Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Breaking the rules: bacteria that use several DNA polymerase IIIs.

ABSTRACT: Studies using Escherichia coli DNA polymerase (Pol) III as the prototype for bacterial DNA replication have suggested that--in contrast to eukaryotes--one replicase performs all of the main functions at the replication fork. However, recent studies have revealed that replication in other bacteria requires two forms of Pol III, one of which seems to extend RNA primers by only a few nucleotides before transferring the product to the other polymerase--an arrangement analogous to that in eukaryotes. Yet another group of bacteria encode a second Pol III (ImuC), which apparently replaces a Pol Y-type polymerase (Pol V) that is required for induced mutagenesis in E. coli. A complete understanding of complex bacterial replicases will allow the simultaneous biochemical screening of all their components and, thus, the identification of new antibacterial compounds.

SUBMITTER: McHenry CS

PROVIDER: S-EPMC3090020 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Breaking the rules: bacteria that use several DNA polymerase IIIs.

McHenry Charles S CS

EMBO reports 20110408 5

Studies using Escherichia coli DNA polymerase (Pol) III as the prototype for bacterial DNA replication have suggested that--in contrast to eukaryotes--one replicase performs all of the main functions at the replication fork. However, recent studies have revealed that replication in other bacteria requires two forms of Pol III, one of which seems to extend RNA primers by only a few nucleotides before transferring the product to the other polymerase--an arrangement analogous to that in eukaryotes. ...[more]

PMID: 21475246

Similar Datasets

Breaking the Rules: Protein Sculpting in NEIL2 Regulation.

Project description:The canonical DNA glycosylase role is global base damage repair but includes functions in epigenetic gene regulation, immune response modulation, replication, and transcription. In this issue of Structure, Eckenroth et al. (2020) present the NEIL2 glycosylase structure. Its catalytic domain flexibility differentiates it from most other glycosylases and suggests novel regulatory mechanisms.

| S-EPMC7909728 | biostudies-literature

Breaking conversational rules matters to captive gorillas: A playback experiment.

Project description:Across human cultures, conversations are regulated by temporal and social rules. The universality of conversational rules suggests possible biological bases and encourages comparisons with the communicative interactions of nonhuman animals. Unexpectedly, few studies have focused on other great apes despite evidence of proto-conversational rules in monkeys, thus preventing researchers from drawing conclusions on potential evolutionary origins of this behaviour. A previous study showed however that western lowland gorillas engage in soft call interactions that seem temporally- and socially-ruled. Indeed, interactions occurred mainly between individuals close in age who followed a preset response delay, thus preventing call overlap. Here, we experimentally investigated the presence of these rules in a captive gorilla group, using a violation-of-expectation paradigm. Head orientation responses suggest that the respect of response delay matters to subjects, but the importance of the interlocutors' age proximity appeared less clear. The intensity of the response varied with subjects' age in a context-dependent way, supporting a possible role of learning. Our findings support the growing number of studies highlighting the importance of vocal turn-taking in animals and a possible sociogenesis of this ability. The capacity to "converse" might have been a key step in the co-evolution of communication and complex sociality.

| S-EPMC7181860 | biostudies-literature

Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase.

Project description:From supercoiled DNA to the tight loops of DNA formed by some gene repressors, DNA in cells is often highly bent. Despite evidence that transcription by RNA polymerase (RNAP) is affected in systems where DNA is deformed significantly, the mechanistic details underlying the relationship between polymerase function and mechanically stressed DNA remain unclear. Seeking to gain additional insight into the regulatory consequences of highly bent DNA, we hypothesize that tightly looping DNA is alone sufficient to repress transcription. To test this hypothesis, we have developed an assay to quantify transcription elongation by bacteriophage T7 RNAP on small, circular DNA templates approximately 100 bp in size. From these highly bent transcription templates, we observe that the elongation velocity and processivity can be repressed by at least two orders of magnitude. Further, we show that minicircle templates sustaining variable levels of twist yield only moderate differences in repression efficiency. We therefore conclude that the bending mechanics within the minicircle templates dominate the observed repression. Our results support a model in which RNAP function is highly dependent on the bending mechanics of DNA and are suggestive of a direct, regulatory role played by the template itself in regulatory systems where DNA is known to be highly bent.

| S-EPMC2920717 | biostudies-literature

Recurrent evolution of herbivory in small, cold-climate lizards: breaking the ecophysiological rules of reptilian herbivory.

Project description:Herbivory has evolved in many groups of vertebrates, but it is rare among both extinct and extant nonavian reptiles. Among squamate reptiles, (lizards, snakes, and their relatives), <2% of the >7,800 species are considered to be herbivorous, and herbivory is restricted to lizards. Here, we show that within a group of South American lizards (Liolaemidae, approximately 170 species), herbivory has evolved more frequently than in all other squamates combined and at a rate estimated to be >65 times faster. Furthermore, in contrast to other herbivorous lizards and to existing theory, most herbivorous liolaemids are small bodied and live in cool climates. Herbivory is generally thought to evolve only in reptile species that are large bodied, live in warm climates, and maintain high body temperatures. These three well known "rules" of herbivory are considered to form the bases of physiological constraints that explain the paucity of herbivorous reptile species. We suggest that the recurrent and paradoxical evolution of herbivory in liolaemids is explained by a combination of environmental conditions (promoting independent origins of herbivory in isolated cool-climate regions), ecophysiological constraints (requiring small body size in cool climates, yet high body temperatures for herbivores), and phylogenetic history. More generally, our study demonstrates how integrating information from ecophysiology and phylogeny can help to explain macroevolutionary trends.

| S-EPMC534712 | biostudies-literature

CryoET of bacterial RNA polymerase with several detergents

Project description: Not available

| EMPIAR-10214 | biostudies-other

DNA polymerase ? proofreads errors made by DNA polymerase ?.

