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Ln the Mtdna Rnl-Region Within Species of Ophiostomatoid Fungi

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Ln the Mtdna Rnl-Region Within Species of Ophiostomatoid Fungi Bio-prospecting and Characterization of Optional Elements present ln the mtDNA rnl-region within Species of Ophiostomatoid Fungi by Jyothi Sethuraman A Thesis submitted to the Faculty of Graduate Studies of The Univeisity of Manitoba in partial fulfilment of the requirements of the degree of Doctor of Philosophy Department of Microbiology University of Manitoba Winnipeg, Manitoba, Canada Copyright @ 2009 Jyothi Sethuraman THtr UNIVERSITY OF MANITOBA FACULTY OF GRADUATE STUDIBS coPYRrcH;;uorr..ro* Bio-prospecting and characterization of optional Elements present ln the mtDNA rnlregion within species of ophiostomatoid Fungi By Jyothi Sethuraman A Thesis/Practicunl srbn¡itte(l to the Faculty ofGladuate Studics ofThe Unir,er.sity of Manitoba in par.tial firlfillnlcnt of the rcquir.cnrent of the degr.ee of Doctor of Philosophy J¡'othi Sethur.aman02009 Pc'nrission - has been grantetl to the uni'e'sitv of Manitoba Librar.ies to len(l â cop¡, of tlris thesis/plactictrnt, to Lib|ar¡' anrl Archives Canarla (LAC) to lcn(l a cop¡, of this tt,"sislir."cìicuur, antl to LAC's agent (UMI/ProQuest) to nriclofihn, sell co¡ries ana to pirtrtistr an abstr.;ct of this thesis/pr.acticum. This replorluction or cop)' of this thesis has becn matle lvailable b¡, author.it¡, of the copyr.ight on,net'solel¡' for the pur.pose of private study antl resear.ch, and ma5, ånl¡, be r.eproducetl aritt copied as pernritterl bY copylight larvs or rvitlt €xpress rvl'itten autholizaiion fì.om the copyright orvner. ABSTRACT Fungal mitochondrial genomes are in a constant flux due to the presence of mobile elements such as plasrnids, introns and homing endonuclease genes (lIEGs). In this study, two regions of the mitochondrial large ribosomal subunit gene (mt-rrzl), Ul i and U7, were screened for the presence of introns and intron encoded proteins in Ophiostoma ulnti and related species. The rul-U'| region sometimes showed the presence of a group I ìnrron encoding a double-motif LAGLIDADG Horning Endonuclease (LIIE), whereas the Ul l region always contained a group I intron that encoded a ribosomal protein, Rps3. The Ui I intron appears to be essential as it encodes an important host gene (rps3). Sometimes, the Ull intron encodes a complex open reading frame (ORF) where the LHE is either fused to the N or C-terminus coding regions of the rps3 ORF potentially generating in-frame fusions and/or gene within gene alrangements Characterization of one LIIE (I-OnuI) that is fused to the C-termrnus of Rps3 demonstrated that I-Onul is an active endonuclease. The cleavage site mapping for the I- OnuI suggested that the mG upon insertion displaces a segment of the resident rps3gene,but the IIEG brings along a DNA segment that compensates for the displaced sequences. This helps the IIE to be expressed as a fusion protein maintaining the rps3 coding region intact. The presence of cleavage site within the rps3 suggest that these IIEGs are targeting ¡he rps3 gene and are not likely facilitating the mobility of the actual u11 group I intron. This srudy surveyed in detail over 20 different Rps3 type FIEGs and the data showed that the phylogeny of the FIEGs appears to be congruent with the phyìogeny of the host gene (RPS3) suggesting that mcs once inserted in the rps3 appears to be passed aÌong in a vertical manner. The mt-ntl U7 region within species of Ceratocystis showed that the U7 region is very dynamic due to the presence of two types of group I introns inserted at two different siles. These introns encoded either single or double motif LHE and in one occasion a GIY-YIG type FIE inserted within the single-motif LFIE coding region. AIso, identical FIEases were found to be present among distantìy related species of Ceratoc)¡stis suggesting possible horizontal transmission or rapid loss of introns and HEGs; in latter scenario one would assume the ancestors had introns with ORFs. ACKNOWLEDGEMENTS I express my sincere gratitude to Dr. G Hausner, my supervisor in this project Without his support, encouragement, and eminent guidance I could not have completed this project, for which I thank him profusely. I am also thankful for the heìp and suppo¡t he provided for the successful completion of the thesis' I am immensely grateful to Dr. J. Reid, who was generous in providing cultures from his culture collections and culturing many fungi during the course of my study; his suggestions and support, has been of utmost help to me. I wish to thank Dr. D R Edgell for allowing access to his laboratory and training me in protein-related experiments. His expertise and advice has been of enormous help towards the completion of the project. I would also like to thank alì the members in Dr. D R Edgell's