Molecular‐Recognition Characteristics of SAM‐Binding Riboswitches

Lim, Jisun; Winkler, William E.; Nakamura, Shingo; Scott, Valerie; Breaker, Ronald R.

doi:10.1002/anie.200503198

Cited by 54 publications

(71 citation statements)

References 28 publications

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“…For example, in the type I (''SAM box'') riboswitch, the replacement (by hydrogen) of either the a-amino or acarboxyl of SAM methionine reduces its apparent K D by more than 33,000-fold (Lim et al 2006). This is well explained by crystallography of the type I riboswitch SAM aptamer.…”

Section: The Polar Profilementioning

confidence: 94%

“…Red is negative, blue positive. The potential for binding a cation to the top of the ring appears clearly in the lower image (Montange and Batey 2006); the result is about an 80-fold preference for SAM (Lim et al 2006). SAM II adopts a related strategy, using O2 and O4 of two U's from an AUU triple (Gilbert et al 2008) near the sulfur.…”

Section: The Polar Profilementioning

confidence: 99%

“…SAM I has the methyl group pointing along the broad minor groove of a helix (Montange and Batey 2006), added bulk at this position makes little difference as long as the charge is maintained (Lim et al 2006). SAM III points the methyl away from the site, into solvent, and makes little distinction between methyl-and ethyl-sulfonium ion (Lu et al 2008).…”

Section: The Polar Profilementioning

confidence: 99%

“…6) uniquely makes dramatic distinctions between sulfur substituents, rejecting all alternatives to SAM by more than 1000-fold (Lim et al 2006). This is probably because the methionine section of the SAM II site extends along the deep narrow major groove of an RNA helix, and methionine sulfur is hindered further by the third strand of a pseudoknot triplex (Gilbert et al 2008).…”

Section: The Polar Profilementioning

confidence: 99%

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RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

2009

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By combining crystallographic and NMR structural data for RNA-bound amino acids within riboswitches, aptamers, and RNPs, chemical principles governing specific RNA interaction with amino acids can be deduced. Such principles, which we summarize in a ''polar profile'', are useful in explaining newly selected specific RNA binding sites for free amino acids bearing varied side chains charged, neutral polar, aliphatic, and aromatic. Such amino acid sites can be queried for parallels to the genetic code. Using recent sequences for 337 independent binding sites directed to 8 amino acids and containing 18,551 nucleotides in all, we show a highly robust connection between amino acids and cognate coding triplets within their RNA binding sites. The apparent probability (P) that cognate triplets around these sites are unrelated to binding sites is %5.3 9 10 -45 for codons overall, and P % 2.1 9 10 -46 for cognate anticodons. Therefore, some triplets are unequivocally localized near their present amino acids. Accordingly, there was likely a stereochemical era during evolution of the genetic code, relying on chemical interactions between amino acids and the tertiary structures of RNA binding sites. Use of cognate coding triplets in RNA binding sites is nevertheless sparse, with only 21% of possible triplets appearing. Reasoning from such broad recurrent trends in our results, a majority (approximately 75%) of modern amino acids entered the code in this stereochemical era; nevertheless, a minority (approximately 21%) of modern codons and anticodons were assigned via RNA binding sites.A Direct RNA Template scheme embodying a credible early history for coded peptide synthesis is readily constructed based on these observations.

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Section: The Polar Profilementioning

confidence: 94%

Section: The Polar Profilementioning

confidence: 99%

Section: The Polar Profilementioning

confidence: 99%

Section: The Polar Profilementioning

confidence: 99%

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RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

2009

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“…This compaction is likely to be assisted by a pseudoknot, which appears to be formed even in the absence of ligand interactions [26]. Both the length of the methionine chain and the partial positive charge located at the methyl-bound sulfur atom had been predicted to be important features in ligand binding [48]. Indeed, oxygen groups from P1 uridines might contribute to electrostatic interactions to the charged sulfur group.…”

