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Annotation of a hypothetical protein (WP_002969292.1) from Brucella abortus.

ABSTRACT: Brucellosis is a zoonotic disease caused mainly by the bacteria belonging to the genus Brucella, most common of them is Brucella abortus. Genome sequencing of Brucella was completed in 2005. While majority of the proteins were assigned function, a large number of the peptides remained un-annotated and were referred as 'hypothetical'. These hypothetical proteins may contain crucial information about the biology and pathogenesis of the B. abortus. Therefore, it is of interest to annotate one such hypothetical protein as a multiple antibiotic resistance regulator protein, MarR. The physiological parameters, localization and the structural features were predicted for this protein which corroborated as the winged-helix type DNA-binding domain superfamily of transcription factors.

SUBMITTER: Rauthan K

PROVIDER: S-EPMC6589471 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Annotation of a hypothetical protein (WP_002969292.1) from Brucella abortus.

Rauthan Kanchan K Goel Divya D Kumar Sudhir S

Bioinformation 20190430 5

Brucellosis is a zoonotic disease caused mainly by the bacteria belonging to the genus Brucella, most common of them is Brucella abortus. Genome sequencing of Brucella was completed in 2005. While majority of the proteins were assigned function, a large number of the peptides remained un-annotated and were referred as 'hypothetical'. These hypothetical proteins may contain crucial information about the biology and pathogenesis of the B. abortus. Therefore, it is of interest to annotate one such ...[more]

PMID: 31249433

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Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome.

Project description:BACKGROUND: Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data. RESULTS: The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes. CONCLUSIONS: An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.

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Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis.

Project description:Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella. The species, B. abortus and B. melitensis, major causative agents of human brucellosis, share remarkably similar genomes, but they differ in their natural hosts, phenotype, antigenic, immunogenic, proteomic and metabolomic properties. In the present study, label-free quantitative proteomic analysis was applied to investigate protein expression level differences. Type strains and field strains were each cultured six times, cells were harvested at a midlogarithmic growth phase and proteins were extracted. Following trypsin digestion, the peptides were desalted, separated by reverse-phase nanoLC, ionized using electrospray ionization and transferred into an linear trap quadrapole (LTQ) Orbitrap Velos mass spectrometer to record full scan MS spectra (m/z 300-1700) and tandem mass spectrometry (MS/MS) spectra of the 20 most intense ions. Database matching with the reference proteomes resulted in the identification of 826 proteins. The Cluster of Gene Ontologies of the identified proteins revealed differences in bimolecular transport and protein synthesis mechanisms between these two strains. Among several other proteins, antifreeze proteins, Omp10, superoxide dismutase and 30S ribosomal protein S14 were predicted as potential virulence factors among the proteins differentially expressed. All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.

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Project description:Isogenic deletion and truncation of specific genes encoding RNases in Brucella abortus were analyzed for changes in gene expression. The main goal of this work is to determine the mRNAs that exhibit dysregulation when small regulatory RNAs (i.e., Bsr8) or RNases (i.e., RNaseE and RNaseJ) are invactivated in Brucella abortus. Small regulatory RNAs often control gene expression by binding directly to mRNAs to block translation or induce their degradation, and RNA from a deletion of one sRNA gene, bsr8, was analyzed to uncover the mRNAs that may be controlled by BsrB. RNases are enzymes that cleave RNAs during processing, turnover, and regulatory events, and RNaseE and RNaseJ appear to be important for B. abortus virulence. Therefore, to determine the mRNAs potentially targetd by these RNases, RNA from a strain harboring a RNaseE truncation and a strain carrying a deletion of rnaseJ were analyzed. In the end, the objective of this study was to gain insight into the regulatory patterns of specific B. abortus sRNAs and RNases.

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