Current Protein and Peptide Science - Volume 13, Issue 4, 2012

At all steps from transcription to translation, RNA-binding proteins play important roles in determining mRNA function. Initially it was believed that for the vast majority of transcripts the role of RNA-binding proteins is limited to general functions such as splicing and translation. However, work from recent years showed that members of this class of proteins also recognize several mRNAs via cis-acting elements for their incorporation into large motor-containing particles. These particles are transported to distant subcellular sites, where they become subsequently translated. This process, called mRNA localization, occurs along microtubules or actin filaments, and involves kinesins, dyneins, as well as myosins. Although mRNA localization has been detected in a large number of organisms from fungi to humans, the underlying molecular machineries are not well understood. In this review we will outline general principles of mRNA localization and highlight three examples, for which a comparably large body of information is available. The first example is She2p/She3p-dependent localization of ASH1 mRNA in budding yeast. It is particularly well suited to highlight the interdependence between different steps of mRNA localization. The second example is Staufen-dependent localization of oskar mRNA in the Drosophila embryo, for which the importance of nuclear events for cytoplasmic localization and translational control has been clearly demonstrated. The third example summarizes Egalitarian/Bicaudal D-dependent mRNA transport events in the oocyte and embryo of Drosophila. We will highlight general themes and differences, point to similarities in other model systems, and raise open questions that might be answered in the coming years.

A growing body of work demonstrates the importance of post-transcriptional control, in particular translation initiation, in the overall regulation of gene expression. Here we focus on the contribution of regulatory elements within the 5' and 3' untranslated regions of mRNA to gene expression in eukaryotic cells including terminal oligopyrimidine tracts, internal ribosome entry segments, upstream open reading frames and cytoplasmic polyadenylation elements. These mRNA regulatory elements may adopt complex secondary structures and/or contain sequence motifs that allow their interaction with a variety of regulatory proteins, RNAs and RNA binding proteins, particularly hnRNPs. The resulting interactions are context-sensitive, and provide cells with a sensitive and fast response to cellular signals such as hormone exposure or cytotoxic stress. Importantly, an increasing number of diseases have been identified, particularly cancers and those associated with neurodegeneration, which originate either from mutation of these regulatory motifs, or from deregulation of their cognate binding partners.

Protein synthesis is a fundamental biological mechanism bringing the DNA-encoded genetic information into life by its translation into molecular effectors - proteins. The initiation phase of translation is one of the key points of gene regulation in eukaryotes, playing a role in processes from neuronal function to development. Indeed, the importance of the study of protein synthesis is increasing with the growing list of genetic diseases caused by mutations that affect mRNA translation. To grasp how this regulation is achieved or altered in the latter case, we must first understand the molecular details of all underlying processes of the translational cycle with the main focus put on its initiation. In this review I discuss recent advances in our comprehension of the molecular basis of particular initiation reactions set into the context of how and where individual eIFs bind to the small ribosomal subunit in the pre-initiation complex. I also summarize our current knowledge on how eukaryotic initiation factor eIF3 controls gene expression in the gene-specific manner via reinitiation.

Post-transcriptional processes critically affect eukaryotic gene expression. Cells respond to environmental and intrinsic stresses by arresting global translation and inducing the accumulation of mRNAs into cytoplasmic RNA granules such as stress granules (SGs) and processing bodies (PBs), which are thought to participate in the regulation of translation and degradation of mRNAs. Stresses trigger the formation of SGs and increase PB size and abundance, and the two granules can share specific mRNAs and proteins. The protein content and dynamics of RNA granules have been extensively studied, but the mechanisms of interaction of RNA-binding proteins (RBPs) with binding partners and the signaling pathways that regulate these interactions are poorly understood. Post-translational modification of proteins in RNA granules via phosphorylation, glycosylation and methylation, influences their associations, enzymatic activities and intracellular locations. There is evidence that the post-translational modification of RBPs has a major influence on their binding to mRNA as well as on the assembly of RNA granules. In this review, recent findings concerning the post-translational modification of RBPs and their possible roles in the assembly of RNA granules are discussed.

