Universidad Autónoma de Madrid Facultad de Ciencias Departamento de Biología Molecular Analysis of the interaction between chromosomal replication and transposition mediated by sliding clamps Doctoral Thesis Héctor Díaz Maldonado Thesis supervisor: Dr. Francisco J. López de Saro Madrid, 2016 Doctoral thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy . The research here presented was carried out at the Centro de Astrobiología (Instituto Nacional de Técnica Aeroespacial - Consejo Superior de Investigaciones Científicas) under the supervision of Dr. Francisco J. López de Saro and was funded by the Subdirección General de Proyectos de Investigación of the Spanish Ministry for Economy and Competitiveness Grants No. CGL2010-17384. Héctor Díaz Maldonado was supported by a FPI fellowship from the Spanish Ministry for Economy and Competitiveness. INDEX Index of figures iv Index of tables vi Abbreviations vii Abstract ix Resumen xi 1. INTRODUCTION 1 1.1. The genetic transposable elements 3 1.2. Transposase diversity and biochemistry 3 1.2.1. The DDE transposase superfamily 5 1.2.2. The HUH transposase superfamily 6 1.3. IS impact in genomes: IS expansion and genome evolution 7 1.4. IS impact in genomes: horizontal gene transfer 9 1.5. Transposition regulation 12 1.6. Tn5: an auto-regulated transposition paradigm 14 1.6.1 Tn5 structure and transposition mechanism 14 1.6.2 Tn5 transposase biochemistry and DNA binding 15 1.7. With a little help from the host 16 1.8. The replication fork: structure and organization 17 1.9. Sliding clamps 19 1.9.1 Sliding clamps are conserved and universal replication factors 19 1.9.2. Sliding clamps coordinate diverse DNA biochemical mechanisms 21 2. OBJECTIVES 23 3. MATERIALS AND METHODS 27 3.1. Oligonucleotides and peptides 29 3.2. Microbiological techniques 32 3.3. Recombinant DNA techniques 33 3.3.1. Genomic and plasmids DNA extraction 33 3.3.2. RNA isolation 33 3.3.3. Polymerase chain reaction (PCR) 34 3.3.4. DNA cloning 34 3.3.5. Site-directed mutagenesis 35 3.4. In vivo transposition assays 35 3.5. Design and validation of an oligonucleotide-based IS-related genes microarray 38 i 3.5.1. Identification of transposases and related genes 38 3.5.2. Design and construction of the microarray 39 3.5.3. Sample labeling 39 3.5.4. Microarray hybridization and scanning 40 3.5.5. Microarray validation 41 3.5.5.1. Quantitative PCR 41 3.5.5.2. Inverse PCR 42 3.6 Protein techniques 42 3.7 Protein purifications 43 3.7.1 Purification of sliding clamps and related enzymes 43 3.7.1.1 E. coli β 43 3.7.1.2 Acidiphilium.sp PM β 44 3.7.1.3 Leptospirillum ferooxidans β 45 3.7.1.4 Methanosarcina barkeri PCNA 45 3.7.1.5 Human PCNA 45 3.7.1.6 E. coli γ-complex 45 3.7.2 Purification of fusion proteins 48 3.7.2.1 GST-Pol IVLF 48 3.7.2.2 GST- LINE-1Z, PIP1 and PIP2 mutants 48 3.7.3 Purification of transposases 48 3.7.3.1 Acidiphilum sp. IS1634 transposases 48 3.7.3.2 Tn5 transposases 49 3.8 Protein interaction techniques 50 3.8.1 Protein-protein pull-down assays 50 3.8.1.1 Acidiphilium IS1634 Tnp pull-down assay 50 3.8.1.2 Tn5 Tnp pull-down assay 50 3.8.1.3 GST- LINE-1Z pull-down assay 50 3.8.2 Peptide-protein pull-down assays 51 3.8.3 Electrophoretic mobility shift assay 51 3.8.4 Crosslinking assay 52 3.8.5 Fast protein liquid chromatography (FPLC) 52 3.9 Protein-DNA interaction technique 52 3.10 Bioinformatic survey 52 3.10.1 Genomic Data Set and Computational Pipeline 52 ii 3.10.2 IS Detection and Classification 53 3.10.3 Test on the orientation distribution of IS elements in chromosomes 55 3.10.4 Test on the orientation distribution of IS elements at phylum level 55 3.10.5 Detection of β-binding motifs in Escherichia coli transposases 56 4. RESULTS 57 4.1. IS orientation in genomes and its interaction with the replication machinery 59 4.1.1 Orientation biases of IS families in bacterial chromosomes 59 4.1.2 IS orientation biases are not generated by post-insertion selection 64 4.1.3 Interaction of transposases with the β Sliding Clamp 65 4.2 Tn5: Tnp interaction with β and characterization of novel hyperactive mutants 75 4.2.1 Tnp binds to the β sliding clamp 78 4.2.2 Tnp interaction with β promotes DNA binding 80 4.2.3 Characterization of two novel hyperactive Tnp mutants 82 4.3 Transposase interaction with sliding clamp: effects on IS proliferation and transposition rate 84 4.3.1 The transposase and related elements microarray 84 4.3.2 Detection of active IS in a long-term culture of Acidiphilium sp. PM 85 