Diversity and selectivity in mRNA translation on the endoplasmic reticulum

Abstract

Pioneering electron microscopy studies defined two primary populations of ribosomes in eukaryotic cells: one freely dispersed through the cytoplasm and the other bound to the surface of the endoplasmic reticulum (ER). Subsequent investigations revealed a specialized function for each population, with secretory and integral membrane protein-encoding mRNAs translated on ER-bound ribosomes, and cytosolic protein synthesis was widely attributed to free ribosomes. Recent findings have challenged this view, and transcriptome-scale studies of mRNA distribution and translation have now demonstrated that ER-bound ribosomes also function in the translation of a large fraction of mRNAs that encode cytosolic proteins. These studies suggest a far more expansive role for the ER in transcriptome expression, where membrane and secretory protein synthesis represents one element of a multifaceted and dynamic contribution to post-transcriptional gene expression.

Figure 1. Revisiting translational compartmentalization

a | The model for translational compartmentalization that has been generally accepted since the discovery of the signal recognition particle (SRP) is presented. Translation initiation begins in the cytosol. Ribosomes translating mRNAs encoding cytosolic proteins that lack a topogenic endoplasmic reticulum (ER)-targeting signal remain in the cytosol. By contrast, ribosomes translating mRNAs that encode a protein containing a signal peptide or a transmembrane domain (such as secretory and integral membrane proteins) are targeted to the ER co-translationally by the SRP. Briefly, following translation initiation in the cytosol, the emerging topogenic signal serves as a targeting signal to the ER. Following docking on the ER translocon, the secretory and membrane proteins are translocated across or into the ER membrane. Upon completion of protein synthesis, ribosomal subunits are recycled into the cytosol. b | A pan-transcriptomic role for the ER in mRNA translation is depicted. Translation initiation can occur directly on the ER. Moreover, mRNAs that encode cytosolic proteins can also be translated by ER-bound ribosomes. Thus, a large fraction of the proteome can be translated by ER-associated ribosomes. Such a diverse and selective translation of mRNAs redefines this ubiquitous organelle as a primary site of proteome synthesis in the cell. Ribosomes translating mRNAs encoding cytosolic proteins associate with the ER via an unknown ribosome receptor (indicated by the question mark).

Figure 2. Distribution of protein synthesis between the cytosol and the ER

a | The distribution of translation between the cytosol and the endoplasmic reticulum (ER) for each mRNA is displayed as a histogram for HEK293 cells , mouse embryonic fibroblasts (MEFs) and Huh7 cells (R. Campos, S. Bradrick, D.W.R., M. Garcio-Blanco & C.V.N., unpublished observations). The histogram shows two distinct populations of mRNAs: one that is ER-enriched and one that is less so. The ER-enriched group of mRNAs tends to encode secreted or membrane proteins, whereas the other group generally encodes cytosolic or nuclear proteins. Importantly, essentially all mRNAs, even those encoding cytosolic proteins, are translated to a significant degree on the ER. b | In the cytosol, the translation machinery primarily synthesizes cytosolic proteins, as depicted by the nascent chains entering the cytosol. Data suggest that translation on the ER is also primarily directed towards the synthesis of cytosolic proteins and not only towards the synthesis of membrane and secreted proteins.

Figure 3. Assembling the translation machinery on the ER

a | The primary functional unit of translation is the polyribosome, which comprises an mRNA, an array of ribosomes along that mRNA, a series of nascent polypeptide chains in the process of synthesis and a diverse set of associated RNA-binding proteins. A polyribosome may initiate assembly on the endoplasmic reticulum (ER) by any one of its constituent parts. The well-established mechanism for compartmentalizing translation to the ER is the signal recognition particle (SRP) pathway, in which a signal sequence in the nascent polypeptide initiates binding of the ribosome and its elongating polypeptide (FIG. 1a). Several other modes of ER association for ribosomes and mRNAs have also been described. Ribosomes may associate with the ER independently of their encoded nascent chain and with mRNAs subsequent to their association with an ER ribosome receptor. In addition, RNA-binding proteins can confer direct, ribosome-independent mRNA binding. This system requires that only one of these components bind to the ER to enable assembly of an entire polyribosome, and it is also possible that a polyribosome is targeted to the ER via multiple mechanisms in parallel. b | A general framework for ribosome and mRNA movement between the cytosol and the ER is depicted. There are essentially two transitions that occur: first, the association of an mRNA and a ribosome to form an active translational unit and the corresponding dissociation; and second the movement of each of these components between the cytosol and the ER. The rate at which each of these transitions occurs would vary depending on the mechanism of ER recruitment. For example, in the SRP pathway (FIG. 1a), the sequence of events is initiation in the cytosol, movement of the translation unit to the ER and finally dissociation of the ribosomes from the mRNA and release into the cytosol. In an alternative model, ribosomes bind stably to the ER and undergo many successive rounds of mRNA translation without release to the cytosol; that is, rates of ribosome binding and release would be lower than those of translational units that are targeted by the SRP pathway. Measurement of these rates for different classes of mRNAs and ribosomes will be essential for understanding the relative importance of various mechanisms for recruiting translation to the ER.

Figure 4. The ER as a global mRNA translation and regulation hub

In this schematic, the diverse roles of the endoplasmic reticulum (ER) in global mRNA translation and regulation are depicted. The ER is the entry point of mRNAs encoding secretory and membrane proteins into the secretory pathway. Two modes of localization are shown. a | In one pathway, mRNAs encoding secretory and membrane proteins undergo initiation on free, cytosolic ribosomes and are targeted to the ER via the signal recognition particle (SRP) pathway. b | In the other pathway, many mRNAs, including those encoding secretory and cytosolic proteins undergo direct initiation on stably ER-bound ribosomes. c | Also shown are diverse ribosome receptors that are autonomous to translocation channels. These ribosomes can engage in the synthesis of cytosolic protein-encoding mRNAs, as well as mRNAs encoding topogenic signals. We propose that the receptor-bound, translationally active ribosome encounters an open translocation site by lateral diffusion in the ER membrane, with engagement of the nascent protein at the translocation site bringing the bound ribosome to close physical proximity to the protein-conducting channel. d | MicroRNA (miRNA)-mediated silencing is highly dependent on the ER. For endogenous miRNAs, RNA-induced silencing complex (RISC) loading, mRNA binding and Argonaute 2-mediated processing are associated with the ER membrane, whereas the cytosolic miRNAs remain inactive^,. Thus, compartmentalization subjects mRNAs to distinct regulatory environments depending on their localization, in which ER-localized mRNAs are targeted for silencing but the same mRNA in the cytosol may escape.