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  3. MANET database - Wikipedia
MANET database - Wikipedia
From Wikipedia, the free encyclopedia
A collage of the 148 subnetwork diagrams of MANET 3.0 (in the top) and the oldest subnetwork, NUC00230 purine metabolism (in the bottom), highlight how metabolic pathways are enzymatic patchworks of different evolutionary ages.[1]

The Molecular Ancestry Network (MANET) database is a bioinformatics database that maps evolutionary relationships of protein architectures directly onto biological networks.[2] It was originally developed by Hee Shin Kim, Jay E. Mittenthal and Gustavo Caetano-Anollés in the Department of Crop Sciences of the University of Illinois at Urbana-Champaign.[3]

MANET traces for example the ancestry of individual metabolic enzymes in metabolism with bioinformatic, phylogenetic, and statistical methods. MANET currently links information in the Structural Classification of Proteins (SCOP) database, the metabolic pathways database of the Kyoto Encyclopedia of Genes and Genomes (KEGG), and phylogenetic reconstructions describing the evolution of protein fold architecture at a universal level.[4] The database has been updated to reflect the evolution of metabolism at the level of protein fold families.[5] MANET literally "paints" the ancestries of enzymes derived from rooted phylogenetic trees directly onto over one hundred metabolic pathways representations, paying homage to one of the fathers of impressionism. It also provides numerous functionalities that enable searching specific protein folds with defined ancestry values, displaying the distribution of enzymes that are painted, and exploring quantitative details describing individual protein folds. This permits the study of global and local metabolic network architectures, and the extraction of evolutionary patterns at global and local levels.

The database is useful for the study of metabolic evolution. A statistical analysis of the data in MANET showed for example a patchy distribution of ancestry values assigned to protein folds in each subnetwork, indicating that evolution of metabolism occurred globally by widespread recruitment of enzymes.[3] MANET was used to sort out enzymatic recruitment processes in metabolic networks and propose that modern metabolism originated in the purine nucleotide metabolic subnetwork.[6] Analysis of the purine metabolism revealed gradual evolutionary replacement of abiotic chemistries by protein enzymes.[7] The database helped uncover a physical and evolutionary conservation trace in the structure of active sites during the emergence of metabolic activities.[8]

References

  1. ^ Caetano-Anollés, Gustavo; Aziz, M. Fayez; Mughal, Fizza; Koç, Ibrahim; Caetano-Anollés, Kelsey; Caetano-Anollés, Derek (2022-04-18). "Recruitment: A Problem of Entangled Temporal Parts". Frontiers in Bioscience-Landmark. 27 (4): 128. doi:10.31083/j.fbl2704128. ISSN 2768-6698.
  2. ^ "Molecular Ancestry Network, University of Illinois". www.manet.uiuc.edu. Archived from the original on 9 July 2017. Retrieved 14 January 2022.
  3. ^ a b Kim HS, Mittenthal JE, Caetano-Anolles G (2006). "MANET:tracing evolution of protein architecture in metabolic networks". BMC Bioinformatics. 7 351. doi:10.1186/1471-2105-7-351. PMC 1559654. PMID 16854231.
  4. ^ Caetano-Anolles G, Caetano-Anolles D (2003). "An evolutionarily structured universe of protein architecture". Genome Res. 13 (7): 1563–71. doi:10.1101/gr.1161903. PMC 403752. PMID 12840035.
  5. ^ Mughal F, Caetano-Anolles G (2019). "MANET 3.0: Hierarchy and modularity in evolving metabolic networks". PLOS ONE. 14 (10) e0224201. Bibcode:2019PLoSO..1424201M. doi:10.1371/journal.pone.0224201. PMC 6812854. PMID 31648227.
  6. ^ Caetano-Anolles G, Kim HS, Mittenthal JE (2007). "The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture". Proc Natl Acad Sci USA. 104 (22): 9358–63. Bibcode:2007PNAS..104.9358C. doi:10.1073/pnas.0701214104. PMC 1890499. PMID 17517598.
  7. ^ Caetano-Anollés, Kelsey; Caetano-Anollés, Gustavo (2013-03-13). "Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism". PLOS ONE. 8 (3) e59300. Bibcode:2013PLoSO...859300C. doi:10.1371/journal.pone.0059300. ISSN 1932-6203. PMC 3596326. PMID 23516625.
  8. ^ Pollack, J. Dennis; Gerard, David; Makhatadze, George I.; Pearl, Dennis K. (2020-08-12). "Evolutionary conservation and structural localizations suggest a physical trace of metabolism's progressive geochronological emergence". Journal of Biomolecular Structure and Dynamics. 38 (12): 3700–3719. doi:10.1080/07391102.2019.1679666. ISSN 0739-1102. PMID 31608807.
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