Ontology highlight
ABSTRACT:
PROVIDER: PRJNA706822 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Helicobacter pylori, which is known as pathogens of various gastric diseases, have many types of genome sequence variants. That is part of the reason why pathogenesis and infection mechanisms of the H. pylori-driven gastric diseases have not been well clarified yet. Here we performed a large-scale proteome analysis to profile the heterogeneity of the proteome expression of 7 H. pylori strains by using LC/MS/MS-based proteomics approach combined with a customized database consisting of non-redundant tryptic peptide sequences derived from full genome sequences of 52 H. pylori strains. The non-redundant peptide database enabled us to identify more peptides in the database search of MS/MS data, compared with a simply merged protein database. Using the approach we performed proteome analysis of genome-unknown strains of H. pylori in as large-scale as genome-known ones. Clustering of the H. pylori strains using the proteome profiling slightly differed from the genome profiling and more clearly divided the strains into two groups based on the isolated area. Furthermore, we also identified phosphorylated proteins and sites of the H. pylori strains and obtained phosphorylation motif located in the N-terminus, which are commonly observed in bacteria.
2018-12-28 | PXD011364 | JPOST Repository
Project description:Comparative proteomics was conducted for Synechocystis sp. PCC 6803 wild type and engineered ethylene-producing JU547 strains. An novel guanidine-degradation enzyme was identified and characterized to play important roles in genome stability.
2021-03-28 | MSV000087119 | MassIVE
Project description:Trinickia sp. YCB016 Genome sequencing and assembly
| PRJNA1094678 | ENA
Project description:In this study, we have applied the top-down approach to reduce the genome of B. subtilis in order to obtain minimal strains with robust growth on complex medium at 37°C. For this purpose, we have evaluated the function of each gene of the B. subtilis genome and identified essential, important and dispensable genomic regions. Using an efficient markerless and scarless deletion method and a system allowing induction of genetic competence in the complete cell population, we have constructed two genome-reduced strains lacking about 36% of dispensable genetic information. Multi-omics analyses with the genome-reduced strains revealed substantial changes in the transcriptome, the proteome and in the metabolome. The massive reorganization of metabolism in the two genome-reduced strains can be explained by the underlying genotypes that were determined by genome re-sequencing. Moreover, the transcriptome and proteome analyses uncovered novel dispensable genomic regions that can be removed to further streamline the B. subtilis genome. In conclusion, both minimal strains show interesting metabolic features and they serve as excellent starting points to generate an ultimate reduced-genome B. subtilis cell containing only genes required for robust growth on complex medium.
2016-12-06 | PXD004565 | Pride
Project description:Approximatively 75% of the genome of S. aureus (“core” genome) are highly conserved between strains, whereas the remaining 25% (“accessory” genome) are composed of variable regions that are mostly composed of mobile genetic elements (MGE), containing virulence and resistance genes. We have developed a composite DNA-microarray (StaphVar Array) which selectively targets 403 genes located on the accessory or core variable genome. Target genes encode antimicrobial resistance factors (35 %), virulence factors (28 %) and adhesins (31%). This microarray was validated with reference strains and used to characterize the genomic DNA of 13 community-acquired methicillin resistant S. aureus (CA-MRSA) strains representative of all the Multilocus Sequence Types (STs) described to date in Belgium. Analysis of gene content of 8 reference strains by the StaphVar Array matched 96 to 99% of the theoretical results. Analysis of CA-MRSA strains showed that 54.4 % of the genes tested were strain-dependent. Strains presented specific exotoxin, enterotoxin, cytolysin and adhesin gene profile by multi-locus sequence typing (MLST) lineage. One exception to these “lineage-specific” gene profile was the variable presence of the Arginin Catabolic Mobile Element (ACME, characteristic of the USA300 clone) within ST8 strains. In conclusion, this novel StaphVar array enables characterization of more than 400 variable resistance and virulence determinants in S. aureus strains. CA-MRSA strains from Belgium displayed extensive diversity in virulence and resistance profile. The presence of the USA 300 clone in our country was confirmed. Although mainly located on MGE, association of virulence genes were highly conserved within strains of the same MLST lineage.
2009-02-15 | GSE13702 | GEO
Project description:Trinickia symbiotica strain:JPY347 Genome sequencing and assembly
| PRJNA169697 | ENA
Project description:Trinickia dabaoshanensis strain:GIMN1.004 Genome sequencing and assembly
| PRJNA427927 | ENA
Project description:Trinickia terrae strain:7GSK02 Genome sequencing and assembly
| PRJNA534012 | ENA
Project description:Trinickia violacea strain:DHOD12 Genome sequencing and assembly
| PRJNA534064 | ENA
Project description:Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, are known to exhibit diverse phenotypic traits, suggesting significant intraspecies genetic heterogeneity. Using whole-genome Bp microarrays, we experimentally mapped patterns of large-scale genomic variation in 93 South East Asian clinical, environmental, and animal Bp isolates. 14% of the reference Bp K96243 genome was variably present across the strain panel, more than double previous estimates, and both hypothetical proteins and paralogous gene pairs (PGPs) were significantly over-represented in the set of strain-variable genes. Examining patterns of PGP retention and loss, we successfully sub-categorized the PGPs into non-redundant, functionally biased, and completely redundant classes. We then identified 20 novel regions (“islands”) variably present between strains previously missed by computational analysis. Three of these novel islands contained lipopolysaccharide (LPS) biosynthesis genes, and strains lacking one such LPS island demonstrated reduced virulence in mouse infection assays. Clinical isolates associated with human melioidosis were strongly associated with the presence of specific genomic islands, but a common set of virulence-related genes was present in all strains. Our results suggest that most Bp strains possess a core virulence machinery capable of causing disease, but accessory functions provided by mobile elements may predispose distinct host species and ecological niches to specific individual strains. This hierarchical model of Bp virulence reconciles previous conflicting studies comparing Bp environmental and clinical isolates, and suggests novel molecular strategies for disease surveillance and outbreak detection efforts in melioidosis. Keywords: aCGH of 93 Bp strains
2008-12-26 | GSE9491 | GEO