Origins and evolution of modern biochemistry

Insights from genomes and molecular structure

Gustavo Caetano-Anolles, Feng Jie Sun, Minglei Wang, Liudmila Sergeevna Mainzer, Ajith Harish, Hee Shin Kim, Vegeir Knudsen, Derek Caetano-Anolles, Jay E. Mittenthal

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)5212-5240
Number of pages29
JournalFrontiers in Bioscience
Volume13
Issue number14
DOIs
StatePublished - May 1 2008

Fingerprint

Biochemistry
Molecular Structure
Molecular structure
Proteome
Genes
Genome
RNA
Proteins
Molecules
Genetic Code
Phylogeny
Metabolic Networks and Pathways
Macromolecules
Organizations
Machinery
Enzymes
Catalysts
TimeLine

Keywords

  • Archaea
  • Evolution
  • Metabolism
  • Proteins
  • Proteome
  • RNA
  • Review
  • Structure
  • rRNA
  • tRNA

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Origins and evolution of modern biochemistry : Insights from genomes and molecular structure. / Caetano-Anolles, Gustavo; Sun, Feng Jie; Wang, Minglei; Mainzer, Liudmila Sergeevna; Harish, Ajith; Kim, Hee Shin; Knudsen, Vegeir; Caetano-Anolles, Derek; Mittenthal, Jay E.

In: Frontiers in Bioscience, Vol. 13, No. 14, 01.05.2008, p. 5212-5240.

Research output: Contribution to journalArticle

Caetano-Anolles, G, Sun, FJ, Wang, M, Mainzer, LS, Harish, A, Kim, HS, Knudsen, V, Caetano-Anolles, D & Mittenthal, JE 2008, 'Origins and evolution of modern biochemistry: Insights from genomes and molecular structure', Frontiers in Bioscience, vol. 13, no. 14, pp. 5212-5240. https://doi.org/10.2741/3077
Caetano-Anolles, Gustavo ; Sun, Feng Jie ; Wang, Minglei ; Mainzer, Liudmila Sergeevna ; Harish, Ajith ; Kim, Hee Shin ; Knudsen, Vegeir ; Caetano-Anolles, Derek ; Mittenthal, Jay E. / Origins and evolution of modern biochemistry : Insights from genomes and molecular structure. In: Frontiers in Bioscience. 2008 ; Vol. 13, No. 14. pp. 5212-5240.
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