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The Pennsylvania State University The Graduate School Intercollege Graduate Degree Program in Plant Biology FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA A Dissertation in Plant Biology by Penglin Sun 2015 Penglin Sun Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The dissertation of Penglin Sun was reviewed and approved* by the following: Teh-hui Kao Distinguished Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Chair, Intercollege Graduate Degree Program in Plant Biology Michael Axtell Associate Professor of Biology Dawn Luthe Professor of Plant Stress Biology Timothy McNellis Associate Professor of Plant Pathology *Signatures are on file in the Graduate School iii ABSTRACT Many flowering plants possess self-incompatibility (SI), an intraspecific reproductive barrier by which pistils reject self-pollen to prevent inbreeding and accept non-self pollen to promote outcrossing. In Petunia, the polymorphic S-locus, which controls self/non-self recognition, contains an S-RNase gene which regulates pistil specificity and multiple S-locus F-box (SLF) genes which collectively regulate pollen specificity. The collaborative non-self recognition model predicts that, for a given S-haplotype, each SLF recognizes a subset of non-self S-RNases to mediate their ubiquitination and degradation by the 26S proteasome, and multiple SLFs collaboratively recognize and detoxify all non-self S-RNases to allow compatible pollination. The overall goal of my dissertation research is to study how SLF proteins interact with S- RNases in order to understand the biochemical basis of self/non-self recognition during SI interactions. The function of the S-RNase gene in controlling pistil specificity has been established through both gain- and loss-of-function experiments; however, only gain-of-function experiments have been used to demonstrate the function of several types of SLF genes in controlling pollen specificity. In Chapter 2, using a gain-of-function assay, I examined the relationships between S2-SLF1 (S2-allelic product of Type-1 SLF) and four S-RNases. The results suggest that S2-SLF1 interacts with S7- and S13-RNases, and the previously identified S1- and S3- RNases, but not with S5- or S11-RNase. An artificial microRNA expressed by the S2-SLF1 promoter, but not by the vegetative cell specific promoter, Late Anther Tomato 52 (LAT52), suppressed expression of S2-SLF1 in S2 pollen, suggesting that SLF1 is specific to the generative cell. The S2 pollen with S2-SLF1 suppressed was compatible with S3-, S5-, S7-, S11-, and S13- carrying pistils, confirming that other SLF proteins are responsible for detoxifying S5- and S11- RNases, and suggesting that S2-SLF1 is not the only SLF in S2 pollen that interacts with S3-, S7-, iv and S13-RNases. Petunia may have evolved at least two types of SLF proteins to detoxify any non-self S-RNase to minimize the deleterious effects of mutation in any SLF. An SLF is predicted to be the F-box protein component of an SCF complex (composed of Cullin1, Skp1, RBX1 and an F-box protein), which mediates ubiquitination of protein substrates for degradation by the 26S proteasome. However, the precise nature of the complex is unknown. In Chapter 3, I used pollen extracts of a transgenic plant expressing S2-SLF1:GFP for co- immunoprecipitation (Co-IP) followed by mass spectrometry (MS). I identified PiCUL1-P (a pollen-specific Cullin1), PiSSK1 (a pollen-specific Skp1-like protein) and PiRBX1 (an RBX1). Thus, all components but RBX1 of the SLF-containing complex may have evolved specific isoforms in SI. According to the collaborative non-self recognition model, SLFs collectively mediate ubiquitination and degradation of non-self S-RNases. In Chapter 4, I describe a surprising finding that SLF1 of P. inflata itself was subject to degradation via the ubiquitin-26S proteasome pathway (UPP), and identified an 18-amino-acid (18-aa) sequence in the C-terminal domain of S2-SLF1 (SLF1 of S2-haplotype) that contains a degradation motif. Four of the 18 amino acids are conserved among all 17 SLF proteins of S2-haplotype and S3-haplotype involved in pollen specificity, suggesting that the stability of all SLF proteins is likely subject to similar regulation. Deleting the 18-aa sequence from S2-SLF1 stabilized the protein but abolished its function in SI, suggesting that regulation of the stability of SLF proteins is an integral part of their function in SI. I used S2-SLF1:GFP as the bait to perform Co-IP followed by MS, and identified PiDCN1 (defective in cullin neddylation 1) and PiUBC12 (NEDD8-conjugating enzyme) that may be involved in neddylation of PiCUL1-P to activate SCFSLF complexes; and identified PiCAND1 (cullin-associated NEDD8-dissociated protein 