Rethinking the Origin of Auxin Biosynthesis in Plants

Auxin is the first identified and essential phytohormone for plant development and survival (Lee and Cho, 2013; Locascio et al., 2014). The synthesis of naturally occurring auxin indole-3-acetic acid (IAA) in plants can be divided into two categories: tryptophan (Trp)-dependent and Trp-independent pathways (Tivendale et al., 2014). Genetic studies have demonstrated the Trp-dependent pathway as the main route for auxin biosynthesis in plants. Among the four distinctive biosynthesis routes downstream of Trp, the indole-3-pyruvic acid (IPA) pathway is the most crucial one. TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) catalyzes the formation of IPA from L-Trp and flavin-containing monooxygenase enzymes (YUCCA) further transform IPA into IAA. Although, these auxin biosynthesis routes are well illustrated in higher plants, the origin of auxin biosynthesis in plants is still unclear. Within the last 1 year, four different Opinions or Letters published in the journal Trends in Plant Science argue whether or not Trp-dependent auxin biosynthesis in plants originates from the which are freshwater plants closely related to land plants during evolution. The major discrepancy among these arguments lie in whether or not charophytes have functional TAA1 (Stepanova et al., 2008; Tao et al., 2008). Being key players in auxin biosynthesis, TAA1 and YUCCA have been adopted as queries for searching the origin of auxin biosynthesis. In the search, Wang et al. identified one TAA1 homolog (kfl00051_0080) and one YUCCA homolog (kfl00109_0340) in Klebsormidium flaccidum (Klebsormidiales, Charophyta) with the help of the recently released K. flaccidum draft genome sequence (Hori et al., 2014). They performed phylogenetic analysis and stated that auxin biosynthesis originates from charophytes. However, their conclusion quickly came under attack due to two major issues. Firstly, TAA1 can only be found in K. flaccidum, but not in the other four charophyte species (Mesostigma viride, Coleochaete orbicularis, Spirogyra pratensis, and Nitella mirabilis), according to a recent report on charophyte transcriptome data (Ju et al., 2015). Secondly, phylogenetic analysis and protein structure prediction results show that K. flaccidum TAA1 (KfTAA1) is more similar to alliinase but not Arabidopsis TAA1 (AtTAA1) (Huang et al., 2014; Turnaev et al., 2015). Nevertheless, we think it is still too early to conclude that auxin biosynthesis does not originate from charophytes. Firstly, although TAA1 homologs have not been identified in other charophyte species, it does not necessarily mean that they do not contain TAA1. Since interpretation of transcriptomic data highly depends on the sample collection stage, the absence of TAA1 …