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Review
. 2009:63:27-44.
doi: 10.1146/annurev.micro.091208.073514.

Regulation of translation initiation by RNA binding proteins

Paul Babitzke  1 , Carol S Baker, Tony Romeo
Affiliations
Review

Regulation of translation initiation by RNA binding proteins

Paul Babitzke et al. Annu Rev Microbiol. 2009.

Abstract

RNA binding proteins are capable of regulating translation initiation by a variety of mechanisms. Although the vast majority of these regulatory mechanisms involve translational repression, one example of translational activation has been characterized in detail. The RNA recognition targets of these regulatory proteins exhibit a wide range in structural complexity, with some proteins recognizing complex pseudoknot structures and others binding to simple RNA hairpins and/or short repeated single-stranded sequences. In some instances the bound protein directly competes with ribosome binding, and in other instances the bound protein promotes formation of an RNA structure that inhibits ribosome binding. Examples also exist in which the bound protein traps the ribosome in a complex that is incapable of initiating translation.

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Figures

Figure 1
Figure 1
Feedback regulation of E. coli ribosomal protein operons. Structures of the mRNA (a–e) and rRNA (a–d ) binding sites for each protein are shown. (a) L20 binding sites in the rpmI leader and 23S rRNA transcripts (23). (b) S8 binding sites in the spc and 16S rRNA transcripts (39). (c) L10-(L12)4 binding sites in the rplJ leader and 23S rRNA transcripts (29). (d ) S15 binding sites in the rpsO and 16S rRNA transcripts (17). (e) Pseudoknot involved in S4 binding to the rpsM transcript (48).
Figure 2
Figure 2
Feedback regulation of Escherichia coli thrS. In the absence of bound ThrRS, ribosomes can bind to the split ribosome binding site (domains 1 and 3) and initiate translation of thrS. Dimeric ThrRS can bind to two tRNAThr molecules for aminoacylation. Alternatively, ThrRS can bind to two sites in thrS (domains 2 and 4), which inhibits ribosome binding and represses translation. The ThrRS binding sites in thrS, as well as thrS Shine-Dalgarno (SD) sequence and initiation codon, are shown. The anticodon loop of tRNAThr is shown for comparison (44). The critical anticodon (tRNAThr) and anticodon-like (thrS) residues are shown.
Figure 3
Figure 3
Autogenous translational repression of mRNAs containing structured binding sites. The bound regulatory protein competes with ribosome binding in each case. Protein binding sites and/or critical residues involved in protein-RNA interaction are highlighted. Shine-Dalgarno (SD) sequences and initiation codons (Met) of the mRNAs are shown. (a) Binding sites for the coat proteins of bacteriophages Qβ, MS2, and PP7 (33). (b) Binding site for bacteriophage T4 gp32 (5). (c) Binding site for bacteriophage T4 gp43 (40). (d) Binding site for Mycobacterium smegmatis PyrR. The distance between the putative SD sequence and the AUG codon (13 nt) is unusually long (18).
Figure 4
Figure 4
Translational repression of Bacillus subtilis tryptophan metabolism genes. (a) Model of the trpE translational repression mechanism. RNA polymerase pausing during transcription provides additional time for binding of tryptophan-activated trp RNA binding attenuation protein (TRAP). In the absence of bound TRAP (limiting tryptophan), the RNA adopts a structure such that the trpE Shine-Dalgarno (SD) sequence is single stranded and available for ribosome binding. In the presence of excess tryptophan, TRAP binding promotes formation of the trpE SD-sequestering hairpin. (b) TRAP binding sites in the trpG, trpP, and ycbK transcripts. In each case, bound TRAP competes with ribosome binding and represses translation. The SD sequence and initiation codon (Met) for each mRNA is marked.
Figure 5
Figure 5
CsrA binding sites in CsrC and pgaA leader transcripts. (a) CsrC contains 13 putative CsrA binding sites (numbered ) and functions as a CsrA antagonist. Because several of the binding sites have slight overlaps, only the highly conserved GGA motifs are colored to improve clarity. (b) The pgaA leader transcript contains six CsrA binding sites (numbered), three of which are present in RNA hairpins. Bound CsrA competes with ribosome binding and represses translation. The pgaA Shine-Dalgarno (SD) sequence and initiation codon (Met) are shown. A high-affinity SELEX-derived RNA target is shown for comparison. Note that this motif is AGA in binding site 4.
Figure 6
Figure 6
Translational activation model of the bacteriophage Mu mom transcript. In the absence of bound Com protein, the RNA adopts an RNA hairpin that sequesters the mom Shine-Dalgarno (SD) sequence and initiation codon (Met). Bound Com stabilizes an alternative RNA hairpin such that the mom SD sequence and initiation codon are single-stranded and available for ribosome binding (26).
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