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Title: Genome-level and biochemical diversity of the acyl-activating enzyme superfamily in plants

Author
item Shockey, Jay
item BROWSE, JOHN - Washington State University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2011
Publication Date: 3/28/2011
Citation: Shockey, J., Browse, J. 2011. Genome-level and biochemical diversity of the acyl-activating enzyme superfamily in plants. Plant Journal. (66):143-160.

Interpretive Summary: All organisms on earth contain at least one protein that carries out the function of activating one or more kinds of organic acids by attaching a cofactor group called coenzyme A. Most higher plants and animals contain large families of these genes. Collectively, this family are called the AAEs, for Acyl Activating Enzymes. While the size and number of the AAE gene families in many organisms has been determined due to the explosion of genome sequencing projects, the functions of most of AAE proteins are still not known. This article provides new information about the numbers of AAE genes in three types of plants (algae, cottonwood tree, and moss) not previously analyzed. The genetic mechanisms that have contributed to the increase in AAE gene copy number during evolution is also discussed. Finally, the current state of knowledge regarding the biochemical functions of various AAE proteins that have been studied in more detail is presented.

Technical Abstract: In higher plants, the superfamily of carboxyl-CoA ligases and related proteins, collectively called acyl activating enzymes (AAEs), has evolved to provide enzymes for many pathways of primary and secondary metabolism and for the conjugation of hormones to amino acids. Across the superfamily there is only limited sequence similarity, but a series of highly conserved motifs, including the AMP-binding domain, make it easy to identify members. These conserved motifs are best understood in terms of the unique domain-rotation architecture that allows AAE enzymes to catalyze the two distinct steps of the CoA ligase reaction. Arabidopsis AAE sequences were used to identify the AAE gene families in the sequenced genomes of green algae, mosses, and trees; the size of the respective families increased with increasing degree of organismal cellular complexity, size, and generation time. Large-scale genome duplications and small-scale tandem gene duplications have contributed to AAE gene family complexity to differing extents in each of the multicellular species analyzed. Gene duplication and evolution of novel functions in Arabidopsis appears to have occurred rapidly, because acquisition of new substrate specificity is relatively easy in this class of proteins. Convergent evolution has also occurred between members of distantly related clades. These features of the AAE superfamily make it difficult to use homology searches and other genomics tools to predict enzyme function.