Riboswitches and the RNA World

Breaker, Ronald R.

doi:10.1101/cshperspect.a003566

Cited by 572 publications

(548 citation statements)

References 74 publications

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“…11,35 The SAM riboswitch class is one of the most abundant, 36 especially in Gram-positive organisms, and is unique in that six distinct SAM riboswitch families have been reported to date that bind SAM in diverse ways. 3,11,24,36 The large diversity of SAM riboswitches likely reflects the importance of regulating SAM-related metabolic pathways. 3 SAM riboswitches exhibit very high affinity for SAM and strongly discriminate against SAM-related analogs such as S-adenosylhomocysteine (SAH), 33,34 which differs from SAM by the absence of a single methyl group and the associated positive charge on the sulfur atom.…”

Section: S-adenosylmethionine (Sam) Riboswitchesmentioning

confidence: 99%

“…3,11,24,36 The large diversity of SAM riboswitches likely reflects the importance of regulating SAM-related metabolic pathways. 3 SAM riboswitches exhibit very high affinity for SAM and strongly discriminate against SAM-related analogs such as S-adenosylhomocysteine (SAH), 33,34 which differs from SAM by the absence of a single methyl group and the associated positive charge on the sulfur atom. A study has reported the existence of SAH-sensing riboswitches, 37 indicating that SAM/SAH riboswitches exploit chemical differences between closelyrelated metabolites to prevent cellular misregulation, which is consistent with recently obtained crystal structures.…”

Section: S-adenosylmethionine (Sam) Riboswitchesmentioning

confidence: 99%

“…[3][4][5][6][7] Riboswitches are composed of two modular domains: an aptamer and an expression platform. 8 While the very conserved aptamer domain is involved in signal detection, the expression platform varies widely as it controls gene expression at various biological levels, such as transcription or translation.…”

Section: Folding Of the Sam-i Riboswitchmentioning

confidence: 99%

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Folding of the SAM-I riboswitch

et al. 2012

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Section: S-adenosylmethionine (Sam) Riboswitchesmentioning

confidence: 99%

Section: S-adenosylmethionine (Sam) Riboswitchesmentioning

confidence: 99%

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Folding of the SAM-I riboswitch

et al. 2012

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“…Thus, the unacylated tRNA Gly UCC is similar to the much smaller metabolic products that affect the riboswitch mechanisms controlling gene expression; the 5′UTR undergoes a conformational change with the binding of the ligand. 82 The tRNA Gly UCC is also predicted to bind to the 5′-GGA-3′ Specifier codon in Bacillus and Staphylococcus species glycyl T-box riboswitches. 83 …”

Section: Unmodified Wobble Position 34 and The Importance Of Position 32mentioning

confidence: 99%

Celebrating wobble decoding: Half a century and still much is new

et al. 2017

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A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.

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“…The ability of RNA to engage in intramolecular base pairing is well established (Busan & Weeks, 2013). RBS elements can be disabled by intramolecular RNA folding, as is the case in riboswitches (Breaker, 2012). The RNA in riboswitches adopts an OFF state when the RBS is bound by a complementary anti-RBS sequence within the mRNA.…”

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confidence: 99%

rClone: A Synthetic Biology Tool That Enables the Research of Bacterial Translation

Eckdahl¹,

Neal²,

Campbell³

et al. 2017

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Celebrating 20 years of undergraduate research mRNA, called the ribosome binding site (RBS; Figure 1). After the small ribosomal subunit binds to the RBS, the large ribosomal subunit attaches to the small subunit to begin translation of the mRNA into a chain of amino acids. The mRNA bases are read as triplet codons that interact by base pairing with anticodons in transfer RNA (tRNA) molecules, which carry amino acids to the growing protein chain (Malys & McCarthy, 2010). As shown in Figure 1, RNA-RNA base pairing typically involves the Watson-Crick base pairs of G with C, and A with U, but G can also base pair with U. The conventional understanding is that the strength of a given RBS is determined by the strength of its base pairing interactions with the 16S rRNA (Shine & Dalgarno, 1974). In natural bacterial genomes, there is a wide variety of RBS sequences and RBS translational strengths that have resulted from natural selection for global patterns of gene expression. The relationship between RNA base pairing and the strength of an RBS also explains how synthetic RBSs can be produced with widely varying strengths.In addition to intermolecular base pairing, intramolecular base pairing affects the strengths of RBSs. The ability of RNA to engage in intramolecular base pairing is well established (Busan & Weeks, 2013). RBS elements can be disabled by intramolecular RNA folding, as is the case in riboswitches (Breaker, 2012). The RNA in riboswitches adopts an OFF state when the RBS is bound by a complementary anti-RBS sequence within the mRNA. For the ON state, a small molecule ligand binds to the folded RNA and changes the RNA shape so that the RBS is available for interaction with the 16S rRNA.Understanding the function of RBSs informs the discipline of synthetic biology, which uses engineering principles and molecular cloning methods for the construction of parts, devices, and systems, INTRODUCTIONGene expression, the process by which the inherited information of genes is used to direct the function of cells, is regulated in all cells because not all genes are needed all the time or under all circumstances (Hijum, Medema, & Kuipers, 2009). Gene expression begins with transcription, the process by which the DNA base sequence of a gene is converted into RNA sequence information. For genes that encode proteins, the messenger RNA (mRNA) product of transcription is used during translation to encode the sequence of amino acids in a protein. The sequence of bases in mRNA is translated by the ribosome, which is composed of a large (50S) and a small (30S) subunit. Translation is initiated when the 16S ribosomal RNA (rRNA) of the small ribosomal subunit base pairs to a conserved sequence in the Understanding bacterial translation is of interest to many high school and college biology students, but hands-on research of this process has traditionally been inaccessible because of the expertise required for molecular cloning. There is also a need for more and better translational control elements that can be used for genetic ...

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Riboswitches and the RNA World

Cited by 572 publications

References 74 publications

Folding of the SAM-I riboswitch

Folding of the SAM-I riboswitch

Celebrating wobble decoding: Half a century and still much is new

rClone: A Synthetic Biology Tool That Enables the Research of Bacterial Translation

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