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Theory and Modelling of Biological Systems

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Retracing the evolution of complex cells

We are interested in the ancient origins of the eukaryotic compartmentalized cell plan. Surprisingly little is known about this key phase of the evolution of life: eukaryotes began to diverge from bacteria during the global oxygenation event 2.5 billion years ago, but all living eukaryotes share a more recent common ancestor dating from about 1.5 billion years ago. Data from modern eukaryotic genomes might allow us to reconstruct the intervening billion-year period during which quintessential eukaryotic features emerged: the nucleus, mitochondria, compartmentalized organelles, the cytoskeletal machinery, and vesicle traffic. In particular, we are pursuing two complementary research directions. Forward in time: we analyze potential origin scenarios using biophysical and evolutionary simulations, to uncover general principles about the evolution of compartmentalized cells. Backward in time: we study the evolution of the molecular machinery underlying compartmentalization using sequence data and phylogenetic techniques; we especially concentrate on molecules that underwent eukaryote- specific gene family expansions, including Rabs, coat proteins, and SNAREs. The population- genetic mechanisms that generated the earliest compartmentalized cells continue to drive the diversification of eukaryotes. Our evolutionary perspective might therefore shed light both on ancient events as well as on modern lineage-specific and tissue-specific elaborations of traffic systems. 

 

  • Ramadas R, Thattai M (2013) New organelles by gene duplication in a biophysical model of eukaryote evolution. Biophys. J. 104: 2553.
  • Anand R, Thattai M (2013) Interactions among quorum sensing inhibitors. PLoS ONE 8: e62254.
  • Thattai M (2013) Using topology to tame the complex biochemistry of genetic networks. Phil. Trans. Roy. Soc. A 371: 20110548.
  • Brodsky F, Thattai M, Mayor S (2012) Evolutionary cell biology: Lessons from diversity. Nature Cell Biol. 14: 651.
  • Rai N, Anand R, Ramkumar K, Sreenivasan V, Dabholkar S, Venkatesh KV, Thattai M (2012) Prediction by Promoter Logic in Bacterial Quorum Sensing. PLoS Comp Biol 8: e1002361.

 

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Simons Centre for the Study of Living Machines