Magnesium-Induced Nucleophile Activation in the Guanylyltransferase mRNA Capping Enzyme

ABSTRACT The Saccharomyces cerevisiae mRNA capping enzyme consists of two subunits: an RNA 5′-triphosphatase (RTPase) and GTP::mRNA guanylyltransferase (GTase). The GTase subunit (Ceg1) binds to the phosphorylated carboxyl-terminal domain of the largest subunit (CTD-P) of RNA polymerase II (pol II), coupling capping with transcription. Ceg1 bound to the CTD-P is inactive unless allosterically activated by interaction with the RTPase subunit (Cet1). For purposes of comparison, we characterize here the related GTases and RTPases from the yeasts Schizosaccharomyces pombe and Candida albicans. Surprisingly, the S. pombe capping enzyme subunits do not interact with each other. Both can independently interact with CTD-P of pol II, and the GTase is not repressed by CTD-P binding. The S. pombe RTPase gene (pct1 +) is essential for viability. Pct1 can replace the S. cerevisiae RTPase when GTase activity is supplied by the S. pombe or mouse enzymes but not by the S. cerevisiae GTase. The C. albicans capping enzyme subunits do interact with each other. However, this interaction is not essential in vivo. Our results reveal an unexpected diversity among the fungal capping machineries.

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Thermodynamics of ligand binding by the yeast mRNA-capping enzyme reveals different modes of binding

Biochemical Journal ◽

10.1042/bj20041112 ◽

2004 ◽

Vol 384 (2) ◽

pp. 411-420 ◽

Cited By ~ 8

Author(s):

Isabelle BOUGIE ◽

Amélie PARENT ◽

Martin BISAILLON

Keyword(s):

Ligand Binding ◽

Entropy Change ◽

Enthalpy Change ◽

Mrna Capping ◽

Capping Enzyme ◽

Eukaryotic Mrnas ◽

Entropic Effect ◽

A Minor ◽

Rna Capping ◽

Capping Enzymes

RNA-capping enzymes are involved in the synthesis of the cap structure found at the 5′-end of eukaryotic mRNAs. The present study reports a detailed study on the thermodynamic parameters involved in the interaction of an RNA-capping enzyme with its ligands. Analysis of the interaction of the Saccharomyces cerevisiae RNA-capping enzyme (Ceg1) with GTP, RNA and manganese ions revealed significant differences between the binding forces that drive the interaction of the enzyme with its RNA and GTP substrates. Our thermodynamic analyses indicate that the initial association of GTP with the Ceg1 protein is driven by a favourable enthalpy change (ΔH=−80.9 kJ/mol), but is also clearly associated with an unfavourable entropy change (TΔS=−62.9 kJ/mol). However, the interaction between Ceg1 and RNA revealed a completely different mode of binding, where binding to RNA is clearly dominated by a favourable entropic effect (TΔS=20.5 kJ/mol), with a minor contribution from a favourable enthalpy change (ΔH=−5.3 kJ/mol). Fluorescence spectroscopy also allowed us to evaluate the initial binding of GTP to such an enzyme, thereby separating the GTP binding step from the concomitant metal-dependent hydrolysis of GTP that results in the formation of a covalent GMP–protein intermediate. In addition to the determination of the energetics of ligand binding, our study leads to a better understanding of the molecular basis of substrate recognition by RNA-capping enzymes.

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Isolation of the mRNA-capping enzyme and ferric-reductase-related genes from Candida albicans

Microbiology ◽

10.1099/00221287-142-9-2515 ◽

1996 ◽

Vol 142 (9) ◽

pp. 2515-2523 ◽

Cited By ~ 38

Author(s):

T. Yamada-Okabe ◽

O. Shimmi ◽

R. Doi ◽

K. Mizumoto ◽

M. Arisawa ◽

...

Keyword(s):

Candida Albicans ◽

Ferric Reductase ◽

Mrna Capping ◽

Capping Enzyme

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Phenotypic analysis of a temperature sensitive mutant in the large subunit of the vaccinia virus mRNA capping enzyme

Virology ◽

10.1016/j.virol.2008.01.028 ◽

2008 ◽

Vol 375 (1) ◽

pp. 236-252 ◽

Cited By ~ 6

Author(s):

Amber N. Shatzer ◽

Sayuri E.M. Kato ◽

Richard C. Condit

Keyword(s):

Vaccinia Virus ◽

Large Subunit ◽

Temperature Sensitive ◽

Phenotypic Analysis ◽

Sensitive Mutant ◽

Temperature Sensitive Mutant ◽

Mrna Capping ◽

Capping Enzyme

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A55 Molecular systematics of sturgeon nucleocytoplasmic large DNA viruses

