What we do
From New Start for Protein Synthesis to Plant-Virus interaction
Plants respond to pathogen attack by activating defense-related gene expression to confer pathogen resistance. On the other side, when plant viruses infect plants, they hijack host systems to drive expression of their genes for virus functions. Both of these types of gene expression can be achieved through modulating the mRNA translation process, which determines when and how a gene is translated to enable rapid and reversible control of protein expression diversity. Thus my lab has a long-term interest in the translational control for plant defense response and plant virus pathogenesis. We especially focus on exploring novel translation initiation sites and hidden genes and, by integrating molecular and computational biology techniques, we aim to elucidate the mechanistic basis of how these novel initiation sites are specified and the biological basis of how these hidden genes functions in plant-virus interactions.
In order to apply scientific discoveries from the laboratory to the field, we employ two plant model systems: Arabidopsis, the most well-studied plant species with extensive, experimentally derived gene annotations/functions and mutant resources, and Solanum lycopersicum (tomato), an economically important crop with good genome quality for investigating plant-pathogen interaction and its impact in crop growth and fruit quality. Plant begomovirus is a DNA virus that primarily infects various dicotyledonous crops such as tomato and cucumber and causes leaf curling/chlorosis, stunted growth and consequently significant loss of crop yield. Thus the systemic investigation of plant defense response in both Arabidopsis and tomato and of pathogenic mechanisms in plant viruses are timely and critical; knowledge gained will facilitate the development of defensive strategies to be applied in agriculture.
Specific research lines
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Exploring hidden AUG/non-AUG translation initiation sites (TISs) and translational pausing for plant gene expressions:
To fulfil the knowledge gaps from genome sequences to gene annotation and from the hidden open-reading frames (ORFs) to the biological importance, my group (1) employs a state-of-the-art technique, ribosome profiling, that based on deep sequencing of ribosome–protected mRNA fragments enables the global profiling of in vivo TISs and the characterization of the ORFs translated on genomes; (1.2) develops bioinformatics and prediction biology approaches to identify the hidden non-canonical (i.e., unannotated) ORFs and their underlying recognition mechanisms; (1.3) performs molecular and genetics approaches to investigate the biological impacts of non-canonical ORFs.
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Decipher the pathogenic mechanisms of novel ORFs in plant begomoviruses:
Plant viruses employ non-canonical translational strategies to increase their coding capacity of genomes. However, the diverse translational strategies pose a great challenge to defining the full set of viral genes. Using plant begomovirus as a model system, we address two main questions: (2.1) to what extent the unanticipated ORFs occur in plant virus genomes; and (2.2) what their functional significance and mechanistic basis are in viral pathogenicity. We have successfully identified a dozen of hidden viral ORFs by experimentally mapping TISs and demonstrated that these ORFs encode novel viral factors that influence pathogenesis in begomovirus. These findings facilitate the next step of elucidating the mechanistic basis of how these new factors coordinate viral life cycles and pathogenesis in plants and how plant viruses preferentially employ specific TISs through the control of alternative transcription/translation initiation sites.
