Evolution of Purine Metabolism Open Access
Keebaugh, Alaine Case (2009)
Abstract
Abstract Evolution of Purine Metabolism Alaine C. Keebaugh
Gene duplication has long been accepted as playing a major role in evolution. Recently, it has been hypothesized that gene loss might also play an important role in evolution. While this hypothesis has not systematically been tested, it is becoming clear that gene loss has played a role in recent human evolution. One pathway that has been repeatedly modified by both gene duplication and gene loss is purine metabolism. The goal of this dissertation is to use purine metabolism as a model system to explore the biological significance of gene duplication and gene loss with respect to evolution and disease. Through characterization of the purine catabolic pathway in mammals we identified a novel genetic difference between placental mammals and marsupials/monotremes. We hypothesize that this genetic difference distinguishes purine catabolism between these lineages. By performing a more detailed characterization of the purine catabolic pathway in vertebrates we discovered an unexpected fate following loss of UOX in the bird/reptile lineage. The patterns of gene retention and gene loss allowed us to hypothesize a new model of gene loss by which a single gene loss event can have long-term, indirect consequences on the evolutionary potential of many genes in the genome. Mutations in HPRT1, a salvage enzyme of purine metabolism, cause Lesch-Nyhan disease in humans; however, the clinical phenotype has not been successfully recapitulated in a mouse model. In this work, we reconstruct the evolutionary history of the HPRT-gene family and hypothesize that the lack of a disease phenotype in mouse is due to the absence of an HPRT1 paralog, PRTFDC1, in this species. To this end, we have developed a more humanized mouse model carrying the human PRTFDC1 locus. In this dissertation we provide empirical evidence to support the theory of adaptive gene loss and highlight the importance of understanding the history of gene duplication and gene loss when modeling human disease.
Table of Contents
Table of Contents 1 INTRODUCTION 1 1.1 Gene duplication 4 1.1.1 Mechanisms of gene duplication. 4 1.1.2 Physical properties of gene duplication. 6 1.1.3 Classical models of adaptive gene duplication. 8 1.2 Gene Loss 12 1.2.1 Mechanisms of gene loss. 12 1.2.2 Classic models of adaptive gene loss. 14 1.2.3 Adaptive gene loss. 16 1.3 Purine Metabolism. 24 1.3.1 Gene duplication. 24 1.3.2 Gene Loss. 28 1.3.3 Human disease. 29 1.3.4 Modeling disease in mouse. 32 1.3.5 Objectives of this dissertation. 34 2 THE GENOMES OF THE SOUTH AMERICAN OPOSSUM (MONODELPHIS DOMESTICA) AND PLATYPUS (ORNITHORHYNCHUS ANATINUS) ENCODE A MORE COMPLETE PURINE CATABOLIC PATHWAY THAN PLACENTAL MAMMALS 35 2.1 INTRODUCTION 36 2.2 MATERIALS AND METHODS 41 2.2.1 Identification of orthologs encoding the purine catabolic pathway 41 2.2.2 Classification of orthologs 42 2.2.3 Sequence Evolution 42 2.3 RESULTS 43 2.3.1 The opossum and platypus genomes encode a more complete set of genes for purine catabolism than do placental mammals 43 2.3.2 Loss of ALLN is specific to placental mammals 47 2.4 Discussion 47 3 EVOLUTION OF THE PURINE CATABOLIC PATHWAY: AN EXPANDED VIEW OF THE EVOLUTIONARY SIGNIFICANCE OF GENE LOSS 51 3.1 Introduction 52 3.2 MATERIALS AND METHODS 57 3.2.1 Identification of orthologs encoding the purine catabolic pathway 57 3.2.2 Classification of orthologs 58 3.2.3 Sequence Evolution 58 3.2.4 Dating 60 3.2.5 RNA isolation and Sequencing 60 3.3 Results 62 3.3.1 Predicted gene content of the purine catabolic pathway in hominoids, birds and reptiles 62 3.3.2 Timing of the gene inactivation events in the hominoid lineage 69 3.3.3 Molecular characterization of the bird and reptile UOX loci 70 3.4 Discussion 72 4 GENE DUPLICATION AND INACTIVATION IN THE HPRT-GENE FAMILY 78 4.1 INTRODUCTION 79 4.2 METHODS 82 4.2.1 Targeted mapping and sequencing 82 4.2.2 Database searches for additional HPRT-gene family members 83 4.2.3 Genomic sequence annotation and analysis 83 4.2.4 Protein domain analysis 84 2.2.5 Phylogenetic analysis 85 4.2.6 Sequencing the mouse PRTFDC1 exons 86 4.2.7 Molecular dating of the mouse PRTFDC1 inactivation event 87 4.3 RESULTS 88 4.3.1 Compilation of the HPRT-gene family data set 88 4.3.2 Phylogeny of the HPRT-gene family 89 4.3.3 Genomic structure of the HPRT-gene family 92 4.3.4 Predicted enzymatic activity 96 4.3.5 Evolutionary rates in the HPRT-gene family 97 4.3.6 Inactivation of PRTFDC1 in mouse 99 4.4 DISCUSSION 101 5 INITIAL CHARACTERIZATION OF A NOVEL MOUSE MODEL FOR LESCH-NYHAN DISEASE 107 5.1 Introduction 108 5.2 Methods 113 5.2.1 Identification and characterization of a human PRTFDC1 BAC clone. 113 5.2.2 Generation of the TgPrtfdc1+/0 transgenic mouse. 113 5.2.3 Breeding & genotyping strategy. 114 5.2.4 Gross phenotyping. 115 5.2.5 Tissue collection. 115 5.2.6 Protein analysis. 116 5.2.7 Expression studies. 116 5.2.8 Statistical analysis. 118 5.3 Results 118 5.3.1 Relative Transcript Abundance in Human. 118 5.3.2 Generation of the PRTFDC1 transgenic mouse. 119 5.3.3 Gross phenotyping. 120 5.3.4 Protein analysis. 121 5.3.5 Relative Transcript Abundance in Transgenic Mice. 123 5.4 Discussion 125 6 DISCUSSION 130 7 REFERENCES 137 8 APPENDIX 156 8.1 Supplementary Table 1 156 8.2 Supplementary Table 2 158 8.3 Supplementary Table 3 160 8.4 Supplementary Figure 4 161
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