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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):...
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Bacterial cells were initially considered simple, randomly organized structures lacking a cytoskeleton. However, the discovery of cytoskeleton homologs in bacteria led to the change of this opinion. Bacterial cytoskeletal filaments regulate the cell shape, cell polarity, cell division, and partitioning of plasmids during cell division. It was later discovered that bacterial cytoskeletal proteins, mainly actin and tubulin homologs, are diverse compared to their eukaryotic counterparts. On the...
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Related Experiment Video

Updated: May 19, 2026

A Visual Assay to Monitor T6SS-mediated Bacterial Competition
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A Visual Assay to Monitor T6SS-mediated Bacterial Competition

Published on: March 20, 2013

AtlasT4SS: a curated database for type IV secretion systems.

Rangel C Souza1, Guadalupe del Rosario Quispe Saji, Maiana O C Costa

  • 1The National Laboratory for Scientific Computing LNCC, Getúlio Vargas, Petrópolis, Rio de Janeiro, Brazil.

BMC Microbiology
|August 11, 2012
PubMed
Summary

The AtlasT4SS database organizes and classifies type IV secretion systems (T4SS) proteins from bacteria and archaea. This resource aids in understanding these crucial macromolecule transporters and their functions.

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Last Updated: May 19, 2026

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Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation
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Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation

Published on: January 4, 2017

Area of Science:

  • Microbiology
  • Molecular Biology
  • Bioinformatics

Background:

  • Type IV secretion systems (T4SS) are essential macromolecule transporters with diverse functions, including genetic material transfer and effector protein transport.
  • T4SS are found across Bacteria and Archaea, playing critical roles in microbial interactions and pathogenicity.
  • Existing knowledge on T4SS is fragmented, necessitating a centralized resource for comprehensive analysis.

Purpose of the Study:

  • To create the first public database, AtlasT4SS, dedicated to organizing and classifying prokaryotic type IV secretion systems.
  • To integrate diverse T4SS data from genomic analyses into a single, accessible platform.
  • To provide a standardized classification scheme for T4SS proteins and their functions.

Main Methods:

  • Manual curation of a comprehensive dataset of T4SS proteins from various bacterial and archaeal species.
  • Development of the AtlasT4SS database using RDBMS MySQL and the Catalyst Framework (Perl) with an MVC design pattern.
  • Application of bi-directional best hit (BBH) analysis for identifying orthologous gene clusters encoding T4SS proteins.

Main Results:

  • The AtlasT4SS database currently contains 1,617 T4SS proteins from 58 bacterial species, one archaeal species, and 11 plasmids.
  • Identification of 134 clusters of orthologous genes encoding T4SS proteins through pairwise genome comparison.
  • Establishment of a three-level hierarchical classification scheme for T4SS, categorizing proteins by genetic organization, homology, evolutionary relationships, and cellular processes.

Conclusions:

  • The AtlasT4SS database provides a novel hierarchical classification system for T4SS, facilitating deeper understanding of their diversity and function.
  • The database offers open access to a valuable resource for researchers studying prokaryotic secretion systems.
  • AtlasT4SS serves as a foundational tool for future research into the evolution, mechanisms, and applications of type IV secretion systems.