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University of California Santa Cruz Characterization Of UNIVERSITY OF CALIFORNIA SANTA CRUZ CHARACTERIZATION OF ARCHAEAL SPECIES THROUGH RNASE P AND TRANSFER RNAS A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOINFORMATICS by Patricia Pak Lee Chan December 2010 The Dissertation of Patricia P. L. Chan is approved: ________________________________ Professor Todd M. J. Lowe, Chair ________________________________ Professor David Haussler ________________________________ Professor Karen M. Ottemann ________________________________ Professor Manuel Ares, Jr. _____________________________ Tyrus Miller Vice Provost and Dean of Graduate Studies Copyright © by Patricia Pak Lee Chan 2010 Table of Contents List of Figures...............................................................................................................vi List of Tables................................................................................................................ix Abstract..........................................................................................................................x Acknowledgments ..................................................................................................... xiii Chapter 1 Introduction ............................................................................................1 1.1 Archaea, the third domain of life....................................................................2 1.2 A mix of bacterial and eukaryotic features.....................................................2 1.3 Ribonuclease P, a “nearly” universal ribozyme .............................................4 1.4 Disrupted transfer RNAs – how common are they?.......................................6 1.5 Atypical genes in nature .................................................................................9 Chapter 2 Transcriptional and Translational Signal Detection in Archaea.....17 2.1 Introduction ..................................................................................................18 2.2 Results ..........................................................................................................20 2.2.1 Absence of transcription factor B recognition element.......................21 2.2.2 Low conservation of Shine-Dalgarno motifs in Pyrobaculum, Cenarchaeum, and Nanoarchaeum .....................................................22 2.2.3 A mixture of leadered and leaderless transcripts in Crenarchaeota and Euryarchaeota ...............................................................................23 2.2.4 Highly variable 5′ UTR length in methanogens ..................................26 2.2.5 Evidence of gene coordinate mis-annotations.....................................27 2.2.6 Internal promoters leading to two modes of transcription...................28 2.2.7 Search for Shine-Dalgarno-less 5′ UTRs.............................................30 2.3 Discussion.....................................................................................................32 2.4 Materials and Methods .................................................................................35 Chapter 3 Discovery of a minimal form of RNase P in Pyrobaculum................55 3.1 Abstract.........................................................................................................56 3.2 Introduction ..................................................................................................57 3.3 Results and Discussion .................................................................................58 3.3.1 Pre-tRNAs in Pyrobaculum have 5ʹ leaders........................................58 iii 3.3.2 Pyrobaculum aerophilum cell extract processes 5ʹ leader from pre- tRNA....................................................................................................60 3.3.3 Evidence for three out of four known archaeal RNase P proteins in Pyrobaculum........................................................................................61 3.3.4 Discovery and in vitro activity of the minimized Pyrobaculum RNase P RNA......................................................................................62 3.3.5 Phylogenetic distribution of the minimized form of RNase P RNA ...64 3.3.6 Search for RNase P RNA in Aquifex and Related Species.................66 3.4 Conclusions ..................................................................................................67 3.5 Materials and Methods .................................................................................68 3.6 Author Contributions....................................................................................81 3.7 Acknowledgments ........................................................................................82 Chapter 4 Modeling the Thermoproteaceae RNase P RNA...............................97 4.1 Introduction ..................................................................................................98 4.2 Results and Discussion .................................................................................99 4.2.1 Common features of type T RNase P RNAs .......................................99 4.2.2 Type T RNase P RNA variants .........................................................100 4.2.3 Search with type T RNase P RNA covariance model .......................101 4.2.4 Type M RNase P RNA variants ........................................................102 4.3 Conclusions ................................................................................................103 4.4 Materials and Methods ...............................................................................104 Chapter 5 Discovery of Permuted and Recently Split Transfer RNAs in Archaea ..............................................................................................................111 5.1 Abstract.......................................................................................................112 5.2 Introduction ................................................................................................113 5.3 Results ........................................................................................................116 5.3.1 Split tRNAAsp(GUC) in Aeropyrum and Thermosphaera consist of adjacent halves...................................................................................116 5.3.2 tRNALys(CUU) in Staphylothermus resembles its ortholog in Nanoarchaeum ..................................................................................119 5.3.3 Permuted tRNAs in Thermofilum pendens have the same structure as in red alga......................................................................................121 5.4 Discussion...................................................................................................123 5.5 Materials and Methods ...............................................................................128 5.6 Author Contributions..................................................................................132 5.7 Acknowledgments ......................................................................................132 Chapter 6 GtRNAdb: A database of transfer RNA genes detected in genomic sequence.....................................................................................................148 6.1 Abstract.......................................................................................................149 iv 6.2 Introduction ................................................................................................149 6.3 Database Features.......................................................................................151 6.3.1 tRNA identification information .......................................................151 6.3.2 tRNA secondary structures and alignments ......................................152 6.3.3 tRNA search and BLAST server .......................................................153 6.3.4 Error and request tracking .................................................................154 6.4 Future Directions ........................................................................................155 6.5 Funding.......................................................................................................156 Chapter 7 Chracterization of a crenarchaeal-rich metagenome through RNase P and tRNAs.................................................................................................160 7.1 Introduction ................................................................................................161 7.2 Results and Discussion ...............................................................................163 7.2.1 At least six crenarchaeal species co-exist in Cistern Spring .............163 7.2.2 Search for RNase P RNAs in metagenome .......................................164 7.2.3 Majority of tRNAs in Cistern Spring have introns............................165 7.2.4 Trans-spliced split tRNAs in Caldivirga...........................................167 7.2.5 Novel intron-bearing split tRNA in Thermoproteus .........................169 7.3 Future Directions ........................................................................................170 7.4 Materials and Methods ...............................................................................171 Chapter 8 Conclusions .........................................................................................186 Bibliography.............................................................................................................190
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