A hallmark of the eukaryotic cell is its organization into organelles, spatial compartments that house specialized chemical environments needed to carry out critical biochemical reactions for the cell. The array of different organelles requires vastly different internal components. Regulated protein import into organelles is a defining property of a given organelle, and is thus a major step in the functioning of a healthy cell. The process of import machinery gene expression and organelle biogenesis must therefore be coordinated in space and time. Failure of this coordination can be severely detrimental to the cell: many import machinery proteins are known to have an intrinsic ability to aberrantly insert into incorrect organelle membranes. This observation begs the following questions: how is import machinery gene expression spatiotemporally quantitatively coordinated with organelle biogenesis within individual cells? To answer these questions, we turn to the peroxisome of Saccharomyces cerevisiae as a model system. The peroxisome is central for fatty acid metabolism in yeast. There are several key properties that render the peroxisome import machinery (PIM) an attractive model system to answer our overarching question, but perhaps the most intriguing is that many PIM mRNAs exhibit strong localization to the peroxisome upon culture of cells in fatty acid rich media. This suggests that mRNA localization might play a major role in coordinating PIM gene expression with peroxisomes by spatially linking translation with the organelle. The results of the experiments proposed below will for the first time quantitatively illuminate the role of spatial control of gene expression in a defining aspect of organelle biogenesis, regulated protein import, and thus function.
Our Specific Aims are organized around addressing the following question: what is the functional role of localizing PIM mRNAs to the peroxisome? The overall hypothesis we will test in each Aim is that localization of the PIM mRNAs coordinates gene expression with peroxisome biogenesis in order to prevent mislocalization of the encoded proteins to non-peroxisomal membranes.
In Specific Aim 1 we detail a broad, quantitative characterization of spatiotemporal PIM gene expression dynamics following induction of peroxisomal function by the fatty acid oleic acid.
In Specific Aim 2 we test whether specifically mislocalizing the transcripts studied in Specific Aim 1 decreases the efficiency or precision of PIM protein targeting to the peroxisome. The results from this Aim will allow us to conclude how much of the precision of PIM protein targeting to peroxisomes is a consequence of spatial proximity of the PIM mRNA to the peroxisomal surface.
In Specific Aim 3 we determine whether the components responsible for trafficking peroxin mRNAs to the peroxisome act on cis sequence elements on the mRNA or in trans following initiation of translation.

Public Health Relevance

Regulating the function of cell organelles by spatially localizing the mRNAs that encode their proteins is thought to control a surprisingly diverse set of biological processes, from learning and memory to tumor cell growth advantages. Using fluorescence imaging techniques capable of visualizing individual mRNA and protein molecules, we will characterize the ability of localized control of gene expression to regulate organelle function using as a model system the Saccharomyces cerevisiae peroxisome, an organelle responsible for fatty acid metabolism and many of whose proteins are encoded by localized mRNAs. We hope to capture this quantitative data in a general framework that describes the precision with which the cell can regulate peroxisomal import machinery content by localizing their mRNAs to the organelle, with the hope that this framework will also inform studies on mRNA localization in contexts ranging from neuroscience to cancer.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Postdoctoral Individual National Research Service Award (F32)
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Special Emphasis Panel (ZRG1-F08-Q (20))
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Sakalian, Michael
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Harvard University
Schools of Arts and Sciences
United States
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Mukherji, Shankar; O'Shea, Erin K (2014) Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance. Elife 3:e02678
McDonald, Richard I; Guilinger, John P; Mukherji, Shankar et al. (2014) Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat Chem Biol 10:1049-54