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UC Riverside UC Riverside Electronic Theses and Dissertations UC Riverside UC Riverside Electronic Theses and Dissertations Title The Role of Cross Pathway Control-2 (cpc-2) in Filamentous Fungus Neurospora Crassa Permalink https://escholarship.org/uc/item/5p192453 Author Garud, Amruta Vikas Publication Date 2013 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA RIVERSIDE The Role of the Cross Pathway Control (cpc)-2 Gene in the Filamentous Fungus Neurospora Crassa A Thesis submitted in partial satisfaction of the requirements for the degree of Master of Science in Genetics, Genomics and Bioinformatics by Amruta Vikas Garud June 2013 Thesis Committee: Dr. Katherine Borkovich, Chairperson Dr. Linda Walling Dr. Wenbo Ma Copyright by Amruta Vikas Garud 2013 The Thesis of Amruta Vikas Garud is approved: Committee Chairperson University of California, Riverside ABSTRACT OF THE THESIS The Role of the Cross Pathway Control (cpc)-2 Gene in the Filamentous Fungus Neurospora Crassa by Amruta Vikas Garud Master of Science, Graduate Program in Genetics, Genomics and Bioinformatics University of California, Riverside, June 2013 Dr. Katherine Borkovich, Chairperson In the filamentous fungus Neurospora crassa, heterotrimeric G protein pathways are major signaling cascades through which the fungus senses and adapts to its environment. The characterized Gβ subunit of N. crassa, GNB-1, has seven tryptophan-aspartate (WD) repeats, predicted to result in a β propeller structure. Another related N. crassa protein, called Cross Pathway Control-2 (CPC-2), also has a seven WD repeat structure and possesses 70% positional identity with Receptor for Activated C Kinase-1(RACK-1), a multifaceted scaffolding protein in mammals. Accumulating evidence in many organisms shows that RACK1 homologs can act as Gβ subunits. Previous work demonstrated that CPC-2 plays an important role during general amino acid control in N. crassa, along with having a role in overall growth and female fertility. My research investigated a possible role for cpc-2 in the G protein signaling pathway, and also investigated genetic epistasis between cpc-2, gnb-1 and the Gα genes in N. crassa. iv In Chapter 2, genetic analysis revealed that gna-3 is epistatic to gnb-1 with regard to control of submerged conidiation. gnb-1 is epistatic to gna-2 and gna-3 for aerial hyphal height, while gnb-1 appears to act upstream of gna-1 and gna-2 during aerial conidiation. None of the activated Gα alleles restored female fertility to Δgnb-1 mutants, and the gna-3Q208L allele inhibited formation of female reproductive structures, consistent with a need for Gα proteins to cycle through the inactive GDP-bound form for these processes. In Chapter 3, genetic epistasis genes showed that gna-3 is epistatic to cpc-2 during conidiation in submerged culture. gna-1 exhibited partial epistasis to cpc-2 during submerged culture conidiation. gna-3, gnb-1 and gng-1 operate downstream of cpc-2 during aerial hyphae height development. Apical extension assays showed that cpc-2 is epistatic to gnb-1 and gng-1. Similar to the results for gnb-1 in Chapter 2, none of the activated Gα alleles restored fertility to the sterile Δcpc-2 mutant. Analysis of apical extension rates on medium supplemented with -amino triazole (3AT) revealed a previously unknown role for gna-1 and gna-3 in general amino acid control. Yeast two hybrid mating assays revealed that CPC-2 interacts with GNA-1 and GNA-3. v Table of Contents Title page Copywright page Approval page Abstract of thesis................................................................................................................iv Table of contents................................................................................................................vi List of figures....................................................................................................................viii List of tables.......................................................................................................................ix Chapter 1. Introduction Neurospora crassa, an excellent model organism ..............................................................1 Heterotrimeric G protein signaling in N. crassa. ................................................................3 The Gβ subunit GNB-1 and the Gβγ heterodimer....................................................................4 RACK-1,a Gβ-related polypeptide......................................................................................5 Fungal homologs of RACK1...............................................................................................6 The Cross Pathway Control-2 (CPC-2) protein in N. crassa...............................................9 Objectives..........................................................................................................................11 Chapter 2. Genetic interaction between the Gβ subunit, gnb-1 and the three Gα genes- gna-1, gna-2 and gna-3 Introduction........................................................................................................................13 Materials and methods .......................................................................................................15 vi Results................................................................................................................................18 Discussion..........................................................................................................................25 Chapter 3. Analysis of the Cross Pathway Control-2 (cpc-2) gene Introduction ........................................................................................................................38 Materials and methods .......................................................................................................42 Results................................................................................................................................56 Discussion..........................................................................................................................96 Chapter 4. Future Directions........................................................................................103 vii List of figures Chapter 2 Fig 1. Analysis of progeny from a cross of Δgna-2 to Δgnb-1 strains using diagnostic PCR....................................................................................................................................33 Fig 2. Scheme for determining epistasis............................................................................34 Fig 3. Phenotypes during asexual growth and development.............................................35 Fig 4. Sexual phase phenotypes.........................................................................................36 Fig 5. Models for interactions between Gα proteins and the Gβγ dimer in Neurospora...37 Chapter 3 Figure 1: Phylogenetic analysis of CPC-2, RACK1, Gβ proteins and RACK1-like proteins...............................................................................................................................88 Figure 2. Phenotypes during asexual growth and development........................................89 Figure 3. Germination patterns of certain mutant strains..................................................90 Figure 4- Sexual phase phenotypes...................................................................................91 Figure 5- CPC-2 interacts with GNA-1 and GNA-3 in a yeast two hybrid assay.............92 Fig 6- Immunoprecipitation experiments...........................................................................93 Figure 7- Apical extension on media containing 3AT.......................................................94 viii List of Tables Chapter 2 Table 1- N. crassa strains used in this study.....................................................................30 Table 2: Oligonucleotides used in this study.....................................................................32 Chapter 3 Table 1: N. crassa strains used in this study......................................................................69 Table 2- Oligonucleotides used in this study.....................................................................71 Table 3- Statistical significance for Aerial Hyphae height Data.......................................72 Table 4- Statistical significance for Apical Extension Data..............................................76 Table 5- Statistical significance for Apical Extension Data on 3 AT................................79 ix Chapter 1: Introduction Neurospora crassa, a multicellular eukaryote, belongs to the ascomycete class of fungi. It has been used as model organism to study genetics, cell biology and biochemistry due to its simple growth requirements, non-pathogenicity, genetic tractability and a short life cycle (9). The famous one-gene-one-enzyme hypothesis by Beadle and Tatum in the 1940s was the result of a study on vitamin biosynthesis in this fungus (6). More recently, N. crassa has emerged as a model system to study pathogenic fungi, and its evolutionary relatedness to animal and mammalian systems makes it an attractive model organism (9). N. crassa grows by extension, branching and fusion of vegetative basal hyphae to form the thick mat called the mycelium. N. crassa has two asexual sporulation pathways- macroconidiation and microconidiation (64).Macroconidiation is the major pathway and involves production of aerial hyphae
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