Self-Incorporation of coenzymes by ribozymes

Breaker, Ronald R.; Joyce, Gerald F.

doi:10.1007/bf00160500

Cited by 50 publications

(37 citation statements)

References 41 publications

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“…When the limited catalytic repertoire of natural ribozymes is considered, the notion that complex networks of metabolic reactions could be guided entirely by RNA appears tenuous. Ancient ribozymes, however, may have created a larger catalytic repertoire by using various divalent metals (5) and by using nucleotide-like cofactors (6)(7)(8) to supplement the limited set of chemical groups that make up unmodified RNA. In recent years, a surprising number of artificial ribozymes have been created by using in vitro selection (9) that catalyze various chemical reactions including alkylation, acylation, phosphorylation, and ester and amide bond formation.…”

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confidence: 99%

An amino acid as a cofactor for a catalytic polynucleotide

Roth

Breaker

1998

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

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Natural ribozymes require metal ion cofactors that aid both in structural folding and in chemical catalysis. In contrast, many protein enzymes produce dramatic rate enhancements using only the chemical groups that are supplied by their constituent amino acids. This fact is widely viewed as the most important feature that makes protein a superior polymer for the construction of biological catalysts. Herein we report the in vitro selection of a catalytic DNA that uses histidine as an active component for an RNA cleavage reaction. An optimized deoxyribozyme from this selection requires L-histidine or a closely related analog to catalyze RNA phosphoester cleavage, producing a rate enhancement of Ϸ1-million-fold over the rate of substrate cleavage in the absence of enzyme. Kinetic analysis indicates that a DNA-histidine complex may perform a reaction that is analogous to the first step of the proposed catalytic mechanism of RNase A, in which the imidazole group of histidine serves as a general base catalyst. Similarly, ribozymes of the ''RNA world'' may have used amino acids and other small organic cofactors to expand their otherwise limited catalytic potential.The ''RNA world'' theory for the origins of life holds that RNA was able to replicate in the absence of DNA and proteins (1). Some manifestations of this theory (1-3) include the view that, during the latter stages of the RNA world, ribozymes were not primitive and ineffectual but were directing a complex metabolic state replete with RNA and DNA synthesis machinery and a host of RNA enzymes necessary to catalyze supportive chemical reactions. Proponents of this view argue that a sophisticated metabolism mediated entirely by RNA would have been necessary for ribozymes to give rise to encoded protein synthesis-a precursor to the complex system of translation that is present in all extant organisms. To achieve maximum catalytic rate enhancements, natural ribozymes require Mg 2ϩ or other metal ion cofactors to induce structure formation or to participate directly in the catalytic process (4), perhaps defining a limitation to the catalytic potential for polynucleotide-based enzymes. When the limited catalytic repertoire of natural ribozymes is considered, the notion that complex networks of metabolic reactions could be guided entirely by RNA appears tenuous. Ancient ribozymes, however, may have created a larger catalytic repertoire by using various divalent metals (5) and by using nucleotide-like cofactors (6-8) to supplement the limited set of chemical groups that make up unmodified RNA. In recent years, a surprising number of artificial ribozymes have been created by using in vitro selection (9) that catalyze various chemical reactions including alkylation, acylation, phosphorylation, and ester and amide bond formation. In addition, the catalytic rates of ribozymes can be tightly regulated by using allosteric mechanisms (10), indicating that the potential for extensive and sophisticated catalysis by nucleic acids is large. Moreover, the full range of reac...

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mentioning

confidence: 99%

An amino acid as a cofactor for a catalytic polynucleotide

Roth

Breaker

1998

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

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168

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“…A few modified nucleotidelike coenzymes such as nicotinamide guanine dinucleotide and dephosphorylated CoA have been incorporated into a modified Tetrahymena group I ribozyme through the sugar hydroxyl group (8). The ribozyme recognizes guanosine and adenosine with free 2Ј,3Ј-hydroxyl groups that must be introduced by the experimenters.…”

