Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes

Mol Phylogenet Evol. 2014 Jun;75:154-64. doi: 10.1016/j.ympev.2014.02.015. Epub 2014 Mar 3.

Abstract

Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.

Keywords: Domain architectures; Horizontal gene transfer; Pathway evolution; Phylogenetic analysis; Shikimate pathway.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3-Phosphoshikimate 1-Carboxyvinyltransferase / genetics
  • Aldehyde-Ketone Transferases / genetics
  • Archaea / enzymology
  • Archaea / genetics*
  • Bacteria / enzymology
  • Bacteria / genetics*
  • Biological Evolution*
  • Computational Biology
  • Gene Transfer, Horizontal
  • Markov Chains
  • Metabolic Networks and Pathways / genetics
  • Multigene Family
  • Phosphorus-Oxygen Lyases / genetics
  • Phosphotransferases (Alcohol Group Acceptor) / genetics
  • Phylogeny*
  • Proteome / analysis
  • Sequence Analysis, DNA
  • Shikimic Acid / metabolism*

Substances

  • Proteome
  • Shikimic Acid
  • Aldehyde-Ketone Transferases
  • 3-Phosphoshikimate 1-Carboxyvinyltransferase
  • Phosphotransferases (Alcohol Group Acceptor)
  • shikimate kinase
  • chorismate synthase
  • Phosphorus-Oxygen Lyases