1), UPL1-like protein (a mono-subunit E3 ligase v containing a HECT domain) and an E2 ubiquitin-conjugating enzyme, that may mediate dissociation of SLF proteins from their SCFSLF complexes and degradation. In Chapter 5, I describe an ongoing project to validate the role of PiDCN1 and PiUBC12 in neddylation of PiCUL1-P, and the function of PiCAND1 in dissociation of SLF proteins from their SCFSLF complexes, based on the results obtained from Chapter 4. I also discuss some of the experiments I carried out to further pinpoint the degradation motif of S2-SLF1 in yeast. Finally, in Chapter 6, I summarize all the major findings of my dissertation research, and describe how these findings have advanced our understanding and laid a foundation for future studies of S-RNase-based SI. vi TABLE OF CONTENTS List of Figures .......................................................................................................................... ix List of Tables ........................................................................................................................... xii Acknowledgements .................................................................................................................. xiii Chapter 1 Literature Review ................................................................................................ 1 1.1 Major Types of SI Mechanisms ................................................................................. 3 1.2 Identification and Characterization of the S-RNase Gene .......................................... 4 1.3 Identification of the First S-Locus F-Box Gene, SLF1 ............................................... 7 1.4 Protein Degradation Model Based on the Assumption that Pollen Specificity Is Controlled by a Single SLF Gene ............................................................................. 9 1.4.1 Protein Degradation Model ............................................................................. 9 1.4.2 Biochemical Characterization of the SLF-Containing Complex ..................... 10 1.5 Evidence against SLF1 Being Solely Responsible for Controlling Pollen Specificity ................................................................................................................ 13 1.5.1 Evolutionary Consideration ............................................................................. 13 1.5.2 Experimental Data .......................................................................................... 15 1.6 Involvement of Additional SLF Genes in Controlling Pollen Specificity ................. 16 1.7 Collaborative Non-Self Recognition Model ............................................................. 17 1.8 Hypotheses and Objectives ....................................................................................... 18 1.9 References .................................................................................................................. 27 Chapter 2 Self-Incompatibility in Petunia inflata: the Relationship between a Self- Incompatibility-Locus F-box Protein and Its Non-Self S-RNases ............................. 34 2.1 Introduction ................................................................................................................ 35 2.2 Methods ...................................................................................................................... 37 2.2.1 Plant Material .................................................................................................. 37 2.2.2 Construction of AmiS2-SLF1 and AmiGFP Stem-Loop Precursors ................. 37 2.2.3 Generation of Ti Plasmid Constructs and Plant Transformation ..................... 38 2.2.4 Visualization of GFP Fluorescence ................................................................. 39 2.2.5 Real-Time PCR Analysis to Determine Levels of S2-SLF1 Transcript and Mature amiRNA, and Copy Numbers of Transgene ........................................ 39 2.2.6 Genomic DNA Isolation and Blotting ............................................................. 41 2.2.7 Genotyping of Progeny by PCR ...................................................................... 41 2.2.8 Accession Numbers ......................................................................................... 42 2.3 Results ........................................................................................................................ 42 2.3.1 Examining the Relationships between S2-SLF1 and Four Non-Self S- RNases by Gain-of-Function Transgenic Functional Assay ............................ 42 2.3.2 Suppression of Expression of LAT52P:S2-SLF1:GFP Transgene by LAT52 Promoter-Driven AmiRNAs Targeting Either S2-SLF1 or GFP

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