Simple, recurring RNA binding sites for L-arginine

Janas, Tadeusz; Widmann, Jeremy; Knight, Rob; Yarus, Michael

doi:10.1261/rna.1979410

Cited by 37 publications

(53 citation statements)

References 30 publications

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“…This implies that this core peptidyl transferase sequence came from selection on a molecule very like modern RNA (because RNA activities are usually disrupted by minor modification of their nucleotides [Paul et al 2006]). Similarly, in all four cases so far examined, successively squeezed selection shows that the simplest binding sites for Ile (Lozupone et al 2003), Trp , His , and Arg (Janas et al 2010) contain essential cognate coding triplets. Thus, the finding (Yarus et al , 2009Johnson and Wang 2010) that codons and anticodons occur broadly in modern RNAamino acid interactions strongly suggests that biological ; these values are collected in Table 4.…”

Section: Rna Chemistry and Evolutionary Questionsmentioning

confidence: 71%

Chiral histidine selection by D-ribose RNA

Illangasekare

Turk²,

Peterson³

et al. 2010

RNA

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The invariant choice of L-amino acids and D-ribose RNA for biological translation requires explanation. Here we study this chiral choice using mixed, equimolar D-ribose RNAs having 15, 18, 21, 27, 35, and 45 contiguous randomized nucleotides. These are used for simultaneous affinity selection of the smallest bound and eluted RNAs using equal amounts of L-and D-His immobilized on an achiral glass support, with racemic histidine elution. The experiment as a whole therefore determines whether RNA containing D-ribose binds L-histidine or D-histidine more easily (that is, by using a site that is more abundant/ requires fewer nucleotides). The most prevalent/smallest RNA sites are reproducibly and repeatedly selected and there is a four-to sixfold greater abundance of L-histidine sites. RNA's chiral D-ribose therefore yields a more frequent fit to L-histidine. Accordingly, a D-ribose RNA site for L-His is smaller by the equivalent of just over one conserved nucleotide. The most prevalent L-His site also performs better than the most frequent D-His site-but rarer D-ribose RNAs can bind D-His with excellent affinity and discrimination. The prevalent L-His site is one we have selected before under very different conditions. Thus, selection is again reproducible, as is the recurrence of cognate coding triplets in these most probable L-His sites. If our selected RNA population were equilibrated with racemic His, we calculate that L-His would participate in seven of eight His:RNA complexes, or more. Thus, if D-ribose RNA were first chosen biologically, translational L-His usage could have followed.

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Section: Rna Chemistry and Evolutionary Questionsmentioning

confidence: 71%

Chiral histidine selection by D-ribose RNA

Illangasekare

Turk²,

Peterson³

et al. 2010

RNA

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“…The binding site contains (enriched in) the codon and/or the anticodon for the cognate amino acid. This was shown for arginine (Connell et al, 1993;Janas et al, 2010); histidine Turk-MacLeod et al, 2012); tryptophan ; isoleucine (Legiewicz and Yarus, 2005;Lozupone et al, 2003;Majerfeld and Yarus, 1998) (some of the aptamers can also discriminate against valine and norleucine); phenylalanine (Illangasekare and Yarus, 2002); and tyrosine (Mannironi et al, 2000). On the other hand, no such enrichment were observed for leucine, valine and glutamine.…”

Section: The Stereochemical Hypothesismentioning

confidence: 95%

The evolution of the genetic code: Impasses and challenges

Kun

Radványi

2018

Biosystems

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The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. The stereochemical, the coding coenzyme handle, the coevolution, the four-column theory, the error minimization and the frozen accident hypotheses are discussed. The integration of these hypotheses can account for the origin of the genetic code. But experiments are badly needed. Thus we suggest a host of experiments that could (in)validate some of the models. We focus especially on the coding coenzyme handle hypothesis (CCH). The CCH suggests that amino acids attached to RNA handles enhanced catalytic activities of ribozymes. Alternatively, amino acids without handles or with a handle consisting of a single adenine, like in contemporary coenzymes could have been employed. All three scenarios can be tested in in vitro compartmentalized systems.

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“…HeLa cell RNA and RNA from sucrose gradient fractions (3s, 8s, 12s) were extracted by TRIzol-LS Reagent using the manufacturer's protocol and 39-end radiolabeled (Janas et al 2010) if needed.…”

Section: Extraction Of Rna and Lipids From Hela Cellsmentioning

confidence: 99%

Human tRNA^Secassociates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers

Janas

Yarus

2012

RNA

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We have shown previously that simple RNA structures bind pure phospholipid liposomes. However, binding of bona fide cellular RNAs under physiological ionic conditions is shown here for the first time. Human tRNA Sec contains a hydrophobic anticodon-loop modification: N 6 -isopentenyladenosine (i 6 A) adjacent to its anticodon. Using a highly specific double-probe hybridization assay, we show mature human tRNA Sec specifically retained in HeLa intermediate-density membranes. Further, isolated human tRNA Sec rebinds to liposomes from isolated HeLa membrane lipids, to a much greater extent than an unmodified tRNA Sec transcript. To better define this affinity, experiments with pure lipids show that liposomes forming rafts or including positively charged sphingosine, or particularly both together, exhibit increased tRNA Sec binding. Thus tRNA Sec residence on membranes is determined by several factors, such as hydrophobic modification (likely isopentenylation of tRNA Sec ), lipid structure (particularly lipid rafts), or sphingosine at a physiological concentration in rafted membranes. From prior work, RNA structure and ionic conditions also appear important. tRNA Sec dissociation from HeLa liposomes implies a mean membrane residence of 7.6 min at 24°C (t 1 ⁄ 2 = 5.3 min). Clearly RNA with a 5-carbon hydrophobic modification binds HeLa membranes, probably favoring raft domains containing specific lipids, for times sufficient to alter biological fates.

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Simple, recurring RNA binding sites for L-arginine

Cited by 37 publications

References 30 publications

Chiral histidine selection by D-ribose RNA

Chiral histidine selection by D-ribose RNA

The evolution of the genetic code: Impasses and challenges

Human tRNA^Secassociates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers

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Simple, recurring RNA binding sites for L-arginine

Cited by 37 publications

References 30 publications

Chiral histidine selection by D-ribose RNA

Chiral histidine selection by D-ribose RNA

The evolution of the genetic code: Impasses and challenges

Human tRNASecassociates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers

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Product

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Human tRNA^Secassociates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers