The auxins are an important class of plant hormones involved in many aspects of plant development The most common naturally occurring auxin is indole-3-acetic acid, or IAA. In Arabidopsis, up to 95% of the IAA pool is found conjugated to small molecules such as sugars and amino acids. However, the genes and enzymes involved in IAA conjugate metabolism are not yet well understood. A mutant, iar1, that is resistant to the inhibitory effects of multiple IAA-amino acid conjugates on root elongation was identified. The IAR1 gene encodes a protein with numerous transmembrane domains and several histidine-rich regions. The IAR1 protein has homologs in other organisms, including Drosophila, C. elegans, and mammals, and is similar in molecular structure to the ZIP family of zinc transporters from Arabidopsis and yeast. Plant reproduction requires precise control of the transition to flowering in response to environmental cues. We have isolated a late-flowering Arabidopsis mutant, fkf1, that is rescued by vernalization or gibberellin treatment. The mutant also exhibits a light-dependent hypocotyl elongation defect. We used a positional approach to clone FKF1, which encodes a novel protein with an N-terminal PAS domain similar to the flavin-binding region of certain photoreceptors, an F-box motif characteristic of proteins that target ubiquitin-mediated degradation, and six kelch repeats predicted to fold into a beta-propeller. FKF1 mRNA levels oscillate with a circadian rhythm and the fkf1 deletion mutation alters the rhythmic expression of other clock-regulated genes, implicating FKF1 in regulation of the circadian clock.