Bartonella henselae
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD000153
PROVIDER: PRJNA190078 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR748893.fastq.gz | Fastqsanger.gz | |||
| SRR748894.fastq.gz | Fastqsanger.gz | |||
| SRR748895.fastq.gz | Fastqsanger.gz | |||
| SRR748896.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Using a discovery proteomics approach, the expressed proteome of Bartonella henselae, a Gram-negative prokaryotic model organism was exhaustively studied under two conditions that mimic those encountered in different hosts. Using the analysis-driven experimentation (ADE) feedback-loop strategy, we were able to virtually eliminate the biases of commonly under-represented short, basic, and particularly lower abundant and membrane protein classes, all of which are experimentally tractable. Based on a very stringent FDR at the PSM level, we identified 85% of all distinct, annotated proteins and above 90% compared to the expressed protein-coding genes in the two conditions. Several lines of evidence indicated that this is very close to all proteins that can be identified by a discovery proteomics approach with current technology Our experimental strategy relied on four elements: First, we used a combination of sub-cellular fractionation (Cyt, TM, IM, OM) with additional biochemical fractionation regimens (gelfiltration, OGEpep, OGEprot, ProteoMiner) to reduce the overall sample complexity. Second, an exclusion list approach was applied, where each sample is measured twice in a mass spectrometer. Third, we relied on the ADE strategy to target typically under-represented areas of the proteome. Finally, we also used chymotrypsin as enzyme in addition to trypsin for all membrane-derived fractions. For computational analysis, we combined results from two database search engines (Mascot and MS-GF+).Mass spectra were searched against a protein sequence database containing 1488 NCBI RefSeq annotated B. henselae proteins (NC_005956.1), 3336 sheep proteins, a positive control (myc-gfp), as well as protein sequences of 256 common contaminants. Spectra were searched against this database using the target/decoy option either with Mascot (version 2.3.0, Matrix Science) or with MS-GF+ (MS-GFDB v7747, kindly provided by Dr. Sangtae Kim, UCSD, USA) using the following parameters: Carbamidomethylation was set as a fixed modification on all Cysteines, oxidation of Methionines, deamidation of Asparagines and Glutamines, as well as cyclization of N-terminal Glutamines were considered as optional modifications. Spectra were searched for a match to fully-tryptic and semi-tryptic peptides with up to two missed cleavage sites. Precursor ion mass tolerance was set to 5 ppm, fragment ion mass tolerance was set to 0.8 Da, and the automatic decoy search option was enabled. For Mascot, data were further post-processed with Percolator (Brosch et al. 2009). Additional RNA-seq data are at GEO under the accession: GSE44564.
2013-07-18 | PXD000153 | Pride
Project description:Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant and membrane localized, we could eliminate their initial under-representation compared to the estimated endpoint. A total of 1,250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and around 90% of the expressed protein-coding genes. Genes, whose transcripts were detected, but not their corresponding protein products, were found highly enriched in several genomic islands. Additionally, genes that lacked an ortholog and a functional annotation were not detected at the protein level, and possibly include over-predicted genes in genome annotations. Furthermore, a dramatic membrane proteome re-organization was observed including differential regulation of autotransporters, adhesins and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor. Transcriptome and proteome analysis of B.henselae in two conditions and duplicates: uninduced and induced for host invasion.
2013-04-23 | E-GEOD-44564 | biostudies-arrayexpress
Project description:Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant and membrane localized, we could eliminate their initial under-representation compared to the estimated endpoint. A total of 1,250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and around 90% of the expressed protein-coding genes. Genes, whose transcripts were detected, but not their corresponding protein products, were found highly enriched in several genomic islands. Additionally, genes that lacked an ortholog and a functional annotation were not detected at the protein level, and possibly include over-predicted genes in genome annotations. Furthermore, a dramatic membrane proteome re-organization was observed including differential regulation of autotransporters, adhesins and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.
2013-04-23 | GSE44564 | GEO
Project description:We report detection of Bartonella henselae DNA in blood samples from 2 harbor porpoises (Phocoena phocoena). By using real-time polymerase chain reaction, we directly amplified Bartonella species DNA from blood of a harbor porpoise stranded along the northern North Carolina coast and from a pre-enrichment blood culture from a second harbor porpoise. The second porpoise was captured out of habitat (in a low-salinity canal along the northern North Carolina coast) and relocated back into the ocean. Subsequently, DNA was amplified by conventional polymerase chain reaction for DNA sequencing. The 16S-23S intergenic transcribed spacer region obtained from each porpoise was 99.8% similar to that of B. henselae strain San Antonio 2 (SA2), whereas both heme-binding phage-associated pap31 gene sequences were 100% homologous to that of B. henselae SA2. Currently, the geographic distribution, mode of transmission, reservoir potential, and pathogenicity of bloodborne Bartonella species in porpoises have not been determined.
| S-EPMC3367652 | biostudies-literature
Project description:Bartonella henselae or Bartonella elizabethae DNA from EDTA-anticoagulated blood samples obtained from four dogs was amplified and sequenced. The results showed that B. elizabethae should be added to the list of Bartonella species (i.e., B. vinsonii subsp. berkhoffii, B. henselae, and B. clarridgeiae) that are currently recognized as infectious agents in dogs. Furthermore, these results may have potential zoonotic implications, particularly if dogs can serve as a previously unrecognized reservoir for B. henselae. Although the clinical relevance of these observations remains to be determined, it is possible that molecular diagnostic techniques such as PCR may help to implicate a spectrum of Bartonella spp. as a cause of or a cofactor in chronic canine and human diseases of poorly defined causation.
| S-EPMC154595 | biostudies-literature
Project description:Bartonella henselae Genome sequencing and assembly
| PRJNA295147 | ENA
Project description:Draft genome sequencing of Bartonella henselae strains from sheltered cats in Osaka, Japan
| PRJDB20485 | ENA
Project description:A genome-wide study of recombination rate variation in Bartonella henselae
| PRJNA274779 | ENA