Project description:During eukaryotic replication, DNA polymerases ? (Pol?) and ? (Pol?) synthesize the leading and lagging strands, respectively. In a long-known contradiction to this model, defects in the fidelity of Pol? have a much weaker impact on mutagenesis than analogous Pol? defects. It has been previously proposed that Pol? contributes more to mutation avoidance because it proofreads mismatches created by Pol? in addition to its own errors. However, direct evidence for this model was missing. We show that, in yeast, the mutation rate increases synergistically when a Pol? nucleotide selectivity defect is combined with a Pol? proofreading defect, demonstrating extrinsic proofreading of Pol? errors by Pol?. In contrast, combining Pol? nucleotide selectivity and Pol? proofreading defects produces no synergy, indicating that Pol? cannot correct errors made by Pol?. We further show that Pol? can remove errors made by exonuclease-deficient Pol? in vitro. These findings illustrate the complexity of the one-strand-one-polymerase model where synthesis appears to be largely divided, but Pol? proofreading operates on both strands.

| S-EPMC7084062 | biostudies-literature

The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames.

Project description:A previous report described the discovery of a group I, self-splicing intron in the DNA polymerase gene of the Bacillus subtilis bacteriophage SPO1 (1). In this study, the DNA polymerase genes of three close relatives of SPO1: SP82, 2C and phi e, were also found to be interrupted by an intron. All of these introns have group I secondary structures that are extremely similar to one another in primary sequence. Each is interrupted by an open reading frame (ORF) that, unlike the intron core or exon sequences, are highly diverged. Unlike the relatives of Escherichia coli bacteriophage T4, most of which do not have introns (2), this intron seems to be common among the relatives of SPO1.

| S-EPMC308352 | biostudies-other

Assessment of the rules related to gaining activity against Gram-negative bacteria.

Project description:In the search for new antibacterial compounds, we repositioned an antimalarial compound class by derivatising it based on the so-called "eNTRy" rules for enhanced accumulation into Gram-negative bacteria. We designed, synthesised and evaluated a small library of amino acid modified compounds together with the respective Boc-protected analogues, leading to no substantial improvement in antibacterial activity against Escherichia coli wild-type K12, whereas more distinct activity differences were observed in E. coli mutant strains ΔtolC, D22, ΔacrB and BL21(DE3)omp8. A comparison of the activity results of the E. coli mutants with respect to the known rules related to enhanced activity against Gram-negative bacteria revealed that applicability of the rules is not always ensured. Out of the four amino acids used in this study, glycine derivatives showed highest antibacterial activity, although still suffering from efflux issues.

| S-EPMC8128065 | biostudies-literature

Use HypE to Hide Association Rules by Adding Items.

Project description:During business collaboration, partners may benefit through sharing data. People may use data mining tools to discover useful relationships from shared data. However, some relationships are sensitive to the data owners and they hope to conceal them before sharing. In this paper, we address this problem in forms of association rule hiding. A hiding method based on evolutionary multi-objective optimization (EMO) is proposed, which performs the hiding task by selectively inserting items into the database to decrease the confidence of sensitive rules below specified thresholds. The side effects generated during the hiding process are taken as optimization goals to be minimized. HypE, a recently proposed EMO algorithm, is utilized to identify promising transactions for modification to minimize side effects. Results on real datasets demonstrate that the proposed method can effectively perform sanitization with fewer damages to the non-sensitive knowledge in most cases.

| S-EPMC4466550 | biostudies-literature

Single-run, parallel detection of DNA from three pneumonia-producing bacteria by real-time polymerase chain reaction.

Project description:A molecular assay for parallel detection of three bacteria, Chlamydia (C.) pneumoniae, Legionella (L.) spp., and Mycoplasma (M.) pneumoniae, in clinical specimens by a set of real-time polymerase chain reactions (PCRs) in a single run was evaluated. Bacterial DNAs were extracted by an automated DNA extraction protocol on the MagNA Pure LC System. Amplification and detection were done by real-time PCR on the LightCycler (LC) instrument. For amplification, specific oligonucleotides derived from the 16s rRNA genes of C. pneumoniae, L. spp., and M. pneumoniae were used. The three assays were complemented with an internal control (IC), a specially designed DNA fragment which contains the specific primer binding sites for the three PCRs. The IC was added to the samples, co-extracted, and co-amplified. Primers and hybridization probes were designed to suit one LC PCR program. LC PCRs were established, detection limits were determined, and clinical samples were tested. The detection limits were found between 5.0 and 0.5 IFU/CFU per PCR reaction for each of the bacteria. A total number of 100 clinical specimens were tested for validation of the molecular assay. Tested samples included 63 bronchoalveolar lavages (BALs) and 37 induced sputa specimens. The internal control was detected in all negative and low-positive samples; no inhibition was found throughout the whole study. Additionally, samples underwent testing by culture for L. spp., and M. pneumoniae; for C. pneumoniae, the serological microimmunofluorescence (MIF) test was used. In conclusion, the developed set of LC PCR assays permits parallel detection of C. pneumoniae, L. spp., and M. pneumoniae in a single LC run. This molecular assay may lead to accurate and early diagnosis of pneumonia produced by these three types of bacteria. The assay proved to be suitable for the high-throughput routine diagnostic laboratory.

| S-EPMC1867508 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data