RNA-Dependent Cysteine Biosynthesis in Archaea

Sauerwald, Anselm; Zhu, Wenhong; Major, Tiffany A.; Roy, Hervé; Palioura, Sotiria; Jahn, Dieter; Whitman, William B.; Yates, John R.; Ibba, Michael; Söll, Dieter

doi:10.1126/science.1108329

Cited by 234 publications

(293 citation statements)

References 30 publications

Supporting

Mentioning

286

Contrasting

Unclassified

Order By: Relevance

“…MJ1660 and its orthologs form a monophyletic gene family that is obviously unrelated to the typical class I CysRS (9). The story was soon confirmed and elaborated by the elegant biochemical and genetic work of Söll and colleagues (10), who showed that the suspected class II CysRS, now properly renamed SepRS (O-phosphoseryl-RS), actually loaded O-phosphoserine (Sep), a precursor of cysteine, onto tRNA Cys . The noncognate Sep-tRNA Cys is then converted to the cognate pairing by the enzyme Sep-tRNA:Cys-tRNA synthase (SepCysS) (MJ1678).…”

mentioning

confidence: 56%

The evolutionary history of Cys-tRNA ^Cys formation

O’Donoghue

Sethi

Woese

et al. 2005

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

100

View full text Add to dashboard Cite

The recent discovery of an alternate pathway for indirectly charging tRNA Cys has stimulated a re-examination of the evolutionary history of Cys-tRNA Cys formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA Cys with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA Cys aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.aminoacyl-tRNA synthetase ͉ cysteine ͉ methanogenic archaea ͉ O-phosphoserine ͉ structure and sequence-based phylogeny

show abstract

mentioning

confidence: 56%

The evolutionary history of Cys-tRNA ^Cys formation

O’Donoghue

Sethi

Woese

et al. 2005

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

100

View full text Add to dashboard Cite

show abstract

“…For both Class I and Class II aminoacyl-tRNA synthetases, the pre-steady state kinetics of aminoacylation can be simplified using a two step irreversible mechanism: (7) For this mechanism, the time dependence of product formation is given by a single exponential followed by a linear phase: (8) In this form of the equation, [P] represents the concentration of product formed, and [E 0 ] represents the concentration of enzyme in the reaction. The quotient [P]/[E 0 ] is a useful way to express the moles of product formed per active site, and is thus independent of the amount of enzyme used in the experiment.…”

Section: Rapid Quench Methods For Studying the Half Reactions Of Aminmentioning

confidence: 99%

“…In some taxa, there is an aaRS corresponding to each of the 20 standard amino acids. However, only 17 canonical aaRS are conserved in all organisms: for asparagine, glutamine, and cysteine, indirect pathways exist by which the AA-tRNA AA is synthesized on the tRNA, after initial aminoacylation by a noncognate or noncanonical aaRS [7,8]. Each aaRS obligatorily interacts with three distinct substrates: ATP, amino acid and tRNA.…”

Section: Introductionmentioning

confidence: 99%

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases

Francklyn

First

Perona

et al. 2008

Methods

110

120

View full text Add to dashboard Cite

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion.

show abstract

“…In the first step, O-phosphoseryl-tRNA synthetase (SepRS), a novel class II aaRS encoded by MJ1660, forms Sep-tRNA Cys . Then a second enzyme, Sep-tRNA:Cys-tRNA synthase (SepCysS), converts this tRNA to correctly charged Cys-tRNA Cys (27). This indirect mechanism of Cys-tRNA formation is confined to certain members of the Euryarchaea (Fig.…”

mentioning

confidence: 99%

“…An initial suggestion (25), later supported by bioinformatic analysis (26), predicted a class II tRNA synthetase (encoded by MJ1660) would cysteinylate tRNA Cys . However, biochemical work established that in M. jannaschii Cys-tRNA is formed by a two-step pretranslational amino acid modification (27). In the first step, O-phosphoseryl-tRNA synthetase (SepRS), a novel class II aaRS encoded by MJ1660, forms Sep-tRNA Cys .…”

mentioning

confidence: 99%

Emergence of the universal genetic code imprinted in an RNA record

Hohn¹,

Park²,

O’Donoghue³

et al. 2006

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

View full text Add to dashboard Cite

The molecular basis of the genetic code manifests itself in the interaction of the aminoacyl-tRNA synthetases and their cognate tRNAs. The fundamental biological question regarding these enzymes' role in the evolution of the genetic code remains open. Here we probe this question in a system in which the same tRNA species is aminoacylated by two unrelated synthetases. Should this tRNA possess major identity elements common to both enzymes, this would favor a scenario where the aminoacyl-tRNA synthetases evolved in the context of preestablished tRNA identity, i.e., after the universal genetic code emerged. An experimental system is provided by the recently discovered O-phosphoseryl-tRNA synthetase (SepRS), which acylates tRNA Cys with phosphoserine (Sep), and the well known cysteinyl-tRNA synthetase, which charges the same tRNA with cysteine. We determined the identity elements of Methanocaldococcus jannaschii tRNA Cys in the aminoacylation reaction for the two Methanococcus maripaludis synthetases SepRS (forming Sep-tRNA Cys ) and cysteinyl-tRNA synthetase (forming Cys-tRNA Cys ). The major elements, the discriminator base and the three anticodon bases, are shared by both tRNA synthetases. An evolutionary analysis of archaeal, bacterial, and eukaryotic tRNA Cys sequences predicted additional SepRS-specific minor identity elements (G37, A47, and A59) and suggested the dominance of vertical inheritance for tRNA Cys from a single common ancestor. Transplantation of the identified identity elements into the Escherichia coli tRNA Gly scaffold endowed facile phosphoserylation activity on the resulting chimera. Thus, tRNA Cys identity is an ancient RNA record that depicts the emergence of the universal genetic code before the evolution of the modern aminoacylation systems.aminoacyl-tRNA synthetase ͉ evolution ͉ O-phosphoseryl-tRNA synthetase ͉ tRNA identity

show abstract

RNA-Dependent Cysteine Biosynthesis in Archaea

Cited by 234 publications

References 30 publications

The evolutionary history of Cys-tRNA ^Cys formation

The evolutionary history of Cys-tRNA ^Cys formation

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases

Emergence of the universal genetic code imprinted in an RNA record

Contact Info

Product

Resources

About

RNA-Dependent Cysteine Biosynthesis in Archaea

Cited by 234 publications

References 30 publications

The evolutionary history of Cys-tRNA Cys formation

The evolutionary history of Cys-tRNA Cys formation

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases

Emergence of the universal genetic code imprinted in an RNA record

Contact Info

Product

Resources

About

The evolutionary history of Cys-tRNA ^Cys formation

The evolutionary history of Cys-tRNA ^Cys formation