Selenoproteins are defined as proteins containing the 21st proteinogenic amino acid, selenocysteine (Sec). Sec is encoded by UGA (STOP) codons which are re-coded to Sec by the presence of a selenocysteine insertion sequence (SECIS) element in the 3'-untranslated region of selenoprotein mRNAs. The SECIS element is bound by several proteins, including SECIS-binding protein 2 (SBP2). Translation of selenoproteins critically depends on the integrity of the SECIS element – SBP2 interaction. Mutations in a SECIS element can abrogate expression of the respective selenoprotein. Mutations in SBP2 impinge on biosynthesis of a subset of selenoproteins and lead to a syndrome including hormonal, neurological, immunological symptoms as well as myopathy. Several other RNA-binding proteins are involved in selenoprotein translation and mediate the hierarchical response of selenoproteins to selenium deficiency. Global inhibition of selenoprotein translation is lethal in the mouse and hypomorphic mutations in selenocysteine synthase in humans leads to Progressive Cerebello Cerebral Atrophy, a neurodevelopmental and neurodegenerative disease in pediatric patients.

The mechanisms that drive the expression of a gene into its final protein product can be sub-divided into three levels: transcriptional, post-transcriptional and post-translational events. To facilitate the development and maintenance of a multi-cellular organism precise regulatory circuits are needed to ensure the survival of the organism and its ability to respond to changes in its environment. The key element of post-transcriptional regulation is RNA. Within the cell RNA exists in the form of ribonucleoproteins (RNPs), which are characterised by the underlying RNA and the proteins that are associated to it. The eukaryotic cell contains a vast plethora of RNA-binding proteins (RBPs) that control the complex fate of cellular RNAs. One of such RBPs is Guanine-rich sequence binding factor 1 (Grsf1). Grsf1 belongs to a group of heterogeneous nuclear RNPs that are characterised by the presence of an RNA binding domain designated RNA recognition motif (RRM). Grsf1 is present in most eukaryotic cells and is located in the nucleus as well as in the cytoplasm. Thus, its activity has been related to nuclear processes (RNA splicing) as well as cytoplasmic events (translation initiation). However, its full functional significance is not yet understood. Grsf1 has been implicated in the influenza viral life cycle, embryonic brain development and the regulation of apoptosis. Moreover, Grsf1 is a functional component of several cellular signalling pathways as well as of the regulation of the cellular redox homeostasis. This review summarises the present knowledge of Grsf1 biology to bring the scattered reports of Grsf1 function into a proper context.

We begin by reviewing the first characterization of fragile X syndrome, which ultimately led to cloning of the FMR1 gene. Discovery of the molecular basis of this disorder, including expansion of a trinucleotide repeat, gave insight not only into fragile X syndrome but also into the premutation syndromes. Features of fragile X syndrome are discussed including the patient phenotype down to the neuronal phenotype. The domain features of the fragile X mental retardation protein FMRP are described, as are the mRNAs bound by FMRP and the role of post-translational modifications as regulators of FMRP function. The relatively new role of FMRP in progenitor cells is reviewed, as is FMRP localization in cells and how FMRP is regulated by glutamatergic signaling in the brain. Understanding how metabotropic glutamate receptors impact FMRP has led to novel therapeutic approaches in treating this disorder.

The mammalian RNA-binding protein (RBP) HuR associates with numerous mRNAs encoding proteins with roles in cell division, cell survival, immune response, and differentiation. HuR was known to stabilize many of these mRNAs and/or modulated their translation, but the molecular processes by which HuR affected the fate of target mRNAs was largely unknown. Evidence accumulated over the past five years has revealed that the influence of HuR on many bound transcripts depends on HuR's interplay with microRNAs which associate with the same mRNAs. Here, we review the interactions of HuR and microRNAs – both competitive and cooperative – that govern expression of shared target mRNAs. Competition between HuR and microRNAs typically results in enhanced gene expression if the HuR-mRNA interaction prevails, and in repression if the microRNA remains associated. Cooperation between HuR and microRNAs leads to lower expression of the shared mRNA. We also describe the regulation of HuR levels by microRNAs as well as the regulation of microRNA levels by HuR. Finally, we discuss transcriptome-wide analyses of HuR-bound mRNAs with neighboring microRNA sites, and review the emerging mechanisms whereby microRNAs confer versatility and robustness to the post-transcriptional outcomes of HuR targets.