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confidence: 99%

Structural features of metabolite-sensing riboswitches

Wakeman

Winkler

Dann

2007

Trends in Biochemical Sciences

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Riboswitches, metabolite-sensing RNA elements found in untranslated regions of the transcripts they regulate, possess extensive tertiary structure to couple metabolite binding to genetic control. Herein, we discuss recently published structures from four riboswitch classes and compare these natural RNA structures to those of in vitro selected RNA aptamers, which bind similar ligands to those of the riboswitches. Additionally, we examine the glmS riboswitch, the first example of a ribozyme-based riboswitch. This RNA provides the latest twist in the riboswitch field and portends exciting advances in the coming years. Our knowledge of the mechanisms of genetic regulation by riboswitches has increased mightily in recent years and will continue to grow as new riboswitch classes and ligands are discovered and structurally characterized. KeywordsRNA structure; riboswitch; ribozyme; transcription attenuation; noncoding RNAs; posttranscriptional regulation; crystallography; NMR Riboswitches: Remnants of an ancient mode of genetic regulation?The "central dogma" states that information is stored as DNA, transcribed into RNA, and translated into proteins, which are traditionally thought to satisfy most cellular structural and catalytic requirements. Genetic control of these steps is believed to occur primarily through the action of regulatory proteins; however, the importance of noncoding RNAs in these processes has become increasingly appreciated in recent years [1]. In eubacterial organisms, regulatory RNAs can elicit control of gene expression through regulation of transcription attenuation, translation initiation [reviewed in 2,3], or mRNA stability [4]. These eubacterial regulatory RNAs function via diverse intermolecular (trans) or intramolecular (cis) mechanisms to regulate the target mRNA. Trans-acting regulatory RNAs interact with target mRNAs to control translation, mRNA stability, or transcription termination [reviewed in 5,6, 7], whereas others regulate gene expression through specific sequestration of RNA-binding proteins [8]. Cis-acting RNAs, which are the focus of this review, are located within untranslated regions (UTRs) of the mRNA transcript that they regulate. Genetic control by the latter RNA elements can be accomplished either through the sole action of the RNA molecule or in conjunction with recruited protein factors.A classic example of a cis-acting regulatory RNA is the transcription attenuation control of tryptophan biosynthesis genes in certain Gram-negative bacteria [9]. For this mechanism, the kinetics of translation of a short leader peptide dictates the conformational state of the overall 5′-UTR. Under tryptophan-depleted conditions the translating ribosome stalls at tryptophan codons within the leader peptide thereby allowing for formation of an antiterminator helix and [24-26; reviewed in 27,12]. Given their ability to function as sensitive sentinels for intracellular metabolites in a protein-independent manner, these RNAs are likely to require exquisite structural sophistication....

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Methionine Adenosyltransferase (S‐Adenosylmethionine Synthetase)

Pajares

Markham

2011

Advances in Enzymology - And Related Areas of Molecular Biology

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10.3. Thermal Unfolding 10.4. Association of MAT III to form MAT I: Role of the Disulfide C35-C61 10.5. Complementary Folding Data Obtained in MAT Proteins of Different Origins 11. MAT Inhibitors 12. Role of MAT in Diseases 12.1. Cognitive and Neurodegenerative Diseases 12.2. Human Mutations in MAT1A Gene: Hypermethioninemia and Demyelination 12.3. MAT and Cancer 12.4. MAT and Ethanol 2. MAMMALIAN MATs Early studies on mammalian MATs showed the existence of this activity in all the tissues studied, the highest being observed in liver. However, complex kinetics were obtained which made the results difficult to interpret until the presence of several isoenzymes was realized. Separations carried out on phenyl Sepharose columns showed elution of three peaks with different hydrophobic character; these were named according to the order of elution as MAT I, II and III. All these isoenzymes share some characteristics such as the Mg 2+ dependence of their 9/14/2012 Page 6 of 80 activity (S 0.5 !1 mM), stimulation by K + ions, and their AdoMet-inducible tripolyphosphatase activity [4, 5]. 2.1. MAT I/III isoenzymes Since their discovery, these isoenzymes were known as liver-specific forms of MAT, until Lu et al. in 2003 [6] showed their presence also in pancreas. Several laboratories have reported in depth studies of MAT I and III which have been carried out using adult liver. The differences can be summarized as follows: i) MAT I is a tetramer whereas MAT III is a dimer, with respective Mr appearing as 200 and 110 kDa upon gel filtration chromatography, ii) their Km values for methionine are in the micromolar range for MAT I (60-120 µM) and in the millimolar range for MAT III (1 mM) [7, 8]; iii) MAT III can be activated by DMSO at physiological concentrations of methionine (60 µM) and is highly hydrophobic (eluting from phenyl Sepharose columns at 50% DMSO (v/v)); and, iv) AdoMet inhibits MAT I and activates MAT III. Some of these differences are normally used to distinguish between isoenzymes in activity assays. Both purified proteins show a common single band (designated "1) of approximately 48 kDa on SDS-PAGE, and antibodies raised against the dimer form recognized both, thus suggesting that a single type of subunit arranged in two assemblies could explain the presence of both oligomers [7]. Further experiments that supported this hypothesis included peptide mapping of the purified isoenzymes [7], dissociation of the tetramer to the dimer using LiBr [9] or N-ethylmaleimide (NEM) modification [10]. The final confirmation came upon cloning of a single cDNA [11, 12] followed by overexpresion in E. coli cells [13], which showed in vivo production of dimers and tetramers. This single subunit type is a product of the MAT1A gene that contains nine exons and eight introns spanning !20 kb [14], and has been localized by fluorescence in situ hybridization to the human chromosome 10q.22 [15]. Animal models, as well as the analysis of human samples, led to the identification of changes in the MAT I/III ratio in pathological conditi...

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Molecular‐Recognition Characteristics of SAM‐Binding Riboswitches

Cited by 54 publications

References 28 publications

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

Structural features of metabolite-sensing riboswitches

Methionine Adenosyltransferase (S‐Adenosylmethionine Synthetase)

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