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Characterization of Developmental Mutants of Phoma

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Characterization of Developmental Mutants of Phoma CHARACTERIZATION OF DEVELOPMENTAL MUTANTS OF PHOMA MEDICAGINIS By KIHYUCK CHOI Bachelor of Science in Applied Biology Dong-A University Busan, South Korea 2006 Master of Science in Agricultural Biology Dong-A University Busan, South Korea 2008 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY December, 2014 CHARACTERIZATION OF DEVELOPMENTAL MUTANTS OF PHOMA MEDICAGINIS Dissertation Approved: Dr. Stephen Marek Dissertation Adviser Dr. Carla Garzon Dr. Haobo Jiang Dr. Ramamurthy Mahalingam ii ACKNOWLEDGEMENTS I would first like to thank my advisors, Dr.’s Moon and Lee during undergraduate and master degree for introducing of Plant Pathology study. I would also like to extend the deepest appreciation to my advisor, Dr. Stephen Marek, for all his support, guidance, encouragement and patience through research and dissertation writing. I wish to express my appreciation to Dr. Garzon for her invaluable guidance and help for my family. I want to thank the committees, Dr. Haobo Jiang and Dr. Ramamurthy Mahalingam who offered their support and expertise. I also want to thank the previous and current students in the lab and Plant Pathology department including Ian Moncrief, Patricia Garrido, Francisco Flores, Andres Espíndola, Gabriela Orquera, Jessica Pavlu and Mary Gard. The most important people supported me behind the scenes. Thank you to my parents, Sunseop and Youngsuk, for always supporting, believing and praying me to keep studying my research. Lastly, I would like to thank my two pricesses, Taeyoun and Kaylee for their unconditional love and encouragement. Especially, Taeyoun has always deserved to get same Ph.D degree in terms of her support and sacrifice. Acknowledgements reflect the views of the author and are not endorsed by committee members or Oklahoma State University. iii Name: KIHYUCK CHOI Date of Degree: DECEMBER, 2014 Title of Study: CHARACTERIZATION OF DEVELOPMENTAL MUTANTS OF PHOMA MEDICAGINIS Major Field: Plant Pathology Abstract: Phoma medicaginis causes spring black stem and leaf spot, an important disease of alfalfa and annual medics. P. medicaginis forms uninucleate conidia in melanized pycnidia and is genetically tractable using Agrobacterium mediated transformation (ATMT), resulting in random integration of T-DNA that occasionally generates pycnidial mutants. One mutant (P265) displays smaller pycnidia and more aerial hyphae than the wild type. A single T-DNA disrupts a putative poly(A) RNA polymerase gene, PmCID13, which in yeasts interacts with ribonucleotide reductase (RNR). As in yeast mutants, P265 shows sensitivity to hydroxyurea (HU), a RNR inhibitor. To functionally characterize PmCID13, targeted PmΔcid13 mutants were created using a hygromycin selectable marker flanked by 1 Kbp regions of PmCID13. PmΔcid13 mutants possess similar morphological features to those of P265. The complementation vector pCAM-NAT (nourseothricin selection) was constructed and used to introduce full-length PmCID13 into mutants. Complemented mutants showed partial recovery of wild type and often lost the original T-DNA due to homologous integration. To our knowledge, this is the first CID13 ortholog to be examined in a filamentous fungus. One T-DNA-tagged mutant produced conidia in non-melanized (hyaline) pycnidia. Pycnidial melanization recovered if the mutant was supplemented with phenoloxidase substrates or allowed to age. DNA sequences flanking the insertion did not predict any disrupted open reading frames (ORF) unless a Coccidioides prediction algorithm was used. The Coccidioides predicted ORF (CPO) was expressed in the wild type, but not the mutant (cpo), and has not been annotated in any genomes, to date. Expression of two conserved genes flanking the T-DNA-disrupted cpo was unchanged from the wild type. Knockout of cpo strain displayed same cultural phenotype (non- melinized pycnidia). Complementation of cpo strains with wild type CPO partially recovered pycnidial melanization. Both knockout and complementation transformants were confirmed using RT-PCR. CPO appears to be a novel regulator of pycnidium specific melanization. iv TABLE OF CONTENTS Chapter Page I. INTRODUCTION ......................................................................................................1 Reference ...............................................................................................................18 II. REVIEW OF LITERATURE..................................................................................21 Medicago species and disease ................................................................................21 Model legume, Medicago truncatula .....................................................................22 Spring black stem caused by Phoma medicaginis Malbr. & Roum ......................23 Taxonomy of Phoma medicaginis .........................................................................23 Systematics of Phoma medicaginis and related fungi ...........................................24 Distribution and host range ....................................................................................25 Symptoms and life cycle ........................................................................................26 Biology of Phoma medicaginis ..............................................................................27 Growth in vitro .......................................................................................................27 Reproduction of Phoma medicaginis .....................................................................28 Host-pathogen interaction ......................................................................................28 Secondary metabolites of Phoma spp. ...................................................................29 Management of spring black stem and leaf spot ....................................................30 Transformation of fungi .........................................................................................31 Agrobacterium-mediated transformation (ATMT) ................................................32 Selectable Marker ..................................................................................................32 Poly (A) RNA polymerase cid13 gene ..................................................................33 Melanin of phytopathogenic fungi .........................................................................35 Reference ...............................................................................................................37 III. Construction of Agrobacterium-mediated transformation vector using alternative selectable marker, nouseothricin resistance ...........................................................43 Abstract ..................................................................................................................43 Introduction ............................................................................................................44 Experimental Approach .........................................................................................45 Results ....................................................................................................................51 Discussion ..............................................................................................................56 v Reference ...............................................................................................................58 IV. Characterization of a noncanonical poly (A) RNA polymerase gene in Phoma medicaginis ...........................................................................................................60 Abstract ..................................................................................................................60 Introduction ............................................................................................................61 Experimental Approach .........................................................................................67 Results ....................................................................................................................81 Discussion ............................................................................................................106 Reference .............................................................................................................114 V. Characterization of T-DNA tagged mutant of Phoma medicaginis developing non- melanized pycnidia ..............................................................................................119 Abstract ................................................................................................................119 Introduction ..........................................................................................................120 Experimental Approach .......................................................................................124 Results ..................................................................................................................133 Discussion ............................................................................................................151 Reference .............................................................................................................158 vi LIST OF TABLES Table Page 2.1 Poly (A) polymerase enzymes (PAPs) in Sz. Pombe ...........................................23 3.1
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