Gene-Wei Li

Quantitative Biology of the Central Dogma

Life is made of floppy molecules that live on thermal fluctuations. Yet precise and quantitative behaviors emerge from these materials. Most of us have exactly 5 fingers on each hand. Even at the cellular level, the output of gene products and enzymatic pathways are tuned at a quantitative level. We are working toward deciphering the physical principles behind the precise control of transcription and translation. At the systems level, we are also interested in how these quantitative outputs from genes are optimally interconnected with the entire proteome and metabolome of a cell. Our approach combines technical development of quantitative tools, genomics analysis, and biophysical modeling. Our ultimate goal is to be able to predict and engineer precise protein production and cellular physiology.

Quantitative Control and the Central Dogma

We aim to understand how cells fine-tune their RNA and protein production. When you order meatballs at an Ikea restaurant, you always get exactly 15 meatballs per order (fewer if you are outside the US). That is because your server can count. But how does a cell specify how many proteins it needs? We have uncovered that bacteria and yeast have a remarkable ability to make the right amount of proteins that come together to form a stoichiometric complex. This is coded in their DNA sequence and must be achieved through simple physics and chemistry that we have yet to understand. Our lab is tackling this fundamental problem, which has wide-reaching implications in both basic and synthetic biology.

Assembly of Complex Multiprotein Machinery

Almost every cellular process is mediated by a complex machine made of multiple proteins and/or RNAs (e.g. RNA polymerases and ribosomes). Proper assembly of these machines is critical for their function. Furthermore, mis-assembled proteins are not only wasteful, they are prone to aggregation and can disrupt properly assembled complexes, thus acting as a dominant negative. Because an individual complex is composed of an integer number of each subunit, its assembly is by default a quantitative problem. We are interested in how cells coordinate their expression and assembly under distinct environmental condition or in different cell types. We are also using the principles we have discovered to discover and further characterize the molecular complexes that make life possible.

Quantitative Cell Biology

The ability to precisely measure the rate of protein production and proteome composition gives us a unprecedented opportunity to start understanding cell biology at a quantitative level. In particular, we are interested in how the production of a given protein is connected to the physiology of the entire cell. We use bacteria and yeast as model systems to discover the rationales for protein expression levels. Our goal is to establish a quantitative framework for addressing this question, which can be translated into human diseases where a twofold change in protein expression can have devastating effects.

Li GW, Burkhardt D, Gross CA, Weissman JS. Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources. Cell 157, 624 (2014).

Li GW, Oh E, Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484, 538 (2012).

Wang W*, Li GW*, Chen C*, Xie XS, Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333, 1445 (2011). *equal contribution

Li GW, Xie XS. Central dogma at the single-molecule level in living cells. Nature 475, 308 (2011).

Taniguchi Y*, Choi PJ*, Li GW*, Chen H* et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329, 533 (2010). *equal contribution

Li GW, Berg OG, Elf J. Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nature Physics 5, 294 (2009).

Elf J*, Li GW*, Xie XS. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191 (2007). *equal contribution