Meng Xu, Genome-wide inference of signal transduction pathways in Arabidopsis thaliana identifies new signaling architectures. Luke Mackinder, Systematic high-throughput localization of novel components of the Chlamydomonas carbon concentrating mechanism

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Meng Xu Abstract:

Plant cells typically perceive extracellular signals by receptors and respond by regulating the expression of specific genes. While plants perceive and process a myriad of signals from the environment, only a few signaling pathways have been elucidated at the molecular level. To expedite the discovery of signaling pathways, we developed a statistical framework to predict signaling pathways from protein interaction networks. We focused on the large family of plant receptors called receptor-like kinases (RLKs) to identify the pathways from RLKs to transcription factors (TFs).

We leveraged the recent elucidation of omics data such as large-scale protein interaction data, including those between membrane proteins, protein functional associations and gene co-expression networks to systematically determine potential signaling pathways between RLKs and TFs. The model is built directly from protein-protein interaction (PPI) network by a semi-supervised approach to maximize the discovery of novel signaling pathways. The method successfully rediscovered known signaling pathways, and predicted new ones that will be tested experimentally.

Luke Mackinder Abstract:

Green algae use a carbon concentrating mechanism (CCM) to improve their photosynthetic efficiency; however the mechanism of the CCM remains elusive and few components have been identified. We have developed a high-throughput pipeline for determining the localization of Chlamydomonas proteins by expressing proteins tagged with fluorophores. Using this approach, we have systematically determined the localization of over one hundred candidate proteins. Strikingly, this approach identified several novel CCM components that localize to the pyrenoid, the central carbon-fixing organelle. The proteins show distinct sub-pyrenoid localizations, suggesting that this organelle is more complex than previously thought. These results pave the way for transfer of the green algal CCM into C3 plants to increase their photosynthetic efficiency.