Regulation and outcomes of localized RNA translation

Abstract

Spatial segregation of mRNAs in the cytoplasm of cells is a well-known biological phenomenon that is widely observed in diverse species spanning different kingdoms of life. In mammalian cells, localization of mRNAs has been documented and studied quite extensively in highly polarized cells, most notably in neurons, where localized mRNAs function to direct protein production at sites that are quite distant from the soma. Recent studies have strikingly revealed that a large proportion of the cellular transcriptome exhibits polarized distributions even in cells that lack an obvious need for long-range transport, such as fibroblasts or epithelial cells. This review focuses on emerging concepts regarding the functional outcomes of mRNA targeting in the cytoplasm of such cells. We also discuss regulatory mechanisms controlling these events, with an emphasis on the role of cell mechanics and the organization of the cytoskeleton. This article is categorized under: Translation > Regulation RNA Export and Localization > RNA Localization.

Keywords: RNA localization; RNA transport; cytoskeleton; local translation; mechanical signaling.

FIGURE 1

mRNAs accumulate in various cytoplasmic regions and localization patterns display distinct dependencies on protein synthesis. Schematic depicting cellular regions where mRNAs can localize. Insets detail associations with membrane‐bound organelles, such as the endoplasmic reticulum (a) and mitochondria (b); defined membrane‐less structures, such as centrosomes (c); or cytosolic regions, such as foci (d) or cell protrusions (e), which are not associated with a specific organelle or structure. While in all cases mRNAs are undergoing translation (indicated by the appearance of the encoded nascent polypeptide [solid black line]), targeting can be translation‐dependent or translation‐independent, as indicated. Protein factors involved in each localization mechanism are shown and discussed in the text

FIGURE 2

Biological outcomes upon translation of localized mRNAs. (a) For mRNAs with a single main target destination, translation at the target site can act as a fail‐safe mechanism that ensures a productive biological outcome. For example, mRNA targeting to the endoplasmic reticulum, or on the surface of mitochondria, ensures proper maturation of the encoded polypeptide and its incorporation into the correct organelle. In an analogous way, concentration of mRNAs encoding partner subunits into cytoplasmic foci allows co‐translational interactions that promote correct assembly of multiprotein complexes. Absence of such a mechanism has deleterious consequences. (b) The presence of an mRNA at different cytosolic locations, X and Y, can affect the efficiency of its translation and the corresponding protein output. For example, the β‐actin and ribosomal protein mRNAs exhibit increased translation when found at protrusive lamellipodial regions of migrating cells. Altering the fraction of mRNA distributed between sites X and Y could be used to regulate cognate protein levels. (c) Translation of an mRNA at different cytosolic locations, X and Y, can tune the functional potential of the encoded polypeptide. For example, the RAB13 mRNA, which encodes a protein that can engage with multiple interacting partners (either activators or effectors), can be translated in either peripheral or perinuclear regions. Translation at a particular cytosolic location introduces the newly synthesized polypeptide into a local network of potential interactors, favoring certain interactions over others. Altering the fraction of mRNA distributed between sites X and Y can thereby shift the balance between biological outcomes

FIGURE 3

Mechanical regulation of mRNA localization. (a) The stiffness of the extracellular matrix modulates the distribution of cytosolic mRNAs. Stiff environments promote protrusion localization of APC‐dependent mRNAs (such as Ddr2) via a RhoA‐dependent mechanism that involves detyrosination of the microtubule network. (b) Localization patterns differ among cells in collectively invading 3D groups. During collective invasion of cancer cells, APC‐dependent mRNAs (such as NET1 and RAB13) localize prominently at the front of leader cells. This localization requires integrin‐mediated adhesion to the extracellular matrix (ECM) and coincides with a local accumulation of extracellular laminin. Notably, such an mRNA localization pattern is not observed in follower cells. (c) Spatial confinement modulates mRNA localization patterns. Ribosomal protein mRNAs (such as RPL27α) become more enriched at peripheral protrusions of cells migrating in confining microchannels. The localization of other mRNAs in confinement depends on the mechanical state of the cell. APC‐dependent mRNAs (such as RAB13) become preferentially enriched at leading protrusions of cell types that exhibit higher mechanical activity and stable, detyrosinated microtubules. This localization pattern can contribute to the efficiency of cell migration through confined spaces

FIGURE 4

Crosstalk between mRNA translation and the cytoskeleton. (a) Potential connections between the cytoskeleton and translation factors are shown. The translation elongation factor eEF1A can bind and regulate both microtubules and actin filaments. eEF1A binding to the cytoskeleton can likely reciprocally influence eEF1A's function in translation elongation. Phosphorylation of the translation initiation factor eIF2α is controlled by proteins (such as YIH1/IMPACT and PP1) whose activity is regulated by binding to monomeric G‐actin and can thus be influenced by the polymerization state of the actin cytoskeleton (see text for details). (b) Schematics depicting potential connections between local cytoskeletal organization and cytosolic domains associated with low or high translation of specific mRNAs. Left panel: Polarized migrating cells exhibit heterogeneous organization of the cytoskeleton with branched actin enriched in protrusive lamellipodia, stable microtubules oriented toward the front, and actin stress fibers attached to stable adhesions at the front or disassembling adhesions at the back. Right panels: Heat maps representing efficiency of mRNA translation along a migrating cell. The RAB13 mRNA is translated with similar efficiency in perinuclear regions and peripheral extending protrusions, while it is silenced at retracting areas. β‐actin mRNA translation is upregulated in the vicinity of focal adhesions at protrusive lamellipodia