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University of California, San Diego UNIVERSITY OF CALIFORNIA, SAN DIEGO Comparative Analysis of Piezophilic Bacteria: The Search for Adaptations to Life in the Deep Sea A thesis submitted in partial satisfaction of the requirements for the degree of Master of Science in Biology by Ian McKenzie Kerman Committee in charge: Professor Douglas H. Bartlett, Co-Chair Professor Eric E. Allen, Co-Chair Professor Milton H. Saier 2008 The Thesis of Ian McKenzie Kerman is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ________________________________________________________________________ ________________________________________________________________________ Co-Chair ________________________________________________________________________ Co-Chair University of California, San Diego 2008 iii Epigraph Here too are dreaming landscapes, lunar, derelict. Here too are the masses, tillers of the soil. And cells, fighters, who lay down their lives for all the world. Here too are cemeteries, fame, snow and spates. And I hear murmuring, the revolt of immense estates. Miroslav Holub In the Microscope iv Table of Contents Signature Page .............................................................................................. iii Epigraph ........................................................................................................ iv Table of Contents .......................................................................................... v List of Abbreviations ..................................................................................... vi List of Tables ................................................................................................. vii List of Graphs ................................................................................................ viii List of Figures ............................................................................................... ix Acknowledgments ......................................................................................... xi Abstract ......................................................................................................... xii Introduction ................................................................................................... 1 Chapter 1: Comparative Analysis of Piezophilic Ribosomes ....................... 6 Chapter 2: Modeling of Protein Folding Volume ......................................... 59 Chapter 3: Genomic Sequencing and Analysis of Moritella sp. PE36 ........ 80 References ..................................................................................................... 133 v List of Abbreviations ΔV change in volume BLAST Basic Local Alignment Search Tool bp base pair COG cluster of orthologous groups DHA docosahexaenoic acid DNA deoxyribonucleic acid EC Enzyme Commission EPA eicosapentaenoic acid KEGG Kyoto encyclopedia of genes and genomes IMG Integrated Microbial Genomes ITS internal transcribed spacer mRNA messenger RNA MUSCLE MUltiple Sequence Comparison by Log-Expectation ORF open reading frame PCR polymerase chain reaction PUFA polyunsaturated fatty acid RNA ribonucleic acid RP ribosomal protein rRNA ribosomal RNA RTX repeat in toxin SRP signal recognition particle tRNA transfer RNA vi List of Tables Table 1.1: Pairings of piezophiles and mesophiles for sequence comparison ............................................................................. 32 Table 1.2: List of organisms and the genome accessions used for comparisons ........................................................................... 32 Table 1.3: List of ribosomal operon upstream regulators found in Escherichia coli ...................................................................... 33 Table 2.1: List of the fifteen proteins selected for folding volume comparison ............................................................................. 68 Table 2.2: List of organisms and the genome accessions used for comparisons ........................................................................... 69 Table 2.3: Table indicating which proteins were found and not found in the organisms .................................................................... 70 Table 2.4: Changes in amino acid side chain volume upon protein folding ..................................................................................... 71 Table 2.5: Pairings of piezophiles and mesophiles for sequence comparison ............................................................................. 71 Table 2.6: Calculated change in volume for proteins in Table 2.1 ........ 72 Table 2.7: Average differences in the change in volume and the standard deviation for each protein ...................................... 74 Table 3.1: Summary of the genome of Moritella sp. PE36 .................... 109 Table 3.2: List of ORFs identified as having a frameshift or being truncated ................................................................................ 110 Table 3.3: Summary of Codon Usage in Moritella sp. PE36 ................. 112 Table 3.4: List of COG categories and the occurrence of each in Moritella sp. PE36 and Shewanella frigidimarina .............. 115 Table 3.5: List of KEGG categories and the occurrence of each in Moritella sp. PE36 and Shewanella frigidimarina .............. 116 Table 3.6: List of amino acid metabolism genes duplicated in Moritella sp. PE36, but not, or less so, in Shewanella frigidimarina ......................................................................... 117 Table 3.7: List of genes functionally annotated on Moritella sp. PE36‟s plasmid ...................................................................... 118 Table 3.8: List of resistance genes found in the genome of Moritella sp. PE36 ................................................................................. 119 vii List of Graphs Graph 1.1: Difference in the number of tRNAs in piezophile- mesophile pairs, grouped by amino acid type....................... 34 Graph 2.1: Plot of the changes in volume of the buried amino acids, grouped by protein ................................................................. 75 Graph 2.2: Plot of the changes in volume of the buried amino acids, grouped by piezophile-mesophile pair .................................. 76 Graph 2.3: Plot of the difference in the change in volume of the buried amino acids ................................................................. 77 Graph 2.4: Plot of the average change in volume of the buried amino acids upon protein folding ..................................................... 78 Graph 2.5: Plot of the difference in the change in volume of the buried amino acids for the two most piezophilic organisms, Colwellia sp. MT41 and Shewanella frigidimarina ......................................................................... 79 Graph 3.1: Histogram showing the usage of amino acids in the Moritella sp. PE36 genome and the prevalence of tRNA genes for those amino acids ................................................... 121 Graph 3.2: Distribution of COGs in Moritella sp. PE36 as a percentage of the total number of proteins assigned to at least one COG category ......................................................... 122 Graph 3.3: Histogram comparing the COG category abundances in Moritella sp. PE36 and Shewanella frigidimarina .............. 123 Graph 3.4: Distribution of KEGG categories in Moritella sp. PE36 as a percentage of the total number of proteins assigned to at least one KEGG ..................................................................... 124 Graph 3.5: Histogram comparing the KEGG category abundances in Moritella sp. PE36 and Shewanella frigidimarina .............. 125 viii List of Figures Figure 1.1: Ribbon diagram of the region of the 30S ribosomal subunit surrounding helix 10 ................................................ 35 Figure 1.2: Diagram showing the closeness of helix 10 and ribosomal protein S20 ............................................................................. 36 Figure 1.3: Surface rendering of the region of the 30S ribosomal subunit surrounding helix 10 ................................................ 37 Figure 1.4: Sequence alignment of 23S ribosomal RNA sequences showing insertions #1 and #2 ................................................ 38 Figure 1.5: Sequence alignment of 23S ribosomal RNA sequences showing insertion #3 .............................................................. 39 Figure 1.6: Sequence alignment of 23S ribosomal RNA sequences showing insertion #4 .............................................................. 39 Figure 1.7: Placement of insertions relative to the 5' half of the reference Escherichia coli 23S ribosomal RNA .................... 40 Figure 1.8: Close view of insertions relative to the Escherichia coli 23S ribosomal RNA ............................................................... 41 Figure 1.9: Predicted structures of helix 25 in Escherichia coli, Shewanella benthica KT99, and Photobacterium profundum SS9 ...................................................................... 42 Figure 1.10: Ribbon diagram of the region of the 50S ribosomal subunit surrounding helix 25 ................................................ 43 Figure 1.11: Surface rendering of the region of the 50S ribosomal subunit surrounding helix 25 ................................................ 44 Figure 1.12: Predicted structures of helices 27-30 in Escherichia coli and helices 27-30 and Insertion #2 in Shewanella benthica KT99 ......................................................................................
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