Understanding the Protein Homeostasis Network

Proteins, important building blocks in the human body, must fold into active conformations to perform their biological functions (Fig 1). If proteins mis-fold or unfold cellular protein homeostasis, or proteostasis, is disturbed. When proteostasis is disturbed, whether by genetic mutations, aging, infection, or environmental stressors, a suite of stress-responsive signaling pathways are activated to correct the misfolding defect and promote an adaptive response. For example, when proteostasis is disturbed in cytosol, a transcription factor known as Hsf1 is induced to initiate a signaling pathway known as the heat shock response (HSR, Fig 2).     

When proteostasis is disturbed in the secretory pathway, three endoplasmic reticulum (ER)-resident proteins, Ire1, PERK and Atf6 are activated to initiate a network of signaling pathways, collectively known as the unfolded protein response (UPR). Both HSR and UPR are rapid gene-expression programs to correct disturbed proteostasis, and conserved from yeast to humans. Yet, our understanding of their mechanisms at the molecular level is still limited. With new findings emerging constantly, we must fully elucidate the pathway if we want to eventually target it therapeutically. In a major goal, we are studying at the molecular level how cells maintain proteostasis via stress-responsive signaling pathways. Our model system is the UPR, which maintains secretory pathway proteostasis. We study this conserved pathway in yeast using molecular genetics tools, and extend key findings to metazoan cells. Using elegant yeast genetic system, we have identified that the lipid kinase Vps34 [an ortholog of human phosphoinositide 3 (PI3)-kinase] significantly contribute to the UPR. We are studying how PI3 kinases in both yeast and human cells integrate the UPR pathways and govern the adaptation against the proteostasis disturbances.

            In a second major goal, we are studying how HAC1 mRNA in yeast Saccharomyces cerevisiae is translationally repressed and how transcription factor Hac1 simultaneously activates a suit of protein-folding enzymes and chaperone genes in the chromosomes.  Our specific goals are: to decipher the rules governing the translational control by mRNA 2⁰ structures

            Protein synthesis, or translation, is a conserved process where amino acids are linked together on ribosomes directed by genetic information present in the messenger RNA (mRNA). It is a highly regulated process to produce an optimum amount of protein. A typical matured mRNA (Fig 3) in eukaryotes has a 5′-untranslated region (5′-UTR, leader), a protein-coding domain and a 3′-untranslated region (3′-UTR, trailer) sandwiched by a 5′-cap and a 3′-poly (A) tail. The un-translated regions vary in their lengths and nucleotide (nt) compositions, ranging from a few nucleotides to several thousand nucleotides (median ~53-nt in yeast and ~218-nt in humans). UTRs may fold into a variety of shapes (e.g., simple RNA hairpin to complex tertiary structure),which control transport of mRNA, localization of mRNA and modulate the rate

 of translation. However, the current knowledge about the effects of mRNA 2⁰ structure or fold (mRF) on translation is still limited, even though high-throughput technologies (e.g., RNA-seq and ribosome profiling) have identified the translated regions in the genome and translation efficiency. Indeed, ribosome profiling does not provide any insights into how ribosomes are recruited to mRNA and how cis-regulatory elements (Fig 3) within mRNA (e.g., mRFs) collectively orchestrate the translational output. Moreover, it is not yet clear whether an mRF is sufficient to facilitate or block translation, whether it requires trans-regulatory factor(s), or the relevant mechanism is tailored to the specific structured mRNA. So, gene-specific studies are needed to unravel how each gene is regulated to produce an optimum amount of protein. Our objective is to decipher the rules of translational control by secondary structures. Currently, we have focused on HAC1 mRNA in yeast Saccharomyces cerevisiae, containing a stable RNA 2⁰ structure at its 5′-UTR.