Our lab is interested in how plants respond to changes to both their internal and external environments.

We are elucidating

i) the role of ribosomal biogenesis factors in the synthesis of the plant ribosome and
ii) the molecular plant-pathogen interactions involved in clubroot disease.

Generating a functional ribosome requires several rRNA processing events in co-ordination with 200 ribosome biogenesis factors (RBFs). Synthesis of RBFs is often tightly coupled with cellular growth rate due to cellular homeostasis. Ribosome biogenesis has been extensively studied in bacteria, yeast and to some degree in mammals; however, little has been reported in plants. Does ribosome biogenesis in plants follow a similar pathway to that already established in yeast? Unlike yeast, the Arabidopsis (model dicot plant) genome encodes a number (1-5) of isoforms for each of the ~200 RBFs identified in yeast. Using techniques such as: yeast mutant complementation, yeast two hybrid analysis, confocal microscopy, qRT-PCR, plant knock-out and knock-down mutants, bioinformatics and plant physiology, cell biology and biochemistry, we are identifying the need for each RBF (and isoform) in plant ribosome biogenesis. The RBF work is a new direction for the lab as previously we have focused on large and small subunit ribosomal proteins and their role in a functional ribosome.

Papers on the plant ribosome

• RP Savard & PC Bonham-Smith (2014) Differential transcript accumulation and subcellular localization of Arabidopsis ribosomal proteins, Plant Science 223: 134-145.
• RP Savard & PC Bonham-Smith (2013) Charge versus sequence for nuclear/nucleolar localization of plant ribosomal proteins, Plant Mol Biol 81: 477-493.
• KB McIntosh, RF Degenhardt & PC Bonham-Smith (2011) Sequence context for transcription and translation of the Arabidopsis RPL23aA and -B paralogs, Genome 54:(9) 738-751.
• RF Degenhardt & PC Bonham-Smith (2008) Arabidopsis ribosomal proteins RPL23aA and –B are differentially targeted to the nucleolus and are disparately required for normal development, Plant Physiol 147: 128-142
• RF Degenhardt & PC Bonham-Smith (2008) Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog, Planta 228: 627-640. 

Plasmodiophora brassicae is a soil borne pathogen of cruciferous plants and the causal agent of clubroot, a devastating disease of Brassica crops. While the emphasis in research over the past few years has led to the successful identifications of a few resistance (R) genes in canola and other Brassica species, the matching avirulence (Avr) genes in P. brassicae have still to be identified. The interaction between the pathogen effectors (Avr) and their host targets is crucial for pathogen success, leading to plant susceptibility to disease. We have collected comprehensive RNA-seq data from P. brassicae-infected root tissues of Arabidopsis at several different infection stages and are currently in the process of carrying out a genome-wide identification and functional characterization of P. brassicae effectors, identifying candidate host targets of key effectors and developing P. brassicae pathotype-specific sequence markers to be used to evaluate genetic diversity and population structures of P. brassicae in canola fields across the prairies.

Papers on clubroot

J Tu, J Bush, PC Bonham-Smith & Y Wei* (2018) Live cell imaging of Plasmodiophora brassicae - Host plant interactions based on a novel two-step axenic culture system, MicrobiologyOpen e765. https://doi.org/10.1002/mbo3.765.
E Pérez-López, M Waldner, M Hossain, AJ Kusalik, Y Wei, PC Bonham-Smith & CD Todd* (2018) Identification of Plasmodiophora brassicae effectors – a challenging goal, Virulence 9:1 1344-1353. https://doi.org/10.1080/21505594.2018.1504560
S Irani, B Trost, M Waldner, N Nayidu, J Tu, A Kusalik, C Todd, Y Wei & PC Bonham-Smith* (2018) Transcriptome analysis of response to Plasmodiophora brassicae infection in Arabidopsis shoot and root, BMC Genomics 19: 23. doi : https://doi.org/10.1186/s12864-017-4426-7