Unfolding of mRNA Secondary Structure by the Bacterial Translation Initiation Complex

Studer, Sean M.; Joseph, Simpson

doi:10.1016/j.molcel.2006.02.014

Cited by 168 publications

(226 citation statements)

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“…Without standby, stable structure cannot be overcome in the short time frame of unfolding because free ribosomes need to be recruited from the cytoplasmic pool. 36,37 The standby model, which received further support from in vitro analyses, 39 provided the framework for how tisB is expressed and regulated. The unstructured region present in +42, but absent from +1 or +106 tisB mRNA, is proposed to be a standby site.…”

Section: Inhibition Of Ribosome Standby Explains the Tisb/istr1 Mechamentioning

confidence: 99%

The toxin-antitoxin systemtisB-istR1

Wagner

Unoson

2012

RNA Biology

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Section: Inhibition Of Ribosome Standby Explains the Tisb/istr1 Mechamentioning

confidence: 99%

The toxin-antitoxin systemtisB-istR1

Wagner

Unoson

2012

RNA Biology

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“…How IF3 increases the accuracy of start codon selection remains unclear, but recent studies provide clues about the mechanism (Antoun et al 2006a,b;Studer and Joseph 2006). IF3 negatively regulates formation of the 30S preinitiation complex by destabilizing tRNA (including fMet-tRNA fMet ) in the 30S P site.…”

Section: A790g Decreases the Affinity Of If3 For The 30s Subunitmentioning

confidence: 99%

“…The SD sequence base pairs with the 39 end of the 16S rRNA (termed the anti-ShineDalgarno sequence or ASD) to facilitate positioning of the start codon in the 30S P site) (Steitz and Jakes 1975). The sequence of the SD, sequence of the start codon, number of nucleotides between the SD and start codon, and the mRNA secondary structure influence the efficiency of initiation (Vellanoweth and Rabinowitz 1992;Studer and Joseph 2006), indicating the importance of each of these determinants in the initiation process.…”

Section: Introductionmentioning

confidence: 99%

“…Translation initiation in bacteria is kinetically controlled by three initiation factors (IF1, IF2, and IF3), and recent studies have helped clarify the roles of these factors in the initiation process (Antoun et al 2003(Antoun et al , 2006aStuder and Joseph 2006). The first major step in the process is assembly of the 30S preinitiation complex.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation

Qin¹,

Abdi²,

Fredrick³

2007

RNA

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In bacteria, initiation of translation is kinetically controlled by factors IF1, IF2, and IF3, which work in conjunction with the 30S subunit to ensure accurate selection of the initiator tRNA (fMet-tRNA fMet ) and the start codon. Here, we show that mutations G1338A and A790G of 16S rRNA decrease initiation fidelity in vivo and do so in distinct ways. Mutation G1338A increases the affinity of tRNA fMet for the 30S subunit, suggesting that G1338 normally forms a suboptimal Type II interaction with fMettRNA fMet . By stabilizing fMet-tRNA fMet in the preinitiation complex, G1338A may partially compensate for mismatches in the codon-anti-codon helix and thereby increase spurious initiation. Unlike G1338A, A790G decreases the affinity of IF3 for the 30S subunit. This may indirectly stabilize fMet-tRNA fMet in the preinitiation complex and/or promote premature docking of the 50S subunit, resulting in increased levels of spurious initiation.

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“…Additionally, single-stranded regions upstream of the RBS have been shown to act as standby sites to allow for temporary ribosome binding until the inhibitory secondary structure opens (9,39,40), with subsequent scanning-like movement downstream (17,39,41). Energy-independent 70S scanning initiation has been demonstrated recently, with an emphasis on the requirement of an SD sequence for proper positioning (18).…”

Section: Discussionmentioning

confidence: 99%

Novel Translation Initiation Regulation Mechanism in Escherichia coli ptrB Mediated by a 5′-Terminal AUG

Beck

Janssen

2017

J Bacteriol

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Alternative translation initiation mechanisms, distinct from the ShineDalgarno (SD) sequence-dependent mechanism, are more prevalent in bacteria than once anticipated. Translation of Escherichia coli ptrB instead requires an AUG triplet at the 5= terminus of its mRNA. The 5=-terminal AUG (5=-uAUG) acts as a ribosomal recognition signal to attract ribosomes to the ptrB mRNA rather than functioning as an initiation codon to support translation of an upstream open reading frame. ptrB expression exhibits a stronger dependence on the 5=-uAUG than the predicted SD sequence; however, strengthening the predicted ptrB SD sequence relieves the necessity for the 5=-uAUG. Additional sequences within the ptrB 5= untranslated region (5=-UTR) work cumulatively with the 5=-uAUG to control expression of the downstream ptrB coding sequence (CDS), thereby compensating for the weak SD sequence. Replacement of 5=-UTRs from other mRNAs with the ptrB 5=-UTR sequence showed a similar dependence on the 5=-uAUG for CDS expression, suggesting that the regulatory features contained within the ptrB 5=-UTR are sufficient to control the expression of other E. coli CDSs. Demonstration that the 5=-uAUG present on the ptrB leader mRNA is involved in ribosome binding and expression of the downstream ptrB CDS revealed a novel form of translational regulation. Due to the abundance of AUG triplets at the 5= termini of E. coli mRNAs and the ability of ptrB 5=-UTR regulation to function independently of gene context, the regulatory effects of 5=-uAUGs on downstream CDSs may be widespread throughout the E. coli genome.IMPORTANCE As the field of synthetic biology continues to grow, a complete understanding of basic biological principles will be necessary. The increasing complexity of the synthetic systems highlights the gaps in our current knowledge of RNA regulation. This study demonstrates that there are novel ways to regulate canonical Shine-Dalgarno-led mRNAs in Escherichia coli, illustrating that our understanding of the fundamental processes of translation and RNA regulation is still incomplete. Even for E. coli, one of the most-studied model organisms, genes with translation initiation mechanisms that do not fit the canonical Shine-Dalgarno sequence paradigm are being revealed. Uncovering diverse mechanisms that control translational expression will allow synthetic biologists to finely tune protein production of desired gene products.KEYWORDS 5= upstream AUG, Shine-Dalgarno, noncanonical initiation, translation initiation, translational regulation, upstream open reading frame P rotein synthesis, in which the ribosome translates an mRNA sequence to form polypeptides, is a four-step process that includes initiation, elongation, termination, and ribosome recycling. Translation initiation is energy dependent and the most highly regulated phase of translation (1). The translational machinery interacts with the mRNA at its ribosome binding site (RBS) along with initiator tRNA to form a ternary complex that is equipped for polypeptide productio...

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Unfolding of mRNA Secondary Structure by the Bacterial Translation Initiation Complex

Cited by 168 publications

References 50 publications

The toxin-antitoxin systemtisB-istR1

The toxin-antitoxin systemtisB-istR1

Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation

Novel Translation Initiation Regulation Mechanism in Escherichia coli ptrB Mediated by a 5′-Terminal AUG

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