tRNA-mediated transcription antitermination
            <i>in vitro</i>
            : Codon–anticodon pairing independent of the ribosome

Grundy, Frank J.; Winkler, William E.; Henkin, Tina M.

doi:10.1073/pnas.162366799

Cited by 111 publications

(147 citation statements)

References 29 publications

Supporting

Mentioning

138

Contrasting

Unclassified

Order By: Relevance

“…39), tRNA Gly (REF. 40) and others 41 can selectively activate transcription of the cognate aminoacyl-tRNA synthetase gene via specific interaction of the anticodon and acceptor stem with the so-called T-box region located in the 5′-UTR (FIG. 3d).…”

Section: Rna Controls Rnamentioning

confidence: 99%

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

2007

View full text Add to dashboard Cite

Although various functions of RNA are carried out in conjunction with proteins, some catalytic RNAs, or ribozymes, which contribute to a range of cellular processes, require little or no assistance from proteins. Furthermore, the discovery of metabolite-sensing riboswitches and other types of RNA sensors has revealed RNA-based mechanisms that cells use to regulate gene expression in response to internal and external changes. Structural studies have shown how these RNAs can carry out a range of functions. In addition, the contribution of ribozymes and riboswitches to gene expression is being revealed as far more widespread than was previously appreciated. These findings have implications for understanding how cellular functions might have evolved from RNA-based origins.More than 40 years of extensive research has revealed that RNAs participate in a range of cellular functions. Some RNAs, despite being composed of only four chemically similar nucleotides, can fold into distinct three-dimensional architectures. In many cases, these constitute simple scaffolds that provide binding sites for proteins that function together with the RNAs. However, the discovery of the first catalytic RNAs -later named RNA enzymes, or ribozymes -in the 1980s demonstrated that RNAs can also have important functional roles in their own right 1,2 . The list of naturally occuring ribozymes is short, and additions over the years have been rare, with each new discovery eliciting considerable excitement in the field.Studies of molecular evolution suggest that RNA molecules significantly influenced the development of modern organisms by mediating the genetic flow from DNA to proteins, as well as through their own contribution to catalytic functions. The 'RNA world' hypothesis implies that RNA molecules appeared before DNA and proteins 3 . Nevertheless, even with a head start, RNA catalysts do not prevail in the modern world. Moreover, most ubiquitous ribozymes require proteins for efficient catalysis in vivo, and most true protein-devoid catalytic RNAs have been found in only a few viral-like sources, suggesting that the contribution of protein-free RNAs to the functions of modern cells has been limited.Correspondence to A.S. or D.J.P. serganoa@mskcc.org; pateld@mskcc.org. Competing interests statementThe authors declare no competing financial interests. HHS Public AccessAuthor manuscript Nat Rev Genet. Author manuscript; available in PMC 2015 December 23. Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptThe discovery of riboswitches 4-6 and other RNA-based sensors reignited interest in the roles of protein-devoid RNA-based elements. These RNA sensors can be broadly defined as mRNA regions that are capable of modulating gene expression in response to internal and external inputs, without the initial participation of proteins. Unlike ribozymes, many of these sensors direct gene expression purely through changes in RNA conformation. For instance, riboswitches alter their conformations in response to small metabolite...

show abstract

Section: Rna Controls Rnamentioning

confidence: 99%

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

2007

View full text Add to dashboard Cite

show abstract

“…Cellular inputs, ranging from changes in temperature and pH to the binding of proteins, other RNAs, and ligands, can preferentially stabilize select conformations along the landscape, resulting in dynamic changes in RNA structure that drive the multistep catalytic cycles of ribozymes (3), regulatory activities of riboswitches (4) and other RNA-based switches (5), and the dynamic assembly and disassembly of ribonucleoprotein (RNP) complexes (6).…”

mentioning

confidence: 99%

“…Such secondary structural transitions entail large kinetic barriers, so they are often catalyzed by RNA-binding proteins (9), ATP-dependent chaperones (10), or otherwise occur by modulating cotranscriptional folding (5,11). Recently, NMR R1ρ relaxation dispersion experiments (12)(13)(14)(15) in concert with mutagenesis (16) have helped uncover more labile RNA secondary structural transitions that can take place without assistance from external cofactors at rates that are 2-4 orders of magnitude faster than larger-scale secondary structural rearrangements.…”

mentioning

confidence: 99%

Invisible RNA state dynamically couples distant motifs

Lee

Dethoff

Al‐Hashimi

2014

Proc. Natl. Acad. Sci. U.S.A.

