UC Riverside

Plants are exposed to a variety of environmental cues and internal signals. To maintain distinct physiological responses, plants use diverse signaling mechanisms. The focus of my dissertation is on karrikin signaling and its relationship to plant growth. I begin by describing the type of signals that karrikins are, what roles they have throughout plant development, and discuss mechanistic details of karrikin perception and response. I explore the idea that karrikins are substitutes for an endogenous plant molecule called KAI2 ligand (KL). Furthermore, I challenge the idea that karrikins are direct KAI2 signals, and propose that karrikins are processed by the plant to function as bioactive signals.In my first chapter, we characterize a gene called KARRIKIN-UPREGULATED F- BOX1 (KUF1), which is an upregulated transcriptional marker of karrikin signaling. We generated a loss-of-function kuf1 mutant to understand the function of KUF1. kuf1 seedlings have phenotypes that are consistent with upregulated KAR/KL signaling. These phenotypes are KAI2 dependent, suggesting that KUF1 functions upstream of KAI2. We show that KUF1 represses KL biosynthesis and karrikin metabolism, the effect of karrikins on KUF1 expression is a conserved mechanism, and show KUF1 is part of a negative feedback loop that dampens KAI2 signaling. Finally, we end the chapter by identifying KUF1 as an F-box protein, and propose that the polyubiquitinated targets of KUF1 are essential to further understand KAR/KL metabolism. In my second chapter, we identify ACT DOMAIN REPEAT (ACR) proteins as targets of KUF1. We used affinity purification and mass spectrometry to identify the most likely KUF1 target, which was ACR5. I begin characterizing ACR5 by testing its interaction with KUF1 and whether ACR5 degradation is dependent on KUF1. I genetically characterize ACR5 by testing whether acr5 can suppress kuf1 mutant phenotypes. Despite knocking out acr5 and its closest homolog acr4, I was unable to see robust suppression of kuf1. For the remainder of chapter 2, I propose that 11 other ACRs are functionally redundant with ACR5. I circumvent the effects of functional redundancy by individually overexpressing all 12 ACRs to assess whether they have phenotypes consistent with upregulated KAI2 signaling. I show that overexpressing ACRs causes seedlings to phenocopy kuf1 on a physiological and molecular level. Given that the ACR gene family is largely uncharacterized, I begin exploring potential functions of ACR5 as an energy sensor that links KAI2 signaling to nitrogen abundance. In my third chapter, I explore the identity of ACR5 as an amino acid sensor. ACR5 is a protein solely composed of ACT domains, which function as small molecule binding sites. ACT domains are conserved in eukaryotes, and I discuss several examples of ACT domain-containing proteins that bind amino acids like glutamine and arginine. Keeping in line with KAI2 signaling as a readout of energy status, I test whether karrikin signaling mutants have effects on Glutamine synthetase/Glutamate synthase (GS/GOGAT) signaling, a pathway involved in nitrogen assimilation, and the TARGET OF RAPAMYCIN (TOR) signaling, a pathway that regulates growth in response to environmental signals. My third chapter identifies future lines of research for ACRs.