Changes in environmental conditions can affect gene expression at many levels. In general, alterations in transcription have been the most widely explored consequences of environmental perturbations, but changes at the level of the translation of specific mRNAs can also have profound effects on a cell's ability to respond to environmental stresses and to damage caused by toxins or other external agents. In addition, execution of critical genetic programs that determine a cell's fate and function - including many developmental processes - frequently begins at the translational level. Disregulation of the initiation phase of protein synthesis plays a role in the etiology of a variety of human diseases, from cancers to neurodegenerative disorders. The selection of the start codon in an mRNA by the translational machinery is a critical phase of gene expression because it determines both the N-terminus of the protein that will be produced and the reading frame of decoding. There is considerable circumstantial evidence that the fidelity of start codon recognition can be affected by environmental conditions - for example, exposure to stressors and toxins or changes in the levels of specific nutrients - and that these changes alter gene expression in ways that affect the physiology of the cell. Changes in the fidelity of start codon recognition could result in production of protein isoforms with different N-termini created by translation initiation from alternative start codons in the 5'-leaders of mRNAs. It could also change expression levels of proteins by modulating translation of regulatory upstream open reading frames in mRNAs. These alterations in gene expression could be harmful to the cell, if unprogramed, or beneficial, if they are part of a posttranscriptional gene regulatory mechanism that allows the cell to respond to its altered environment or internal or external signals. Using an established, high-throughput dual-luciferase assay for measuring the fidelity of start codon recognition we will: 1) Test the hypothesis that external conditions, signals and internal cues can modulate the fidelity of start codon recognition to alter gene expression at the translational level;2) Determine the effects of forcing changes in the fidelity of start codon recognition on cell physiology and gene expression. These studies have the potential to uncover a completely new mode of post-transcriptional gene regulation. They will also provide important insights into how environmental conditions affect gene expression at the translational level, as well as the consequences of these changes for cell physiology.

Public Health Relevance

Proteins are the molecular machines that perform most of the important tasks in cells. We will determine how changes in environmental conditions - for example, exposure to toxins - alters the production of proteins from the messenger RNAs that encode them. This information will deepen our understanding of how cells respond to exposure to harmful environmental conditions and how these conditions can produce diseases.

National Institute of Health (NIH)
National Institute of Environmental Health Sciences (NIEHS)
Exploratory/Developmental Grants (R21)
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Molecular Genetics A Study Section (MGA)
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Balshaw, David M
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University of California Berkeley
Schools of Arts and Sciences
United States
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McGlincy, Nicholas J; Ingolia, Nicholas T (2017) Transcriptome-wide measurement of translation by ribosome profiling. Methods 126:112-129
Sen, Neelam Dabas; Zhou, Fujun; Harris, Michael S et al. (2016) eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. Proc Natl Acad Sci U S A 113:10464-72
Sen, Neelam Dabas; Zhou, Fujun; Ingolia, Nicholas T et al. (2015) Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. Genome Res 25:1196-205