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UC San Diego UC San Diego Electronic Theses and Dissertations UC San Diego UC San Diego Electronic Theses and Dissertations Title Common evolutionary pathway for the appearance of the Ca²⁺ : Cation Antiporter (CaCA) family and several other transporter superfamilies Permalink https://escholarship.org/uc/item/5c89x28r Author Zhang, Chenchen Publication Date 2012 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Common Evolutionary Pathway for the Appearance of the Ca2+:Cation Antiporter (CaCA) Family and Several Other Transporter Superfamilies A Thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Biology by Chenchen Zhang Committee in charge: Professor Milton H. Saier, Jr., Chair Professor Lin Chao Professor Charles Elkan 2012 The Thesis of Chenchen Zhang is approved and is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2012 iii TABLE OF CONTENTS Signature Page ................................................................................................................. iii Table of Contents ............................................................................................................. iv List of Tables ................................................................................................................... vi List of Figures ................................................................................................................. vii Abstract ............................................................................................................................ xi Introduction ........................................................................................................................ 1 Methods .............................................................................................................................. 4 Chapter 1 1.1: Phylogenetic Analysis of CaCA Family Homologues ................................... 6 1.2: Phylogenetic Analysis of MPE family Homologues .................................... 12 Chapter 2: 2.1: Orthology Analysis of MPE Family Homologues ......................................... 16 2.2: Orthology Analysis of MPE Family Homologues ......................................... 20 Chapter 3: 3.1: Topological Analyses of CaCA Family Homologues ................................ 24 3.2: Topological Analyses of MPE Family Homologues .................................. 27 Chapter 4: iv 4.1: Establishment of Internal Repeats in CaCA Family Proteins ........................... 30 4.2: Internal Repeats in MPE Family Proteins ........................................................ 33 Chapter 5: Establish Homology Between Superfamilies ................................................. 34 Discussion ........................................................................................................................ 41 Appendix .......................................................................................................................... 47 References ...................................................................................................................... 128 v LIST OF TABLES Table 1. CaCA Family Homologues ................................................................................. 47 Table 2. MPE Family Homologues .................................................................................. 56 Table 3. Paralogues in Cluster 1 (CaCA) .......................................................................... 67 Table 4. Paralogues in Cluster 2 (CaCA) ......................................................................... 68 Table 5. Paralogues in Cluster 3 (CaCA) .......................................................................... 69 Table 6. Paralogues in Cluster 4 (CaCA) .......................................................................... 69 Table 7. Paralogues in Cluster 5 (CaCA) .......................................................................... 71 Table 8. Paralogues in Cluster 6 (CaCA) .......................................................................... 75 Table 9. Paralogues in Cluster 1 (MPE). ......................................................................... 75 Table 10. Paralogues in Cluster 2 (MPE). ....................................................................... 80 Table 11. Paralogues in Cluster 3 (MPE). ....................................................................... 81 Table 12. Paralogues in Cluster 4 (MPE). ....................................................................... 83 Table 13. Paralogues in Cluster 5 (MPE). ....................................................................... 87 Table 14. Paralogues in Cluster 7 (MPE). ....................................................................... 89 Table 15. Obvious HGT (CaCA) ...................................................................................... 90 Table 16. Paralogues In the CaCA Family ...................................................................... 90 vi Table 17. Paralogues In the MPE Family ........................................................... 90 Table 18. Obvious HGT (MPE) ........................................................................................ 90 Table 19. Characteristic of Phylogenetic Clusters from the CaCA Family .................... 91 Table 20. Characteristic of Phylogenetic Clusters from the MPE Family ...................... 91 Table 21.Comparsion Scores Between Superfamilies. .................................................... 91 Table 22.Comparsion Scores Between Potential Repeat of TMSs (MPE). ..................... 92 vii LIST OF FIGURES Figure 1. Protein Tree for all CaCA Family Members .................................................... 93 Figure 2. Protein Tree for Cluster 1 Proteins (CaCA) ...................................................... 94 Figure 3. Protein Tree for Cluster 2 Proteins (CaCA) ...................................................... 95 Figure 4. Protein Tree for Cluster 3 Proteins (CaCA) ..................................................... 96 Figure 5. Protein Tree for Cluster 4 Proteins (CaCA) ...................................................... 97 Figure 6. Protein Tree for Cluster 5 Proteins (CaCA) ...................................................... 98 Figure 7. Protein Tree for Cluster 6 Proteins (CaCA) ...................................................... 99 Figure 8. Protein Tree for all MPE Family Members ..................................................... 100 Figure 9. Protein Tree for Cluster 1 Proteins (MPE) ...................................................... 101 Figure 10. Protein Tree for Cluster 2 Proteins (MPE) .................................................... 102 Figure 11. Protein Tree for Cluster 3 Proteins (MPE) .................................................... 103 Figure 12. Protein Tree for Cluster 4 Proteins (MPE) .................................................... 104 Figure 13. Protein Tree for Cluster 5 Proteins (MPE) .................................................... 105 Figure 14. Protein Tree for Cluster 7 Proteins (MPE) .................................................... 106 Figure 15. 16S rRNA Tree (CaCA) ................................................................................ 107 Figure 16. 16S rRNA Tree (MPE) .................................................................................. 108 Figure 17. AveHAS Plots for all CaCA Family Members ............................................. 109 Figure 18. AveHAS Plots for Cluster 1 Proteins (CaCA) .............................................. 109 viii Figure 19. AveHAS Plot for Cluster 2 Proteins (CaCA) ................................................ 109 Figure 20. AveHAS Plot for Cluster 3 Proteins (CaCA) ................................................ 110 Figure 21. AveHAS Plot for Cluster 4 Proteins (CaCA) ................................................ 110 Figure 22. AveHAS Plots for Cluster 5 Proteins (CaCA) .............................................. 110 Figure 23. AveHAS Plots for Cluster 6 Proteins (CaCA) .............................................. 111 Figure 24. AveHAS Plots for all MPE Family Members ............................................... 111 Figure 25. AveHAS Plots for Cluster 1 Proteins (MPE) ................................................ 112 Figure 26. AveHAS Plots for Cluster 2 Proteins (MPE) ................................................ 112 Figure 27. AveHAS Plots for Cluster 3 Proteins (MPE) ................................................ 113 Figure 28. AveHAS Plots for Cluster 4 Proteins (MPE) ................................................ 113 Figure 29. AveHAS Plots for Cluster 5 Proteins (MPE) ................................................ 114 Figure 30. AveHAS Plots for Cluster 6 Proteins (MPE) ................................................ 114 Figure 31. AveHAS Plots for Cluster 7 Proteins (MPE) ................................................ 115 Figure 32. Alignment of TMSs 2-6 vs TMSs 7-11 (CaCA) ........................................... 115 Figure 33. Alignment of Mla1 and Dac1(CaCA) ........................................................... 116 Figure 34. Alignment of TMSs 1-5 vs TMSs 7-11 (CaCA) ........................................... 117 Figure 35. Alignment of TMSs 1-5 vs TMSs 6-10 (CaCA) ............................................117 Figure 36. Alignment of TMSs 1-2 vs TMSs 3-4
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