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Related Experiment Video

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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SSER: Species specific essential reactions database.

Abraham A Labena1,2,3, Yuan-Nong Ye4, Chuan Dong1,2

  • 1Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.

BMC Systems Biology
|April 20, 2017
PubMed
Summary

A new Species-Specific Essential Reactions database (SSER) centralizes vital cellular reactions. This resource aids synthetic biology, metabolic modeling, and antimetabolic drug discovery by identifying essential reactions across organisms.

Keywords:
DatabaseEssential ReactionsFlux Balance Analysis (FBA)Metabolic NetworksSSER

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Metabolic Engineering

Background:

  • Essential reactions are fundamental to cellular networks, synthetic biology, and drug target identification.
  • Targeting essential reactions is a strategic approach for antimetabolic drug design, especially when reactions are catalyzed by multiple enzymes.
  • Existing databases lack a specific focus on essential reactions, highlighting the need for a centralized repository.

Purpose of the Study:

  • To develop and present a centralized, species-specific essential reactions database (SSER).
  • To provide a valuable resource for researchers in synthetic biology, metabolic modeling, and drug discovery.

Main Methods:

  • Flux Balance Analysis (FBA) was employed to identify essential reactions.
  • Manual curation of experimentally validated metabolic network models was integrated with FBA.
  • The database was populated with data from twenty-six diverse organisms.

Main Results:

  • The SSER database currently includes essential biochemical and transport reactions for twenty-six organisms.
  • Quantitative data on essential reactions, associated enzyme-encoding genes, and shared reactions across species are provided.
  • The database facilitates comparative analysis of essential metabolic components.

Conclusions:

  • SSER serves as a primary resource for essential reaction data, gene, and metabolite information.
  • The database significantly aids in the reconstruction and analysis of metabolic network models.
  • SSER is a valuable tool for advancing drug target discovery studies.