Virus Evolution ◽

10.1093/ve/vez002.054 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

S Clouthier ◽

E Anderson ◽

G Kurath ◽

R Breyta

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Dna Sequences ◽

Small Subunit ◽

Sequence Length ◽

Dna Viruses ◽

Mrna Capping ◽

Capping Enzyme ◽

Nucleocytoplasmic Large Dna Virus ◽

Nucleocytoplasmic Large Dna Viruses

Abstract Namao virus (NV) is a sturgeon nucleocytoplasmic large DNA virus (sNCLDV) that can cause a lethal disease of the integumentary system in lake sturgeon Acipenser fulvescens. As a group, the sNCLDV have not been assigned to any currently recognized taxonomic family of viruses. In this study, a dataset of NV DNA sequences was generated and assembled as two non-overlapping contigs of 306 and 448 base pairs (bp) and then used to conduct a comprehensive systematics analysis using Bayesian phylogenetic inference for NV, other sNCLDV, and representative members of six families of the NCLDV superfamily. The phylogeny of NV was reconstructed using protein homologues encoded by nine nucleocytoplasmic virus orthologous genes (NCVOGs): NCVOG0022—mcp, NCVOG0038—DNA polymerase B elongation subunit, NCVOG0076—VV A18-type helicase, NCVOG0249—VV A32-type ATPase, NCVOG0262—AL2 VLTF3-like transcription factor, NCVOG0271—RNA polymerase II subunit II, NCVOG0274—RNA polymerase II subunit I, NCVOG0276—ribonucleotide reductase small subunit, and NCVOG1117—mRNA capping enzyme. The accuracy of our phylogenetic method was evaluated using a combination of Bayesian statistical analysis and congruence analysis. Stable tree topologies were obtained with datasets differing in target molecule(s), sequence length, and taxa. Congruent topologies were obtained in phylogenies constructed using individual protein datasets and when four proteins were used in a concatenated approach. The major capsid protein phylogeny indicated that ten representative sNCLDV form a monophyletic group comprised of four lineages within a polyphyletic Mimi-Phycodnaviridae group of taxa. Overall, the analyses revealed that Namao virus is a member of the Mimiviridae family with strong and consistent support for a clade containing NV and CroV as sister taxa.

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Sir2 Silences Gene Transcription by Targeting the Transition between RNA Polymerase II Initiation and Elongation

Molecular and Cellular Biology ◽

10.1128/mcb.00019-08 ◽

2008 ◽

Vol 28 (12) ◽

pp. 3979-3994 ◽

Cited By ~ 34

Author(s):

Lu Gao ◽

David S. Gross

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Transcriptional Silencing ◽

Pol Ii ◽

Initiation Factors ◽

Lysine Deacetylase ◽

Evolutionarily Conserved ◽

Mrna Capping ◽

Capping Enzyme

ABSTRACT It is well accepted that for transcriptional silencing in budding yeast, the evolutionarily conserved lysine deacetylase Sir2, in concert with its partner proteins Sir3 and Sir4, establishes a chromatin structure that prevents RNA polymerase II (Pol II) transcription. However, the mechanism of repression remains controversial. Here, we show that the recruitment of Pol II, as well as that of the general initiation factors TBP and TFIIH, occurs unimpeded to the silent HMR a 1 and HMLα1/HMLα2 mating promoters. This, together with the fact that Pol II is Ser5 phosphorylated, implies that SIR-mediated silencing is permissive to both preinitiation complex (PIC) assembly and transcription initiation. In contrast, the occupancy of factors critical to both mRNA capping and Pol II elongation, including Cet1, Abd1, Spt5, Paf1C, and TFIIS, is virtually abolished. In agreement with this, efficiency of silencing correlates not with a restriction in Pol II promoter occupancy but with a restriction in capping enzyme recruitment. These observations pinpoint the transition between polymerase initiation and elongation as the step targeted by Sir2 and indicate that transcriptional silencing is achieved through the differential accessibility of initiation and capping/elongation factors to chromatin. We compare Sir2-mediated transcriptional silencing to a second repression mechanism, mediated by Tup1. In contrast to Sir2, Tup1 prevents TBP, Pol II, and TFIIH recruitment to the HMLα1 promoter, thereby abrogating PIC formation.

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Vesicular Stomatitis Virus mRNA Capping Machinery Requires Specific cis-Acting Signals in the RNA

Journal of Virology ◽

10.1128/jvi.01057-07 ◽

2007 ◽

Vol 81 (20) ◽

pp. 11499-11506 ◽

Cited By ~ 30

Author(s):

Jennifer T. Wang ◽

Lauren E. McElvain ◽

Sean P. J. Whelan

Keyword(s):

Vesicular Stomatitis Virus ◽

Rna Viruses ◽

Translation Strategies ◽

Cis Acting ◽

Specific Manner ◽

Mrna Capping ◽

Capping Enzyme ◽

Vesicular Stomatitis ◽

Rna Capping ◽

Negative Sense

ABSTRACT Many viruses of eukaryotes that use mRNA cap-dependent translation strategies have evolved alternate mechanisms to generate the mRNA cap compared to their hosts. The most divergent of these mechanisms are those used by nonsegmented negative-sense (NNS) RNA viruses, which evolved a capping enzyme that transfers RNA onto GDP, rather than GMP onto the 5′ end of the RNA. Working with vesicular stomatitis virus (VSV), a prototype of the NNS RNA viruses, we show that mRNA cap formation is further distinct, requiring a specific cis-acting signal in the RNA. Using recombinant VSV, we determined the function of the eight conserved positions of the gene-start sequence in mRNA initiation and cap formation. Alterations to this sequence compromised mRNA initiation and separately formation of the GpppA cap structure. These studies provide genetic and biochemical evidence that the mRNA capping apparatus of VSV evolved an RNA capping machinery that functions in a sequence-specific manner.

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