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Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Escherichia coli K-12 Synechocystis sp. PCC 6803

PROVIDER: GSE115135 | GEO | 2018/08/15

REPOSITORIES: GEO

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Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Ecoli]

Project description:We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.

2018-08-15 | GSE115132 | GEO

Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Synechoscystis sp]

2018-08-15 | GSE115134 | GEO

Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors

Project description:Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors

| PRJNA473848 | ENA

High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors.

Project description:The vast majority of organisms possess transcription elongation factors, the functionally similar bacterial Gre and eukaryotic/archaeal TFIIS/TFS. Their main cellular functions are to proofread errors of transcription and to restart elongation via stimulation of RNA hydrolysis by the active centre of RNA polymerase (RNAP). However, a number of taxons lack these factors, including one of the largest and most ubiquitous groups of bacteria, cyanobacteria. Using cyanobacterial RNAP as a model, we investigated alternative mechanisms for maintaining a high fidelity of transcription and for RNAP arrest prevention. We found that this RNAP has very high intrinsic proofreading activity, resulting in nearly as low a level of in vivo mistakes in RNA as Escherichia coli. Features of the cyanobacterial RNAP hydrolysis are reminiscent of the Gre-assisted reaction-the energetic barrier is similarly low, and the reaction involves water activation by a general base. This RNAP is resistant to ubiquitous and most regulatory pausing signals, decreasing the probability to go off-pathway and thus fall into arrest. We suggest that cyanobacterial RNAP has a specific Trigger Loop domain conformation, and isomerises easier into a hydrolytically proficient state, possibly aided by the RNA 3'-end. Cyanobacteria likely passed these features of transcription to their evolutionary descendants, chloroplasts.

| S-EPMC7026648 | biostudies-literature

Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Ecoli]

Project description:Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Ecoli]

| PRJNA473847 | ENA

Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Synechoscystis sp]

Project description:Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Synechoscystis sp]

| PRJNA473849 | ENA

Long patch base excision repair compensates for DNA polymerase ? inactivation by the C4'-oxidized abasic site.

Project description:The C4'-oxidized abasic site (C4-AP), which is produced by a variety of damaging agents, has significant consequences for DNA. The lesion is highly mutagenic and reactive, resulting in interstrand cross-links. The base excision repair of DNA containing independently generated C4-AP was examined. C4-AP is incised by Ape1 ~12-fold less efficiently than an apurinic/apyrimidinic lesion. DNA polymerase ? induces the ?-elimination of incised C4-AP in ternary complexes, duplexes, and single-stranded substrate. However, excision from a ternary complex is most rapid. In addition, the lesion inactivates the enzyme after approximately seven turnovers on average by reacting with one or more lysine residues in the lyase active site. Unlike 5'-(2-phosphoryl-1,4-dioxobutane), which very efficiently irreversibly inhibits DNA polymerase ?, the lesion is readily removed by strand displacement synthesis conducted by the polymerase in conjunction with flap endonuclease 1. DNA repair inhibition by C4-AP may be a partial cause of the cytotoxicity of drugs that produce this lesion.

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Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-12-31 | GSE124644 | GEO

Proofreading dynamics of a processive DNA polymerase.

Project description:Replicative DNA polymerases present an intrinsic proofreading activity during which the DNA primer chain is transferred between the polymerization and exonuclease sites of the protein. The dynamics of this primer transfer reaction during active polymerization remain poorly understood. Here we describe a single-molecule mechanical method to investigate the conformational dynamics of the intramolecular DNA primer transfer during the processive replicative activity of the Phi 29 DNA polymerase and two of its mutants. We find that mechanical tension applied to a single polymerase-DNA complex promotes the intramolecular transfer of the primer in a similar way to the incorporation of a mismatched nucleotide. The primer transfer is achieved through two novel intermediates, one a tension-sensitive and functional polymerization conformation and a second non-active state that may work as a fidelity check point for the proofreading reaction.

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Circadian control of global gene expression by the cyanobacterial master regulator RpaA

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-04 | E-GEOD-50922 | biostudies-arrayexpress