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Title:Origins and evolution of modern biochemistry: insights from genomes and molecular structure.
Author(s):Caetano-Anolles, Gustavo; Sun, Feng-Jie; Wang, Minglei; Yafremava, Liudmila S.; Harish, Ajith; Kim, Hee Shin; Knudsen, Vegeir; Caetano-Anolles, Derek; Mittenthal, Jay E.
Subject(s):biochemistry
genomes
evolution of RNA
protein evolution
evolution of viruses
phylogenetics
proteome architecture
genetic code
Abstract:The survey of components in living systems at different levels of organization enables an evolutionary exploration of patterns and processes in macromolecules, networks, and genomic repertoires. Here we discuss how phylogenetic strategies that generate intrinsically rooted phylogenies impact the evolutionary study of RNA and protein components of the macromolecular machinery that is responsible for biological function. We used these methods to generate timelines of discovery of components in systems, such as substructures in RNA molecules, architectures in proteomes, domains in multi-domain proteins, enzymes in metabolic networks, and protein architectures in proteomes. These timelines unfolded remarkable patterns of origin and evolution of molecules, repertoires and networks, showing episodes of both functional specialization (e.g., rise of domains with specialized functions) and molecular simplification (e.g., reductive tendencies in molecules and proteomes). These observations have important evolutionary implications for origins of translation, the genetic code, modules in the protein world, and diversification of life, and suggest early evolution of modern biochemistry was driven by recruitment of both RNA and protein catalysts in an ancient community of complex organisms.
Issue Date:2008-05-01
Publisher:Frontiers in Bioscience
Citation Info:Frontiers in Bioscience (2008) 13: 5312-5240
Genre:Article
Type:Text
Language:English
URI:http://www.bioscience.org/current/vol13.htm
http://hdl.handle.net/2142/8746
ISSN:1093-4715
DOI:10.2741/3077
Publication Status:published or submitted for publication
Peer Reviewed:is peer reviewed
Rights Information:Copyright held by Gustavo Caetano-Anolles.
This is an, un-copyedited, author manuscript that has been accepted for publication in the Frontiers in Bioscience.
Publishers policy: http://www.bioscience.org/guides/pubmed.htm
Date Available in IDEALS:2008-06-10


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