lab fo¡ the help and support provided. I would like to thank all the committee members, Dr. D Court and Dr. M Pietcey- Normore and Dr. I Oresnik who have reviewed my work in the past, and for their valuable comments and suggestions. I also would like to show my appreciation to Dr. J Kennell for being the external examiner. I thank all of my committee members who read and gave me very helpfuì suggestions regarding the submission. I wish to thank for the friendship and encouragement especialìy to Anna Majer for the immense help she provided with the projects and also to all the former and present lab mates, Sahra-Taylor Mullineux, Shelìy Rudski, Tamara Corkery, Vincent Okoli, Mohamed Abdel-Fattah and Mohamed Iranpour. I also wish to thank all the staff and graduate students for their friendship and suppof, I gratefully acknowledge the financial t support provided by NSERC through its operating grant to Dr. G Hausner. Additionaì suppof by International graduate student scholarship and Faculty of Science bursary is greatly acknowledged. My very special gratitude and respect to my uncle and parents for their support and encouragement during my study. I bestow upon God for all blessings TABLE OF CONTENTS Abstract I Acknowledgements llt Table of Contents List of Figures vl List of Tabìes viii List of Abbreviations ix Introduction i Review of Literature 8 Materials and Methods 53 Chapter i 69 Chapter 2 118 Chapter 3 r63 Chapter 4 r87 Conclusion 223 References 227 Appendix List of Figures Introduction Fig 1: Schematic representation for the positions o'f mt-rnl U7 and Ul I regions Revierv of Literature Fig l: Group I, group II and spliceosomal intron splicing pathway 25 Chapter l: The sporadic occuffence of a group I intron-like elemeht in the mtDNA nrl gene of Opltiostonta novo-ulmi subspecies americatn. Fig lA-lD: Schematic representation of the ml-U1 and rnl-Ul i regions 88 Fig 2: Representative PCR amplification products obtained from members of O. ulmi s.l. and related taxa for primers targeting the rnl-U7 regions 93 Fig 3: Phylogenetic tree based on Bayesian analysis of 55 double motif LAGLIDADG FIEG-li ke elements 99 Fig 4 A-48: Phylogeny of the clade of flEGlike elements that includes the ml-l699 intron encoded ORFs 104 Fig 5: Phylogenic analysis of ml-i699 intron ORF nucleotide sequences obtained from geographically diverse strains of Ophiosloma ulnli and O. ttovo-ulmi subsp. anlencana i07 Fig. 6A-6D: Secondary structure models of the IA 1 r-¡¡l-U7 intron-like elements found in O. novo-ulnti subsp. americana 111 Chapter 2: Multiple LAGLIDADG homing endonucìeases target the rìbosomal protein 53 gene encoded within a group I intron that intemrpts fhe n gene of Ophiostonta and related taxa Fig 1: RT-PCR assay to detect splicing of the mL2449 group I intron in Ophiostonta novo-uhní ssp antericana strain WIN(M) 900 130 Fig2A-2F-: Schematic representation of the n1,2499 intron, the intron-encoded rps3 gene, and FIEG inserlion sites 133 Fig 3A-B: Phylogenetic analyses of 32 double motif LAGLIDADG amino acid sequences 141 Fig 4: Phyìogenetic relationships among 47 mL2449 intron encoded sequences 145 Fig 5: Purification and characterization of I-OnuI l4g Fig 6: Sequence logos generated from an amino acid alignment of Rps3 orthologs 155 Chapter 3: The evolutionary history of mtDNA encoded Rps3 among filamentous ascomycetes fungi with an emphasis on the ophiosromatoid fungi Fig. 1:Diversity found within rps3/var\ gene configurations 170 Fig 2: Phylogenetic relationships among rps3 sequences 174 Fig. 3: Phylogeny of fungal mtDNA rps3 sequences r77 Fig. 4: Phylogenetic analyses of a 36 rps3 gene codon-based alignment covering 1179 positions (393) r83 Chapter 4: The mosaic composition of the mitochondnal ntt-IJ7 region in selected species of Cerat ocystis Fig 1: Overview of mtDNA ml-U'| intronlexon configurations 194 Fig 2: Schematic representation of the insertions present within the ml-I)1 region in Ceratocystis and related taxa 197 Fig 3: Phylogenetic position of the Ceratocyslis rnl-U? llEases 209 Fig 4: Phylogenetic tree based on I 157 postions of the ITS sequence of l2 strains belonging to the species Ceratocystis 213 Fig 5: Phylogenetic position of the C. resinifera mLl923 intron encoded GIY-YIC FIEG 217 Fig 6: Phylogenetic analysis of the group II intron encoded FIEases 220 vIt List of Tables Materials and Methods Primers used for completing the all the sequences used in the study 57 Chapter 1: The sporadic occurrence of a group I intronlike element in the mtDNA rnl gene of Ophiostoma novo-ulntí subspecies atnericana. Table 1: List of strains and summary of PCR survey for insefions within the mtDNA ntl U'l and Ul I regions. '77 Table 2z GenBank accession numbers for the homing endonuclease gene (IIEG)- like elements used in the phyÌogenetic anaìysis 97 Chapter 2: Multiple LAGLIDADG homlng endonucleases
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