4.3.3 An active transposase of the IS1634 family contains a β-binding motif 88 4.3.4 Transposases can bind β sliding clamps from diverse organisms 91 4.3.5 Transposases can bind bidirectionally to β and to the Archaeal PCNA 98 4.3.6 A stronger β-binding motif increases transposition in vivo 99 4.4. PCNA-binding motif in the human retrotransposon LINE-1 102 5. DISCUSSION 109 5.1 The source of IS orientation biases in chromosomes 111 5.2 Sliding clamp as a general link between transposition and replication 112 5.3 Replisome composition could explain the IS orientation biases in Firmicutes 115 5.4 Transposase interaction with β. Implications in transposition self-regulation 117 5.5 IS proliferation and HGT. Role of transposase interaction with sliding clamps 120 5.6 Transposase affinity to β sliding clamp influences transposition rate 122 5.7 Final remarks 123 6. CONCLUSIONS 125 7. REFERENCES 131 8. APPENDICES 147 iii Index of figures Figure 1.1. Mechanisms of DDE-transposas. 6 Figure 1.2. Hypothesized relationship between transposable element activity, host regulatory 9 mechanisms and genomic stability. Figure 1.3. Venn diagram representing the pan-genome of three hypothetical strains. 10 Figure 1.4. Transposon Tn5 structure. 14 Figure 1.5. Schematic representation of the replication fork. 19 Figure 1.6. The structure of sliding clamps is evolutionary conserved. 21 Figure 3.1. pSKT1 plasmid map. 37 Figure 3.2. Optimal hybridization conditions and specificity of the microarray. 40 Figure 3.3. E. coli γ-complex purification. 47 Figure 4.1. Graphic representation of IS orientation biases in bacteria 61 Figure 4.2. Graphic representation of IS orientation biases in bacteria (II) 61 Figure 4.3. Global gene orientation for 1,727 circular bacterial chromosomes 65 Figure 4.4. List of peptides used in the biochemical assays aligned at the β -binding motif. 67 Figure 4.5. E. coli β clamp and GST-PolIVLF purification. 69 Figure 4.6. Transposase-derived peptides interact with E. coli β sliding clamp. 70 Figure 4.7. Transposase-derived peptides compete with PolIVLF for binding E. coli β. 71 Figure 4.8. An archaeal transposase-derived peptide binds archaeal PCNA and E. coli β. 72 Figure 4.9. Two different binding motifs in transposases of IS200 family bind E. coli β clamp 73 with distinct strength. Figure 4.10. Different binding motifs located in transposases of IS66 family, bind E. coli β 74 clamp with distinct affinity. Figure 4.11. X-ray co-crystal structure of Tn5 synaptic complex. 76 Figure 4.12. TnpWt, TnpNΔ7 and Inh purifications. 77 Figure 4.13. Tnp interacts with β sliding clamp. 79 Figure 4.14. Tnp binds DNA in presence of β sliding clamp. 81 Figure 4.15. In vivo assay to study the transposition activity of different Tnp mutants. 83 Figure 4.16. Identification of IS changes in a 600-generation culture of Acidiphilium sp. 87 Figure 4.17. A member of the IS1634 family is active in Acidiphilium sp. PM. 89 Figure 4.18. Unrooted similarity tree of IS1634 transposases and alignment of C-terminal 90 region. Figure 4.19. IS1634 transposase (TnpWt) purification. 92 Figure 4.20. Acidiphilium sp. and Leptospirillum ferrooxidans β sliding clamps purification. 93 iv Figure 4.21. Interaction between Tnp and sliding clamps. 94 Figure 4.22. Chemical crosslinking of Acidiphilium TnpWt and Ecβ. 96 Figure 4.23. Binding of Acidithiobacillus IS1634 transposase to sliding clamps. 97 Figure 4.24. E. coli IS66 transposase also binds sliding clamps from diverse organisms. 98 Figure 4.25. Binding of transposases to Archaeal sliding clamp (PCNA). 99 Figure 4.26. β-binding motifs present in enzymes of E. coli and Acidiphilium sp. PM. 100 Figure 4.27. In vivo transposition assay to study the effect of different β binding motifs in 101 IS1634 transposition rate. Figure 4.28. Human LINE-1 structure and PCNA interaction protein domain (PIP box). 103 Figure 4.29. Human PCNA and GST-LINE 1Z purification. 104 Figure 4.30. Pull down assay of PCNA by LINE-1 derived peptides containing a putative PIP 106 box. Figure 4.31 Pull down assay of PCNA by GST-LINE-1Z. 107 Figure 4.32. FPLC assay. PCNA interacts with GST-LINE-1Z. 108 Figure 5.1. Structure of IS66 and diversity in sequence and location of β -binding motifs. 114 Figure 5.1 Structural and functional asymmetries contributing to biased orientation of ISs in 116 chromosomes. Figure 5.3. Detail of the crystal structure of Tn5 synaptic complex. 119 Figure I.4. Sequences of transposase regions containing the β motif.