Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella

New Phytol. 2008;179(4):987-1003. doi: 10.1111/j.1469-8137.2008.02534.x.

Abstract

The plant enzyme 4-coumarate:coenzyme A ligase (4CL) is part of a family of adenylate-forming enzymes present in all organisms. Analysis of genome sequences shows the presence of '4CL-like' enzymes in plants and other organisms, but their evolutionary relationships and functions remain largely unknown. 4CL and 4CL-like genes were identified by BLAST searches in Arabidopsis, Populus, rice, Physcomitrella, Chlamydomonas and microbial genomes. Evolutionary relationships were inferred by phylogenetic analysis of aligned amino acid sequences. Expression patterns of a conserved set of Arabidopsis and poplar 4CL-like acyl-CoA synthetase (ACS) genes were assayed. The conserved ACS genes form a land plant-specific class. Angiosperm ACS genes grouped into five clades, each of which contained representatives in three fully sequenced genomes. Expression analysis revealed conserved developmental and stress-induced expression patterns of Arabidopsis and poplar genes in some clades. Evolution of plant ACS enzymes occurred early in land plants. Differential gene expansion of angiosperm ACS clades has occurred in some lineages. Evolutionary and gene expression data, combined with in vitro and limited in vivo protein function data, suggest that angiosperm ACS enzymes play conserved roles in octadecanoid and fatty acid metabolism, and play roles in organ development, for example in anthers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / enzymology
  • Arabidopsis / genetics
  • Base Sequence
  • Bryopsida / enzymology
  • Bryopsida / genetics
  • Chloroplasts / chemistry
  • Coenzyme A Ligases / analysis
  • Coenzyme A Ligases / genetics*
  • Coenzyme A Ligases / physiology
  • Computational Biology
  • Evolution, Molecular
  • Gene Expression
  • Genome, Plant*
  • Multigene Family
  • Oryza / enzymology
  • Oryza / genetics
  • Peroxisomes / chemistry
  • Phylogeny
  • Plant Proteins / analysis
  • Plant Proteins / genetics*
  • Plant Proteins / physiology
  • Plants / enzymology
  • Plants / genetics*
  • Plants, Genetically Modified / metabolism
  • Plants, Genetically Modified / ultrastructure
  • Populus / enzymology
  • Populus / genetics
  • Sequence Alignment
  • Tobacco / genetics

Substances

  • Plant Proteins
  • Coenzyme A Ligases