Section: Discussionmentioning

confidence: 99%

Versatile 5′ phosphoryl coupling of small and large molecules to an RNA

Huang

Yarus

1997

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

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A Ca 2؉ -requiring catalytic RNA is shown to create 5 phosphate-phosphate linkages with all nucleotides and coenzymes including CoA, nicotinamide adenine dinucleotide phosphate, thiamine phosphate, thiamine pyrophosphate, and f lavin mononucleotide. In addition to these small molecules, macromolecules such as RNAs with 5-diphosphates, and nonnucleotide molecules like N-phosphate arginine and 6-phosphate gluconic acid also react. That is, the self-capping RNA isolate 6 is an apparently universal 5 phosphate-linker, reacting with any nucleophile containing an unblocked phosphate. These RNA reactions demonstrate a unique RNA catalytic capability and imply versatile and specific posttranscriptional RNA modification by RNA catalysis.RNA molecules are thought to have played prominent roles as both carriers of genetic information and catalysts for chemical transformations in a primordial RNA world (1, 2), from which modern protein-catalyzed metabolism has evolved (3, 4). This RNA world hypothesis requires that RNA molecules be able to catalyze a broad range of chemical reactions that are presently carried out by protein enzymes in modern proteinnucleic acid world. Whereas RNAs have been shown to catalyze a variety of reactions, most of which involve the nucleic acid phosphate-sugar backbone, RNA-catalyzed reactions discovered so far are still quite limited compared with protein-catalyzed reactions. Thus new RNA-catalyzed reactions expand the catalytic RNA repertoire and thereby provide clues to the extent and nature of the RNA world (1, 2).We selected an RNA (isolate 6) that catalyzed a self-capping reaction with free GDP (5) in the presence of Ca 2ϩ , yielding the same 5Ј-capped structure as is formed on eukaryotic mRNA by protein GTP:RNA guanylyltransferase. The RNA self-capping reaction involves the nucleophilic attack on the 5Ј ␣-phosphate of the pppRNA (RNA with 5Ј-triphosphate) by the oxygen of ␤-phosphate of GDP with subsequent release of PP i :[1]We now report that the self-capping RNA catalyst can react via attack on the ␣-phosphate of the pppRNA from an oxygen of any nucleophile's terminal phosphate. The current finding generalizes this catalytic capability of RNA and thereby implies a route to versatile 5Ј RNA posttranscriptional modification. MATERIALS AND METHODSReagents. Mes, 3Ј-NMPs, 5Ј-NMP, NDPs, NTPs, adenosine 5Ј-tetraphosphate (ppppA), guanosine 5Ј-tetraphosphates (ppppG), thiamine phosphate (thiamine-P), thiamine pyrophosphate (thiamine-PP), reduced and oxidized CoA (90-95% purity), acetyl CoA (90-95% purity), 3Ј-NADP (oxidized form, 80-90% purity), N-phosphate arginine (phosphoarginine), and 6-phosphate gluconic acid were from Sigma. FMN (oxidized form) was purchased from Fluka. Calf intestinal alkaline phosphatase (CIAP) was from New England Biolabs. Shrimp alkaline phosphatase (SAP) was from United States Biochemical. G-25 microspin gel filtration columns were from Pharmacia.RNA Preparation. Internally 32 P-labeled 104-mer selfcapping RNA (isolate 6 RNA), 5Ј-ppp ggggaguacgggagaggauacuacac...

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“…To test whether cofactors can be self-incorporated into RNA sequences, Breaker and Joyce have used the Tetrahymena thermophila group I intron ribozyme [25]. This ribozyme normally promotes its own excision from a pre-rRNA molecule by catalyzing two successive phosphoester transfer reactions, resulting in self-splicing of intron and ligation of the flanking 5′-and 3′-exons [1].…”

Section: Self-incorporation Of Redox Cofactors Into Rnamentioning

confidence: 99%

Ribozymes that use redox cofactors

Tsukiji

Ramaswamy

Suga

2004

Pure and Applied Chemistry

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This review summarizes the history and most recent advances in aptamers and ribozymes that bind and use redox(reduction-oxidation) cofactors. Redox reactions, catalyzed by protein enzymes in an extant world, play a central role in the metabolism of numerous biological molecules in the living organisms. The burden of catalyzing these reactions in a preprotein-based world (i.e., the hypothesized RNA World) could have been borne by RNA molecules. To this end, we raise a fundamental question: can RNA accelerate the redox chemical transformation? We hope that this article will be able to shed light on this intriguing question.

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Self-Incorporation of coenzymes by ribozymes

Cited by 50 publications

References 41 publications

An amino acid as a cofactor for a catalytic polynucleotide

An amino acid as a cofactor for a catalytic polynucleotide

Versatile 5′ phosphoryl coupling of small and large molecules to an RNA

Ribozymes that use redox cofactors

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