Evidence from Co-expression Analysis for the Involvement of Amidase and INS in the Tryptophan-Independent Pathway of IAA Synthesis in Arabidopsis.

The reverse genetic approach has uncovered indole synthase (INS) as the first enzyme in the tryptophan (trp)-independent pathway of IAA synthesis. The importance of INS was reevaluated suggesting it may interact with tryptophan synthase B (TSB) and therefore involved in the trp-dependent pathway. Thus, the main aim of this study was to clarify the route of INS through the analysis of Arabidopsis genome. Analysis of the top 2000 co-expression gene lists in general and specific conditions shows that TSA is strongly positively co-expressed with TSB in general, hormone, and abiotic conditions with mutual ranks of 89, 38, and 180 respectively. Moreover, TSA is positively correlated with TSB (0.291). However, INS was not found in any of these coexpressed gene lists and negatively correlated with TSB (- 0.046) suggesting unambiguously that these two routes are separately and independently operated. So far, the remaining steps in the INS pathway have remained elusive. Among all enzymes reported to have a role in IAA synthesis, amidase was found to strongly positively co-expressed with INS in general and light conditions with mutual ranks of 116 and 141 respectively. Additionally, amidase1 was found to positively correlate with INS (0.297) and negatively coexpressed with TSB concluding that amidase may exclusively involve in the trp-independent pathway.

Contribution of the IAM Pathway to IAA Pool in Developing Rice Grains

A possible role for the indole-3-acetamide (IAM) pathway in the indole-3-acetic acid (IAA) production was investigated in developing rice grains. IAM-hydrolase proposed to convert IAM to IAA primarily through the identification of IAM and IAM-hydrolase activity in some plant species. Expression profiles of the two putative rice IAM-hydrolase genes, OsAMI1&2, were compared to the previously quantified IAA level. The abrupt increase in IAA level between 4 and 7 days after anthesis (DAF) was not found to correlate with changes in the expression of OsAMI1 or OsAMID2 suggesting that the IAM pathway may not contribute significantly to IAA pool in rice grains. Production of a biological compound other than IAA may explain the high activity of OsAMI1&2 in developing rice grains. OsAMI1 that reported to be conserved across the plant kingdom showed higher expression level in most analyzed reproductive rice tissues whereas OsAMID2 showed more fluctuation in expression comparing to OsAMI1. Role of the IAM pathway in IAA production was also discussed in other plant systems and Arabidopsis seed was recommended as an ideal tissue to identify enzyme(s) convert(s) tryptophan to IAM as well as physiological effects of IAA produced via this pathway.