Ligase Clades

Clade I – LACS

Much of our work on these genes has been published.

At2g47240
At1g49430
At1g64400
At4g23850
At4g11030
At3g05970
At5g27600
At2g04350
At1g77590
At4g14070
At3g23790

 

Clade II

The members of this clade are under active investigation by our laboratory, using the research approaches described.

At5g36880
At5g23050
At1g55320

 

Clade III

The characterization of JAR1 by Staswick et al. revealed that the 19 genes in clade III are not CoA ligases.

Jasmonate response locus JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation.
Staswick PE, Tiryaki I, and Rowe ML

Jasmonic acid (JA) and related cyclopentanones are critical plant signaling molecules, but their mode of action at the molecular level is unclear. A map-based approach was used to identify the defective gene in the Arabidopsis JA response mutant jar1-1. JAR1 is 1 of 19 closely related Arabidopsis genes that are similar to the auxin-induced soybean GH3 gene. Analysis of fold predictions for this protein family suggested that JAR1 might belong to the acyl adenylate-forming firefly luciferase superfamily. These enzymes activate the carboxyl groups of a variety of substrates for their subsequent biochemical modification. An ATP-PPi isotope exchange assay was used to demonstrate adenylation activity in a glutathione S-transferase-JAR1 fusion protein. Activity was specific for JA, suggesting that covalent modification of JA is important for its function. Six other Arabidopsis genes were specifically active on indole-3-acetic acid (IAA), and one was active on both IAA and salicylic acid. These findings suggest that the JAR1 gene family is involved in multiple important plant signaling pathways.

 

Clade IV 4 CL genes

Also see

Ehlting, J, Buttner, D, Wang, Q, Douglas, CJ, Somssich, IE, and Kombrink, E. 1999. Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms.  Plant J. 19(1):9-20.

And

Schneider, K, Hovel, K, Witzel, K, Hamberger, B, Schomburg, D, Kombrink, E, and Stuible, HP. 2003. The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase. Proc. Natl. Acad. Sci. USA. 100(14):8601-8606.

At1g51680
At3g21240
At1g65060
At3g21230
At1g62940

 

Clade V “4CL-like”

At4g05160, At5g63380 activities reported:

At4g05160 has activity with with medium-chain fatty acids, medium-chain fatty acids carrying a phenyl substitution, long-chain fatty acids, as well as the jasmonic acid precursors 12-oxo-phytodienoic acid and 3-oxo-2-(2′-pentenyl)-cyclopentane-1-hexanoic acid.

At5g63380, showed high activity with long-chain fatty acids and 12-oxo-phytodienoic acid, the latter representing the most efficiently converted substrate.

See

Schneider, K, Kienow, L, Schmelzer, E, Colby, T, Bartsch, M, Miersch, O, Wasternack, C, Kombrink, E, and Stuible, HP.  2005. A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis thaliana has the catalytic capacity to activate biosynthetic precursors of jasmonic acid.  J. Biol. Chem. 280(14):13962-13972. Epub 2005 Jan 26.

At1g20500
At1g20490
At5g38120
At1g20510
At1g20480
At5g63380
At4g05160
At4g19010

 

Clade VI

The members of this clade are under active investigation by our laboaratory, using the research approaches described.

At1g20560
At2g17650
At1g77240
At5g16370
At5g16340
At3g16910
At1g75960
At1g21540
At1g21530
At1g66120
At1g65890
At1g65880
At1g68270
At1g76290

 

Clade VII

The members of this clade are under active investigation by our laboaratory, using the research approaches described.

At3g48990
At3g16170
At1g30520