Ontology highlight
ABSTRACT:
PROVIDER: PRJNA728975 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR26214578_1.fastq.gz | Fastqsanger.gz | |||
| SRR26214578_2.fastq.gz | Fastqsanger.gz | |||
| SRR26214579_1.fastq.gz | Fastqsanger.gz | |||
| SRR26214579_2.fastq.gz | Fastqsanger.gz |
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Project description:Microarray comparative genome hybridization (mCGH) data was collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae, and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491, and FAM18 and N. gonorrhoeae FA1090.
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Project description:Regulation of gene expression by small non-coding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to indirectly control, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant and a complemented derivative were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, mRNA half-lives increased for 12 genes in Fe-depleted growth conditions, compared to FA1090. Biological functions for the 12 genes controlled by NrrF included energy metabolism, oxidative stress, antibiotic resistance, amino acid synthesis and a regulatory protein whose functions are not fully understood, in addition to hypothetical proteins.
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Project description:Neisseria gonorrhoeae is the causative agent of gonorrhea, a leading sexually transmitted disease with severe complications on reproductive health. The U.S. Centers for Disease Control and Prevention has categorized the public health threat induced by N. gonorrhoeae as “urgent”, due to the ease of transmission and the fast emergence of multi-drug resistant strains. The need for development of vaccines and understanding the underlying factors leading to antibiotic resistance is of utmost importance. The proteomic profiles of the 14 WHO N. gonorrhoeae reference strains have been compared to the WHO F reference strain using a mass spectrometry with tandem mass tags (TMT) labeling to analyze the cell envelope and the cytoplasmic fractions extracted from each strain. Identifying novel vaccine candidates and proteomic signatures for antimicrobial resistance will further our understanding of N. gonorrhoeae proteotypes, in relationship to their respective genotypes and phenotypes, and provide deep insights that will impact the development of preventive and therapeutic tools to combat gonorrhea.
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Project description:Regulation of gene expression by small non-coding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to indirectly control, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant and a complemented derivative were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, mRNA half-lives increased for 12 genes in Fe-depleted growth conditions, compared to FA1090. Biological functions for the 12 genes controlled by NrrF included energy metabolism, oxidative stress, antibiotic resistance, amino acid synthesis and a regulatory protein whose functions are not fully understood, in addition to hypothetical proteins. 18 samples. Three separate biological replicates for both growth conditions (Fe deplete and Fe replete) were done for all each isolate (6 samples per isolate); FA1090 wild type strain; NrrF_mutant strain LJ001; NrrF_complemented strain LJ002
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Project description:Protein glycosylation is increasingly recognized as a common protein modification across bacterial species. Within pathogenic members of the Neisseria genus O-linked protein glycosylation is associated with virulence yet the depth of the glycoproteome, or if glycosylation plays additional roles in Neisserial physiology are largely unknown. Recently it was identified that even closely related members of the Neisseria genus can possess O-Oligosaccharyltransferases, pglOs, that possess distinct targeting activities suggesting extensive glycoproteome diversity in terms of the substrates capable of being glycosylated across Neisserial species. Within this work we explore this concept using Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) fractionation and Data-Independent Acquisition (DIA) to allow the characterization of differences in the glycoproteomes and proteomes within N. gonorrhoeae strains expressing differing pglO alleles. We demonstrate the utility of FAIMS to expand the known glycoproteome of N. gonorrhoeae enabling the characterization of the glycoproteomes of wild type N. gonorrhoeae MS11 as well as a recently reported panel of strains expressing different pglO allelic chimeras (15 PglO enzymes) with unique substrate targeting activities. Combining glycoproteomic insights with DIA proteomics we demonstrate that alterations within pglO alleles have widespread impacts on the proteome of N. gonorrhoeae. Examination of peptides known to be targeted by glycosylation using DIA analysis supports alterations in glycosylation occupancy independent of changes in protein levels and that the occupancy of glycosylation is generally low on most glycoproteins. Combined this work expands our understanding of the N. gonorrhoeae glycoproteome and the impact of glycosylation on bacterial species.
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