the expression of single or multiple genes via a Dicer mechanism targeting common transcript sequences. We are also in the process of developing novel approaches to assess and characterize the regulatory pathways that are subject to hierarchical control via the 26S ubiquitinylation-mediated activity of select ASK genes.