1 3 Plant Mol Biol (2014) 84:565–576 DOI 10.1007/s11103-013-0152-y Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.) Luis L. Escamilla‑Treviño · Hui Shen · Timothy Hernandez · Yanbin Yin · Ying Xu · Richard A. Dixon Received: 13 September 2013 / Accepted: 26 October 2013 / Published online: 5 November 2013 © Springer Science+Business Media Dordrecht 2013 hydroxycinnamoyltransferase (HCT) genes (PvHCT1a and PvHCT2a), closely related to lignin pathway HCTs from other species, were characterized biochemically and exhibited the expected HCT activity, preferring shikimic acid as acyl acceptor. We also characterized two switch- grass coumaroyl shikimate 3′-hydroxylase (C3′H) enzymes (PvC3′H1 and PvC3′H2); both of these cytochrome P450s had the capacity to hydroxylate 4-coumaroyl shikimate or 4-coumaroyl quinate to generate caffeoyl shikimate or CGA. Another switchgrass hydroxycinnamoyl transferase, PvHCT-Like1, is phylogenetically distant from HCTs or HQTs, but exhibits HQT activity, preferring quinic acid as acyl acceptor, and could therefore function in CGA bio- synthesis. The biochemical features of the recombinant enzymes, the presence of the corresponding activities in plant protein extracts, and the expression patterns of the corresponding genes, suggest preferred routes to CGA in switchgrass. Keywords Phenylpropanoid pathway · Lignin · Flavonoids · Chlorogenic acid Abstract Studying lignin biosynthesis in Panicum vir- gatum (switchgrass) has provided a basis for generating plants with reduced lignin content and increased saccharifi- cation efficiency. Chlorogenic acid (CGA, caffeoyl quinate) is the major soluble phenolic compound in switchgrass, and the lignin and CGA biosynthetic pathways potentially share intermediates and enzymes. The enzyme hydroxycin- namoyl-CoA: quinate hydroxycinnamoyltransferase (HQT) is responsible for CGA biosynthesis in tobacco, tomato and globe artichoke, but there are no close orthologs of HQT in switchgrass or in other monocotyledonous plants with com- plete genome sequences. We examined available transcrip- tomic databases for genes encoding enzymes potentially involved in CGA biosynthesis in switchgrass. The protein products of two hydroxycinnamoyl-CoA shikimate/quinate Accessions numbers PvHCT1a: AB723827, PvHCT2a: KC696573, PvHCT-Like1: JX845714, PvC3′H1: AB723823, PvC3′H2: AB723824. Electronic supplementary material The online version of this article (doi:10.1007/s11103-013-0152-y) contains supplementary material, which is available to authorized users. L. L. Escamilla-Treviño · H. Shen · T. Hernandez · R. A. Dixon Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA L. L. Escamilla-Treviño · H. Shen · T. Hernandez · Y. Yin · Y. Xu · R. A. Dixon Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN 37831, USA Present Address: L. L. Escamilla-Treviño · H. Shen · R. A. Dixon (*) Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 6203-5017, USA e-mail: Richard.Dixon@unt.edu Y. Yin · Y. Xu Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA Present Address: Y. Yin Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115-2857, USA