Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

2 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative proteomics studies of the wild strain SC1401 and the tfoX deficient strain

ABSTRACT: Natural transformation, as one of the horizontal gene transfer (HGT) modes of bacteria, allows bacteria to actively uptake foreign DNA under natural conditions and integrate it into their genome through homologous recombination. Natural transformation plays an vital role in the rapid spread of pathogen virulence factors and resistance genes, resulting in the emergence of multidrug resistant or highly pathogenic strains.To investigate the mechanism by which tfoX regulates the natural transformation process of Glaesserella parasuis, comparative proteomics studies were performed on the parent wild strain SC1401 and the tfoX deficient strain.

ORGANISM(S): Glaesserella Parasuis

SUBMITTER: Yiping Wen

PROVIDER: PXD032382 | iProX | Thu Mar 17 00:00:00 GMT 2022

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

The molecular diversity of transcriptional factor TfoX is a determinant in natural transformation in Glaesserella parasuis.

Tang Xiaoyu X Yang Zhen Z Dai Ke K Liu Geyan G Chang Yung-Fu YF Tang Xinwei X Wang Kang K Zhang Yiwen Y Hu Bangdi B Cao Sanjie S Huang Xiaobo X Yan Qigui Q Wu Rui R Zhao Qin Q Du Senyan S Lang Yifei Y Han Xinfeng X Huang Yong Y Wen Xintian X Wen Yiping Y

Frontiers in microbiology 20220729

Natural transformation is a mechanism by which a particular bacterial species takes up foreign DNA and integrates it into its genome. The swine pathogen Glaesserella parasuis (G. parasuis) is a naturally transformable bacterium. The regulation of competence, however, is not fully understood. In this study, the natural transformability of 99 strains was investigated. Only 44% of the strains were transformable under laboratory conditions. Through a high-resolution melting curve and p ...[more]

PMID: 35966685

Similar Datasets

Vibrio campbellii DS40M4 is a tractable model strain that diverges from the canonical quorum-sensing regulatory circuit in vibrios

Project description:Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi) is a fundamental model strain for studying population density-based cell-to-cell communication, known as quorum sensing, among gram-negative bacteria. In V. campbellii BB120, sensing of autoinducers at high cell densities activates the expression of the master transcriptional regulator, LuxR, which controls the expression of genes involved in group behaviors. Unlike BB120, the Vibrio campbellii environmental isolate DS40M4 was recently shown to be capable of natural transformation, a process by which bacteria take up exogenous DNA and incorporate it into their genome via homologous recombination. Here, we compare other phenotypes between DS40M4 and BB120. We find that DS40M4 has a faster growth rate and stronger type VI secretion-mediated cell killing, whereas BB120 forms more robust biofilms and is bioluminescent. We exploited the power of natural transformation to rapidly generate >30 mutant strains to explore the function of DS40M4-encoded homologs of the BB120 quorum-sensing system. Our results show that DS40M4 has a similar quorum-sensing circuit to BB120 but with three distinct differences: 1) DS40M4 lacks the canonical HAI-1 autoinducer LuxM synthase but has an active LuxN receptor, 2) the quorum regulatory small RNAs (Qrrs) are not solely regulated by autoinducer signaling through the response regulator LuxO, and 3) the DS40M4 LuxR regulon is <100 genes, which is relatively small compared to the >400 genes regulated in BB120. This work illustrates that DS40M4 is a tractable and relevant model strain for studying quorum-sensing phenotypes in Vibrio campbellii.

2021-06-28 | GSE147616 | GEO

Diversity in natural transformation frequencies and regulation across Vibrio species

Project description:In marine Vibrio species, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in two Vibrio campbellii strains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation in V. campbellii DS40M4. This result is in contrast to Vibrio cholerae that requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar to V. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies among Vibrio species indicates a wide disparity among even closely related strains, with Vibrio vulnificus having the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency in Vibrio vulnificus.

2019-11-14 | GSE136941 | GEO

Unintended side effects of transformation are very rare

Project description:Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based only on circumstantial evidence. We provide the first direct measurement of the effects of transformation on the genome by sequencing the genomes of 29 transformants and 30 untransformed controls to high coverage. Contrary to the received wisdom, our results show that transformation of DNA flanked by long targeting sequences, followed by homologous recombination and selection on a drug marker, is extremely safe. Gene deletion may select for a few mutations that occur after transformation, but even then we found fewer than two point mutations per gene deletion strain. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between wild types and strains with a drug resistance marker inserted. As part of this process, we provide the first published genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99.