113

View full text Add to dashboard Cite

Using on-and off-resonance carbon and nitrogen R1ρ NMR relaxation dispersion in concert with mutagenesis and NMR chemical shift fingerprinting, we show that the transactivation response element RNA from the HIV-1 exists in dynamic equilibrium with a transient state that has a lifetime of ∼2 ms and population of ∼0.4%, which simultaneously remodels the structure of a bulge, stem, and apical loop. This is accomplished by a global change in strand register, in which bulge residues pair up with residues in the upper stem, causing a reshuffling of base pairs that propagates to the tip of apical loop, resulting in the creation of three noncanonical base pairs. Our results show that transient states can remodel distant RNA motifs and possibly give rise to mechanisms for rapid long-range communication in RNA that can be harnessed in processes such as cooperative folding and ribonucleoprotein assembly.NMR spectroscopy | dynamics | R1ρ relaxation dispersion | nucleic acids I t is now well-established that RNA sequences do not code for a single static structure, but rather, many conformations that populate energetic minima along a free-energy landscape (1, 2). Cellular inputs, ranging from changes in temperature and pH to the binding of proteins, other RNAs, and ligands, can preferentially stabilize select conformations along the landscape, resulting in dynamic changes in RNA structure that drive the multistep catalytic cycles of ribozymes (3), regulatory activities of riboswitches (4) and other RNA-based switches (5), and the dynamic assembly and disassembly of ribonucleoprotein (RNP) complexes (6).A common mode of RNA dynamics involves rearrangements in secondary structure that can melt or create entire hairpins, and thereby expose or sequester key regulatory elements that are several nucleotides long (1,4,7,8). Such secondary structural transitions entail large kinetic barriers, so they are often catalyzed by RNA-binding proteins (9), ATP-dependent chaperones (10), or otherwise occur by modulating cotranscriptional folding (5, 11). Recently, NMR R1ρ relaxation dispersion experiments (12-15) in concert with mutagenesis (16) have helped uncover more labile RNA secondary structural transitions that can take place without assistance from external cofactors at rates that are 2-4 orders of magnitude faster than larger-scale secondary structural rearrangements. These transitions entail excursions away from the energetically favorable ground state (GS) toward lowpopulated (typically populations <15%) and short-lived (lifetime < milliseconds) species often referred to as "excited states" (ES) (12, 13). These invisible RNA ES feature localized reshuffling of base pairing in and around noncanonical motifs such as bulges, internal loops, and apical loops (16) which can also expose or sequester functionally important residues or promote ATPindependent large-scale changes in secondary structure (14, 15). These faster and more localized changes in secondary structure may meet unique demands in RNA-based regulatory functions (16).Using...

show abstract

“…Transcription is therefore directed by the concentrationdependent binding of charged and uncharged tRNAs to the T-box, with the level of charging serving as a sensor of the intracellular concentration of the cognate amino acid. By using this feedback mechanism, they control bacterial growth, in response to nutritional stress signals, via regulation of transcription of genes encoding mainly for amino acid biosynthesis enzymes, amino acid transporters, and aminoacyl-tRNA synthetases (8)(9)(10)(11). T-boxes bind specific, cognate tRNA molecules mainly at two conserved sites: the anticodon sequence, which forms base pairs with the codon sequence of the specifier loop (SL); and the tRNA's NCCA 3′ accepting end, which pairs with the UGGN sequence found in the antiterminator bulge (12,13).…”

mentioning

confidence: 99%

“…As the major specificity determinant of a T-box is the unique codon-like nucleotide triplet of the SL, which recognizes only one tRNA anticodon sequence, all T-boxes were considered thus far to be of single specificity, and the possibility of a broader specificity of T-boxes was overlooked (10). However, a closer look at all the available T-box sequences suggests the existence of T-boxes harboring SLs with two putative codon regions (Tables S1 and S2).…”

mentioning

confidence: 99%

Two-codon T-box riboswitch binding two tRNAs

Saad

Stamatopoulou

Brayé

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

T-box riboswitches control transcription of downstream genes through the tRNA-binding formation of terminator or antiterminator structures. Previously reported T-boxes were described as single-specificity riboswitches that can bind specific tRNA anticodons through codon–anticodon interactions with the nucleotide triplet of their specifier loop (SL). However, the possibility that T-boxes might exhibit specificity beyond a single tRNA had been overlooked. In Clostridium acetobutylicum , the T-box that regulates the operon for the essential tRNA-dependent transamidation pathway harbors a SL with two potential overlapping codon positions for tRNA Asn and tRNA Glu . To test its specificity, we performed extensive mutagenic, biochemical, and chemical probing analyses. Surprisingly, both tRNAs can efficiently bind the SL in vitro and in vivo. The dual specificity of the T-box is allowed by a single base shift on the SL from one overlapping codon to the next. This feature allows the riboswitch to sense two tRNAs and balance the biosynthesis of two amino acids. Detailed genomic comparisons support our observations and suggest that “flexible” T-box riboswitches are widespread among bacteria, and, moreover, their specificity is dictated by the metabolic interconnection of the pathways under control. Taken together, our results support the notion of a genome-dependent codon ambiguity of the SLs. Furthermore, the existence of two overlapping codons imposes a unique example of tRNA-dependent regulation at the transcriptional level.

show abstract

tRNA-mediated transcription antitermination in vitro : Codon–anticodon pairing independent of the ribosome

Cited by 111 publications

References 29 publications

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

Invisible RNA state dynamically couples distant motifs

Two-codon T-box riboswitch binding two tRNAs

Contact Info

Product

Resources

About