Biology

Dr. Sanchari Bhattacharyya
Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138, USA

Abstract:

A mechanistic understanding of effect of mutations at the genomic level on fitness (genotype-phenotype relationship, GPR) is a central challenge in modern biology. We address this problem bottom up by probing effect of mutations on molecular properties of macromolecules as well as through multiscale analyses that span several levels of biological organization.

In the first part of this talk, I will describe our recent work to understand fitness effects of synonymous substitutions in prokaryotic genes. We find that synonymous substitutions at the N-terminus as well as far-downstream of genes affect interactions between the coding region and the upstream Shine–Dalgarno (SD) sequence through mRNA folding, which modulates the efficiency of translation initiation to affect intracellular mRNA, protein levels as well as fitness. We also elucidate the crucial role of the transcription termination factor Rho in dictating these effects. Along with a complementary statistical analysis of the E. coli genome which specifically implicates avoidance of intra-molecular base-pairing with the SD sequence, these data shed light into the proteome-wide effects of codon usage bias.

In the next part, I will discuss the mechanistic origin of conservation of protein abundances in the cell. Using bacterial Dihydrofolate Reductase (DHFR) protein as a model system, we find that the fitness landscape of protein abundance has an optimum at physiological concentration, while both up and down-regulation are toxic. In case of down-regulation, loss in DHFR activity triggers a metabolite imbalance which leads to inhibition of an essential pyrimidine biosynthesis enzyme, eventually resulting in loss of a DNA building block and bacterial filamentation. In the over-expression regime, a very similar metabolic imbalance and filamentation is however triggered by a completely different mechanism: interactions of excess DHFR with several functionally related enzymes in a metabolon. Along the same lines, we uncover dramatic difference of over-expression toxicity between “E. coli’s own DHFR” and “orthologous foreign DHFR”, which suggests the crucial role of evolutionary selection in shaping the PPI network in cells. Overall, these studies highlight the pleiotropic nature of mutations and the complex multi-layered feature of genotype-phenotype relationships.