Related Experiment Video
Updated: Jan 5, 2026
07:28
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
3.6K
MANET 3.0: Hierarchy and modularity in evolving metabolic networks
Fizza Mughal1,2, Gustavo Caetano-Anollés1,2
1Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
Plos One
|October 25, 2019
Summary
Enzyme recruitment drives metabolic evolution. The updated Molecular Ancestry Networks (MANET) database reveals ancient enzyme innovations and network growth patterns, supporting a patchwork model of metabolic evolution.
Area of Science:
- Biochemistry and Evolutionary Biology
- Bioinformatics and Systems Biology
Background:
- Enzyme recruitment is a key evolutionary mechanism shaping modern metabolism.
- The Molecular Ancestry Networks (MANET) database tracks the evolutionary history of enzyme structural domains in metabolic pathways.
Purpose of the Study:
- To release version 3.0 of the MANET database with updated data and enhanced evolutionary tracing.
- To investigate the evolutionary patterns of enzyme innovation, diversification, and metabolic network organization.
Main Methods:
- Integrated data from KEGG, SCOP, and PDBsum for comprehensive analysis.
- Utilized structural phylogenomic reconstruction and domain classification at the SCOP fold family level.
- Employed bipartite networks and their projections to study the evolutionary growth of metabolic modules.
Main Results:
- Ancient enzymatic innovations exhibited a biphasic diversification pattern.
- Metabolic networks show increasing hierarchical modularity and scale-free behavior over evolutionary time.
- Identified enzyme sharing across mesonetwork boundaries, supporting the patchwork model of metabolic evolution.
Conclusions:
- The MANET database provides a valuable resource for studying metabolic evolution.
- Metabolic network evolution is characterized by increasing modularity and a 'principle of granularity'.
- Enzyme recruitment and modular innovation are fundamental to the development of complex metabolic systems.
Related Concept Videos
01:23Operon Model
997
The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
997
01:30Introduction to Metabolism
2.5K
Metabolism encompasses all biochemical reactions in a living organism, facilitating both the breakdown and synthesis of biomolecules. These metabolic processes are categorized into catabolic and anabolic pathways, which operate in a coordinated manner to ensure energy balance and cellular function.Catabolic Pathways and Energy ReleaseCatabolic pathways involve the breakdown of complex macromolecules such as carbohydrates, lipids, and proteins into smaller structures like monosaccharides, fatty...
2.5K
01:40Overview of Metabolism
37.5K
Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
37.5K
01:15Metabolism of Chemolithotrophs
691
Chemolithotrophs are microorganisms that obtain energy by oxidizing inorganic molecules such as hydrogen gas (H₂), ammonia (NH₃), reduced sulfur compounds (H₂S, S²⁻), and ferrous iron (Fe²⁺). Unlike heterotrophic organisms that rely on organic carbon, chemolithotrophs transfer electrons from these inorganic donors to the electron transport chain (ETC), generating a proton motive force (PMF) that drives ATP synthesis through oxidative phosphorylation.
691
01:19Regulation of Metabolism
11.3K
Cellular needs and conditions vary from cell to cell and change within individual cells over time. For example, the required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and...
11.3K
01:21Mechanistic Models: Overview of Compartment Models
320
Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
320