Proteome Expression: The Subcellular Organisation of Protein Synthesis

Abstract

Proteome expression is the integrated output of gene transcription, messenger ribonucleic acid (mRNA) stability, mRNA translation and protein stability, and varies between cells, tissues and organs. Proteome expression is dynamic and can be readily modified in response to stress, cell cycle progression, pathogenic infection and malignant transformation. With recent advances in single molecule optical imaging and high‐resolution genomic analyses, increased attention has turned to the spatiotemporal regulation of proteome expression at the subcellular level. With this interest has come a reinvestigation of a fundamental question in cell biology – the subcellular organisation of mRNA transcriptome expression. Although it is widely accepted that eukaryotic cells partition proteome expression, with soluble proteins being synthesised on cytoplasmic ribosomes and secretory/integral membrane proteins on endoplasmic reticulum (ER)‐bound ribosomes, recent data indicate a far broader role for the ER in proteome expression.

Key Concepts

  • Ribosomes, the cellular machines that perform protein synthesis, are present in the two primary protein synthesis compartments of the eukaryotic cell, the cytosol and endoplasmic reticulum (ER).
  • mRNAs are largely partitioned between the cytosol and the ER on the basis of their encoded gene product, with cytosolic protein‐encoding mRNAs being translated by cytoplasmic ribosomes and secretory/membrane protein‐encoding mRNAs undergoing translation on ER‐bound ribosomes.
  • The mechanisms governing mRNA and ribosome partitioning between the cytosol and ER compartments are largely unknown.
  • Recent studies have revealed that ER‐bound ribosomes are broadly engaged in the translation of the mRNA transcriptome.
  • A role for the ER in the expression of the cellular proteome can now be considered.

Keywords: protein synthesis; mRNA localisation; translation; ribosome; endoplasmic reticulum

Figure 1. The signal recognition particle (SRP) pathway: A mechanism formRNAand ribosome localisation to the endoplasmic reticulum. The SRP pathway provides a mechanism for the localisation of secretory/membrane protein‐encoding mRNAs, as ribosome‐engaged transcripts, to the ER. In the SRP model, mRNAs undergo translation initiation in the cytosol, on cytosolic ribosomal subunits. Upon emergence of a topogenic signal (signal sequence or transmembrane domain), SRP associates with the ribosome/mRNA/nascent chain complex and directs its localisation to the ER via interaction with the SRP receptor. Following release of the SRP, the ribosome/mRNA/nascent chain complex then associates with the Sec61 translocon and translation/translocation ensues. At the termination of protein synthesis, ribosomes dissociate into their component subunits and are released into the cytosol. The SRP pathway thus comprises two cycles, a ribosome association/dissociation cycle (ribosome cycle) and an SRP association/dissociation cycle (SRP cycle), that direct mRNA and ribosome partitioning between the cytosol and ER compartments.
Figure 2. The translational landscape of the endoplasmic reticulum is biased to cytosolic protein‐encodingmRNAs: Experimental strategies and results. (a) Experimental strategies. Depicted is the experimental strategy used by the author's laboratory to examine steady‐state mRNA partitioning between the cytosol and ER compartments. Tissue culture cells are first treated with a digitonin‐supplemented buffer to release the cytosolic contents, efficiently releasing cytosolic ribosomes and polyribosomes. The permeabilised cells are then detergent solubilised to release ER‐bound ribosomes. Using RNA‐seq and Ribo‐seq approaches, the subcellular distributions of both mRNAs and their translations can be determined. (b) ThemRNAlandscape of theER. Illustrated are the relative fraction of mRNAs encoding cytosolic proteins (green) and secretory/membrane proteins (red) present on the ER. Data are from the indicated studies and include data sets obtained in human‐derived cell lines and in the yeast S. cerevisiae.
Figure 3. Working model describing the subcellular organisation of proteome expression. In this model, multiple cellular pathways contribute to the steady‐state mRNA partitioning patterns depicted in Figure. In the SRP pathway, secretory/membrane protein mRNAs that undergo translation initiation on cytosolic ribosomes (1) are efficiently localised to the ER (2). In parallel, both cytosolic and secretory/membrane protein‐encoding mRNAs can undergo de novo translation initiation on ER‐bound ribosomes (3). This may be a stochastic process and/or may include direct mRNA localisation to the ER, for subsets of both mRNA cohorts. Because cytosolic mRNAs predominate in the mRNA transcriptome, the translational landscape of the ER is thus primarily devoted to the translation of cytosolic mRNAs. ER‐bound ribosomes that initiate translation of secretory/membrane protein mRNAs diffuse in the ER membrane to access and/or associate with an ER translocon (4). A central prediction of this model is that a large fraction of ER‐bound ribosomes are stably associated with the ER and exchange with the cytosolic pool very slowly (5), perhaps with half‐times of hours. Such stable ribosome–ER interactions are predicted to be a significant if not primary driver of steady‐state mRNA distributions in the cell.
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Hsu, Jack C‐C, and Nicchitta, Christopher V(Jun 2018) Proteome Expression: The Subcellular Organisation of Protein Synthesis. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005718]