The ubiquitous mRNA-binding protein human antigen R (HuR) and its neuronal relatives (HuB, HuC, HuD) participate in the post-transcriptional regulation of many AU-rich element-bearing mRNAs. In addition to its originally described role in controlling mRNA decay, the binding of HuR to target mRNAs can affect many aspects of mRNA processing including splicing, polyadenylation, intracellular trafficking, translation and modulation of mRNA repression by miRNAs. In accordance to the growing list of signalling events which are involved in regulating these different HuR functions, recent data implicate that posttranslational modification, namely protein kinase-triggered phosphorylation of HuR plays a crucial role in connecting extracellular signal inputs to a specific post-transcriptional program by HuR. Notably, in addition to directly targeting HuR functions, posttranslational modifications of HuR have a major impact on the sequestration and binding to various HuR ligand proteins as has been demonstrated e.g. for the 14-3-3 chaperones. However, the detailed mechanisms of how a specific modification of HuR coordinates different aspects in HuR regulation are currently poorly understood. Due to the fact that most of the described HuR activities are closely related to its subcellular localization and the binding to cargo mRNA, this review will focus on these aspects of HuR functions and their control by posttranslational modification, particularly by HuR phosphorylations by different protein kinases.

Studies on the post-transcriptional control of gene expression in hematopoietic cells have uncovered that a subfamily of heterogeneous nuclear ribonucleoproteins (hnRNPs) is involved in cytoplasmic gene regulation. Among them hnRNP K and hnRNPs E1/E2 share common structural motifs, the hnRNP K homology (KH) domains that provide a functional basis for RNA binding. Specific sub-cellular localization and differentiation dependent post-translational modifications modulate the interaction of these proteins with mRNA and proteins in messenger ribonucleoprotein complexes (mRNPs), the latter generating connectivity to cell signaling events. As components of different mRNPs, hnRNP K and hnRNPs E1/E2 function as crucial modulators of mRNA stability and translation in hematopoietic cell differentiation.

Increasing evidence points to the participation of the multifunctional protein Annexin A2 (AnxA2) in mRNA localisation as well as the translation of certain mRNAs on cytoskeleton-bound polysomes, and thereby in the regulation of the biosynthesis of specific proteins, such as c-Myc and AnxA2 itself, which are linked to cellular transformation. AnxA2 is most likely activated by signalling pathways, which result in its post-translational modifications and modulate its binding to various ligands, including specific mRNAs. Positive and polar residues in helices C-D in domain IV of AnxA2 bind to cis-acting elements in the 3’-UTRs of its cognate, c-myc, collagen prolyl 4-hydroxylase-α(I) and N-methyl-D-aspartate R1 mRNAs, thus contributing to post-transcriptional regulation of the expression of specific genes. The cis-acting elements appear to constitute a higher order structure, frequently containing the consensus sequence 5'-AA(C/G)(A/U)G; however, non-canonical AnxA2 binding sites may also be involved. In the case of c-myc mRNA, the association with AnxA2 appears to regulate its localisation and translation. In addition, the binding of AnxA2 to a pseudoknot structure present in infectious bronchitis viral RNA results in reduced efficiency of -1 ribosomal frameshifting, indicating its recruitment as a host protein during viral infection. Finally, the association of AnxA2 with endosomes and exosomes suggests a role in co-ordinated transport of mRNA and vesicles, i.e. processes that respond to extracellular signals and are expected to employ multifunctional proteins.