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Related Concept Videos

Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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Metabolism of Chemolithotrophs

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. However, because inorganic electron donors...
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
Lipid Catabolism01:25

Lipid Catabolism

Triglycerides serve as crucial long-term energy storage molecules in microorganisms, providing a dense source of metabolic energy. Their breakdown is mediated by lipases, which hydrolyze triglycerides into glycerol and free fatty acids. Each of these components follows distinct metabolic pathways, ultimately contributing to ATP synthesis and cellular energy homeostasis.Glycerol MetabolismGlycerol, released from triglyceride hydrolysis, is phosphorylated by glycerol kinase to form...
Fates of Pyruvate01:20

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Introduction to Metabolism01:30

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High-Throughput Metabolic Profiling for Model Refinements of Microalgae
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Published on: December 4, 2021

Reconstructing phylogeny from metabolic substrate-product relationships.

Che-Wei Chang1, Ping-Chiang Lyu, Masanori Arita

  • 1Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Taiwan. freshrogerchang@gmail.com

BMC Bioinformatics
|February 24, 2011
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Metabolic network analysis reconstructs organismal evolutionary trees by examining substrate-product relationships. This method reveals species in unusual environments and aids in understanding species-environment interactions.

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Area of Science:

  • Metabolic pathway analysis
  • Phylogenetic reconstruction
  • Systems biology

Background:

  • Traditional phylogenetic reconstruction relies on genomic annotations.
  • The added value of metabolic networks to genomic data for phylogenetics is underexplored.

Purpose of the Study:

  • To investigate how metabolic network information can enhance phylogenetic reconstruction.
  • To represent metabolic information at a finer resolution than enzymes and compounds.

Main Methods:

  • Enzyme reactions from 1075 organisms were translated into substrate-product relationships.
  • Each organism was represented as a vector of these relationships.
  • Phylogenetic trees were reconstructed using a hierarchical method and compared to other approaches.

Main Results:

  • Phylogenetic trees derived from metabolic network properties effectively identified organisms from anomalous environments.
  • The method provides insights beyond traditional genome-based phylogenetic reconstruction.

Conclusions:

  • Metabolite structural relationships highlight parasitic and symbiont species.
  • This approach enhances the understanding of species-environment interactions when combined with traditional phylogenetic methods.