2017-09-26 | GSE104198 | GEO

A Study of Hansoh (HS)-10502 in Patients With Advanced Solid Tumors

Project description:HS-10502 is a Poly(ADP-ribose) polymerase 1 (PARP1)-specific selective inhibitor. The purpose if this study is to assess the safety, tolerability, pharmacokinetics (PK), and efficacy of HS-10502 in subjects with homologous recombination repair (HRR) gene mutant or homologous recombination deficiency (HRD) positive advanced solid tumors.

| 9330 | ecrin-mdr-crc

Comparative genomic hybridization of Vibrio cholerae serogroup conversion from 01 to 0139

Project description:These experiment were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VCO139-Kan was added after 24h and the cells grwon further for 24h. The VCO139-Kan strain is a MO10 derivative (both O139 serogroup) which harbors a Kanamycin cassette in the O139 region (as part of the operon between wbfA and wbfB w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Two groups of transformants were gained: Group I had a full exchange of the O1 region by the O139 region (clones serogroup-converted: SGC#1-3); the crossovers for the homologous recombination event had occurred within or upstream of the gmhD gene and in most instances within or downstream of the homolog gene of VC0271. This implies an exchange of an at least 33 kb spanning O1 genomic region by more than 42 kb of the O139 region. Group II had only half of the O139 region transfered and therefore half of the O1 region kept (clones HSGC#4-6). We analyzed their genotype and found that all of them had undergone a homologous recombination event with one crossover in or upstream of the gmhD gene and the second one inside the VC0254 and IS1358 gene. The transformation experiment was done three independent times (I - III). Three clones from group I and group II were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone.

2007-08-01 | E-SMDB-3574 | biostudies-arrayexpress

Nucleases Encoded by Integrated Elements CJIE2 and CJIE4 Inhibit Natural Transformation of Campylobacter jejuni

Project description:The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factors coding for DNase activity in absence of dns were identified. DNA arrays indicated that nonnaturally transformable dns-negative strains contain putative DNA/RNA non-specific endonucleases encoded by CJE0566 and CJE1441 of strain RM1221. These genes are located on C. jejuni integrated element 2 and 4. Expression of CJE0566 and CJE1441 from strain RM1221 and a homologous gene from strain 07479 in DNase-negative Escherichia coli and C. jejuni strains indicated that these genes code for DNases. Genetic transfer of the genes to a naturally transformable C. jejuni strain resulted in a decreased efficiency of natural transformation. Modelling suggests that the C. jejuni DNases belong to the Serratia nuclease family. Overall, the data indicate that the acquisition of prophage encoded DNA/RNA non-specific endonucleases inhibits the natural transformability of C. jejuni through hydrolysis of DNA.

2009-11-14 | GSE18399 | GEO

O1->O139 Serogroup conversion / KanR selected (15%)

2007-04-25 | GSE5120 | GEO

Transcriptomic analysis of Lactococcus lactis ssp. cremoris KW2 after ComX constitutive production

Project description:Lactococcus lactis is one of the most important lactic acid bacterium used in the dairy industry. Activation of natural DNA transformation in this species would greatly improve the selection of novel strains with desired industrial traits. Here, we investigate the activation of natural transformation in L. lactis ssp. cremoris KW2, a strain of plant origin whose genome encodes the master competence regulator ComX and the complete set of essential late gene products required for natural transformation under its potential control. In absence of any information on the competence signaling system in this species, activation of natural DNA transformation by the constitutive production of ComX was attempted. Using a reporter strain of late competence phase activation and transcriptomic analyses, we show that all key genes for natural transformation can be induced in strain KW2. Then, we demonstrate that natural DNA transformation is functional in this strain and that this process requires the DNA uptake machinery dedicated to competence. Various chromosomal modifications such as point mutations or gene deletion/insertion could be quickly and efficiently achieved. These results are the first to report the functionality of natural DNA transformation in L. lactis and pave the way for the identification of molecular mechanisms activating competence development in this species.

2017-06-29 | GSE86476 | GEO

Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis

Project description:DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria and required for DNA transformation. However, the interaction of DprA with competence proteins and recombination is poorly understood. Therefore, the proteomes of whole Neisseria meningitidis (Nm) wildtype and dprA mutant cells were compared. Such a comparative proteomic analysis increases our understanding of the interactions of DprA with other Nm components, and may elucidate its potential role beyond DNA processing in transformation. Using label-free quantitative proteomics, a total of 1057 unique Nm proteins were identified out of which 100 were quantified as differentially abundant (P ≤ 0.05 and fold change ≥ |2|) in the dprA null mutant. Proteins involved in homologous recombination (RecA, UvrD and HolA), pilus biogenesis (PilG, PilT1, PilT2, PilM, PilO, PilQ, PilF and PilE), and cell division, including core energy metabolism and response to oxidative stress were downregulated in dprA null mutant Nm. Immunoblotting was employed to validate the differences observed in two selected proteins. The analysis revealed reduced amounts of PilG in the dprA null mutant and reduced amounts of DprA in the Nm pilG null mutant. In conclusion, DprA interacts with proteins essential for Nm DNA recombination in transformation, pilus biogenesis and other functions associated with the inner membrane. Inverse downregulation of Nm DprA and PilG expression in the corresponding mutants indicate a link between DNA processing and pilus biogenesis demonstrated for the first time.

2017-04-26 | PXD006121 | Pride

ASF1 acts with RIF1 to promote DNA end-joining in BRCA1 deficient cells

Project description:RIF1 acts downstream of 53BP1 to coordinate DNA double strand break repair pathway choice between non-homologous end joining (NHEJ) and homologous recombination (HR). Here we identified ASF1 as an endogenous RIF1-associated protein. We showed that ASF1 forms complex with RIF1 and regulates RIF1-dependent functions in DNA damage response.

2022-06-09 | PXD027727 | Pride