Trans-acting translational regulatory RNA binding proteins

Abstract

The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.

Keywords: IRES uORF; RNA binding protein; interactome capture; mRNA translation; protein synthesis; terminal oligopyrimidine tract.

Figure 1

RNA motifs and interactions with trans‐acting factors. Schematic representation of translational regulation mediated by the binding of trans‐acting factors (in grey) to cis‐acting elements along the pseudo‐circularized messenger RNA. Terminal oligopyrimidine motifs (TOPs), internal ribosome entry sites (IRESs) and uORFs in the 5′ UTR; and miRNA‐responsive (MREs), AU‐rich (AREs) and cytoplasmic polyadenylation (CPEs) elements in the 3′ UTR, are known to either stimulate or inhibit cellular protein synthesis. AUG indicates the start of the ORF

Figure 2

uORFs and cellular stress. ATF4 is a transcription factor regulated at the level of transcription and translation in response to stress (Dey et al., 2010), and plays an important role in the integrated stress response (ISR) by enhancing the expression of stress response transcripts (Harding et al., 2000; Vattem & Wek, 2004; Wek, Jiang, & Anthony, 2006). ATF4 mRNA translation is mediated by a delayed re‐initiation mechanism at two uORFs (Vattem & Wek, 2004). (a) ATF4 uORF1 is very short (encoding three amino acids) and functions in a positive manner, enhancing re‐initiation at downstream uORF2 (encoding 59 amino acids) which overlaps with the ATF4 ORF. (b) Under normal conditions, when eIF2‐GTP (and thus TC) availability is high, ribosomes translate uORF1 and the 60S ribosome dissociates. Importantly, the 40S ribosome remains associated and continues to scan the message, reinitiating at the inhibitory uORF2 and bypassing the ATF4 CDS (inhibiting ATF4 translation). (c) In response to cellular stress, when eIF2 is phosphorylated and eIF2‐GTP (and thus TC) availability is low, the scanning 40S ribosome bypasses uORF2 and instead re‐initiates at the start of the ATF4 ORF, increasing ATF4 translation. Therefore, delayed re‐initiation provides a mechanism for cells to selectively enhance the translation of mRNAs, particularly those encoding proteins required for adaptation and recovery from stress, during global protein synthesis inhibition

Figure 3

Comparison of selected RNA‐binding proteins and their domains. Comparison of selected RNA‐binding proteins and their domains. PABPC1 (polyadenylate‐binding protein cytoplasmic 1); PTB (polypyrimidine tract‐binding protein 1); CPEB1 (cytoplasmic polyadenylation element‐binding protein 1); LARP1 (La‐related protein 1); PKR (double‐stranded RNA‐activated protein kinase); FMR1 (Fragile X mental retardation protein 1). Domains: RRM (RNA recognition motif); MLLE (Met‐Leu‐Leu‐Glu motif); NES (nuclear export sequence); NLS (nuclear localization sequence); ZZ (ZZ‐type zinc finger domain); LAM (La motif); RRM‐L5 (RRM‐like motif 5); DSRM (double‐stranded RNA‐binding motif); STK (Ser‐Thr kinase domain); KH (K homology RNA‐binding domain)