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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Gram-negative Bacterial Protein Secretion Systems01:17

Gram-negative Bacterial Protein Secretion Systems

Gram-negative bacteria utilize sophisticated protein secretion systems to transport proteins across their double-membrane envelope into the extracellular environment or host cells. Based on their mechanism of action, these systems are classified into one-step and two-step pathways.One-Step Secretion Systems (Types I, III, IV, and VI)One-step secretion systems bypass the periplasm entirely, forming a continuous channel that spans both the inner and outer membranes:Type I Secretion System (T1SS):...
Bacterial Translocation and Protein Secretion01:26

Bacterial Translocation and Protein Secretion

Bacterial protein secretion involves translocation systems to ensure proteins reach their designated locations, including the plasma membrane, periplasm, outer membrane, or the external environment. These translocation systems are vital for bacterial physiology, supporting processes like membrane assembly, enzymatic activity in the periplasm, and interactions with the external environment. The division of labor between Sec and Tat pathways ensures efficiency in handling proteins with diverse...

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A Tandem Liquid Chromatography&#8211;Mass Spectrometry-based Approach for Metabolite Analysis of Staphylococcus aureus
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Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven

Manuel J Rodríguez-Ortega1, Inmaculada Luque, Carmen Tarradas

  • 1Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071 Córdoba, Spain. q62roorm@uco.es

BMC Genomics
|December 9, 2008
PubMed
Summary

This study presents a proteomics method to accurately annotate protein functions, correcting errors in automated gene sequencing. The approach enhances the identification of bacterial surface proteins, aiding vaccine discovery.

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Area of Science:

  • Proteomics and Bioinformatics
  • Microbiology and Infectious Disease Research

Background:

  • Automated gene annotation relies heavily on sequence homology, often leading to inaccurate protein function predictions.
  • Manual curation is time-consuming, necessitating faster and more reliable methods for correcting annotation errors.
  • Surface proteomes are crucial for understanding bacterial pathogens and identifying vaccine candidates.

Purpose of the Study:

  • To develop and validate a proteomics-based strategy for correcting protein function annotation errors in sequencing projects.
  • To accurately identify and localize surface proteins in bacterial pathogens, specifically focusing on the zoonotic pathogen Streptococcus suis.
  • To improve the discovery of novel vaccine targets by enhancing the annotation of surface-associated proteins.

Main Methods:

  • A surface-shaving proteomics approach using trypsin and proteinase K to digest surface proteins from intact bacterial cells.
  • Liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) for peptide identification.
  • Computational analysis of identified protein sequences, including inspection for exporting or retention signals, combined with experimental evidence.

Main Results:

  • Successfully identified a set of surface proteins in Streptococcus suis with no cytoplasmic contamination, confirmed by the absence of cytoplasmic markers and unaffected cell viability post-treatment.
  • Corrected the function annotation of two proteins, identifying them as putative extracellular adhesins instead of previously misassigned cytoplasmic functions.
  • One of the corrected proteins was identified as a putative component of the bacterial pilus.

Conclusions:

  • The study demonstrates the complementary power of laboratory-based proteomics and computational methods for accurate protein localization and function annotation.
  • The validated proteomics strategy effectively corrects erroneous protein function predictions, improving the annotation of surface proteins.
  • This approach accelerates the discovery of potential vaccine candidates by providing robust experimental evidence for surface protein annotation and aiding Gene Ontology (GO) term assignment.