Related Experiment Video

Updated: Oct 30, 2025

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Bacterial Protein Interaction Networks: Connectivity is Ruled by Gene Conservation, Essentiality and Function

Maddalena Dilucca¹, Giulio Cimini², Andrea Giansanti³

¹Dipartimento di Fisica, Sapienza University of Rome, 00185, Rome, Italy.

Current Genomics

|July 5, 2021

Summary

Gene conservation, essentiality, and function influence protein connectivity in bacterial protein-protein interaction networks. A highly connected core of conserved, essential genes involved in genetic information processing is conserved across species.

Area of Science:

Genomics
Systems Biology
Bioinformatics

Background:

Protein-protein interaction (PPI) networks are fundamental to cellular processes.
Gene properties like conservation, essentiality, and functional repertoire are linked to protein connectivity within PPI networks.

Purpose of the Study:

To investigate how gene conservation, essentiality, and functional repertoire relate to protein connectivity in bacterial PPI networks.
To determine if PPI subnetwork connectivity differs between essential and nonessential genes.
To analyze the influence of evolutionary and functional relationships (Clusters of Orthologous Genes - COGs) on PPI connectivities.

Main Methods:

Analysis of 42 bacterial genomes with diverse sizes and evolutionary paths.
Examination of PPI subnetworks for essential and nonessential genes.
Measurement of gene conservation using evolutionary retention index (ERI) and evolutionary pressures.
Correlation of protein connectivity with evolutionary and functional classifications (COGs).

Main Results:

Gene conservation, essentiality, and functional specialization significantly constrain protein connectivity in bacterial PPI networks.
A conserved core of highly connected proteins (connectivity k≥40) was identified across species.
This core is particularly evident in the degree distributions of bacteria with smaller genomes (<1000 genes).

Conclusions:

Highly connected proteins in the core are predominantly conserved and essential genes.
These core genes are frequently associated with COG cluster J, involved in ribosomal functions and genetic information processing.
The findings highlight the structural and functional importance of highly connected proteins in bacterial cellular machinery.

Keywords:

Protein-protein interactions bacterial genomes cellular processes clusters of orthologous genes evolutionary retention index gene essentiality

More Related Videos

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Related Concept Videos

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein Networks

Protein Networks

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conserved Binding Sites

Conserved Binding Sites

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Protein-Protein Interfaces

Protein-Protein Interfaces

Articles linked to this work by shared authors, journal, and citation graph.

Insights into the role of dynamical features in protein complex formation: The case of SARS-CoV-2 spike binding with ACE2.

Computational and structural biotechnology journal·2025

Highly engaging events reveal semantic and temporal compression in online community discourse.

PNAS nexus·2025

Spontaneous opinion swings in the voter model with latency.

Physical review. E·2024

Network topology mapping of chemical compounds space.

Scientific reports·2024

Modeling cell populations metabolism and competition under maximum power constraints.

PLoS computational biology·2023

Capability accumulation patterns across economic, innovation, and knowledge-production activities.

Scientific reports·2023

See all related articles