Page 67 - CSIR-IGIB Annual Report 2020-21

Linking metabolism to cellular proteostasis Using lab evolution to help proteostasis
Cellular proteostasis is defined as the Laboratory adaptation has been used for a long
homeostasis of protein biogenesis that includes time to obtain mechanistic understanding on
protein translation, folding, translocation, different pathways including drug targets,
modification, and degradation. A large body of cellular metabolism, and disease progression.
literature exists supporting the role of protein This technique, in conjunction with genome
chaperones and quality control machinery that sequencing also have the potential to unravel
aid in these different steps of proteostasis. Our cryptic pathways that may contribute to cellular
group is interested in unraveling the role of proteostasis. Our lab is currently focusing on
small molecules in maintaining the different using this approach to identify pathways that
branches of proteostasis. We were able to are crucial for protein folding in vivo. To develop
develop a deep-mutational scanning based cells that have better protein folding capacities,
technique to monitor proteostasis. This allowed we have evolved cells (E. coli and
us to look at perturbation of intracellular Saccharomyces cerevisiae) to handle thermal
proteostasis with a very high resolution. With stress. Typically heat shock causes proteins to
this technique we were able to show that misfold in addition to other problems. We posit
changes in cellular metabolism affects cellular that chronic heat shock should force cells to
proteostasis. Conversely, we also find changes adapt and upregulate pathways that can take
in cellular metabolism in response to problems care of chronic misfolding without the fitness
in proteostasis. Using in vitro biophysical tools, loss associated with overexpression of
we were able to show that metabolites that chaperones. We have characterized these
change during protein folding problems inside evolved lines using genomic and transcriptomic
the cell have the potential to aid protein folding. tools and based on these, have formulated our
In the future it will be important to delineate hypothesis. We will try to identify the genetic
how changes in protein folding signal changes in components that are responsible for better
metabolism. It will also be important now to proteostasis in these cells. Subsequently we will
check if metabolic alteration could be a viable work towards development of strategies to
route to alleviate protein misfolding problems modulate the activity of these pathways to
in animal models of human diseases. perturb proteostasis in yeast models of human
diseases involving protein misfolding.
Publications

Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis. Verma
K, Saxena K, Donaka R, Chaphalkar A, Rai MK, Shukla A, Zaidi Z, Dandage R, Shanmugam D, Chakraborty K. Nat
Commun. 2020 Jun 10;11(1):2926.

GROEL/ES buffers entropic traps in folding pathway during evolution of a model substrate. Sadat A, Tiwari S, Verma
K, Ray A, Ali M, Upadhyay V, Singh A, Chaphalkar A, Ghosh A, Chakraborty R, Chakraborty K, Mapa K. J Mol Biol.
2020 Sep 18;432(20):5649-5664.

Annual Report 2020-21 64