Table of Contents

I. Introduction

1. A Moveable Feast: An Introduction to Mobile DNA

II. Conservative Site-Specific Recombination

2. An Overview of Tyrosine Site-specific Recombination: From an Flp Perspective

3. The Serine Recombinases

4. The lambda Integrase Site-specific Recombination Pathway

5. Cre Recombinase

6. The Integron: Adaptation On Demand

7. Xer Site-Specific Recombination: Promoting Vertical and Horizontal Transmission of Genetic Information

8. The Integration and Excision of CTnDOT

9. Site-specific DNA Inversion by Serine Recombinases

10. Serine Resolvases

11. Phage-encoded Serine Integrases and Other Large Serine Recombinases

12. Hairpin Telomere Resolvases

13. Biology of Three ICE Families: SXT/R391, ICEBs1, and ICESt1/ICESt3

III. Programmed Rearrangements

14. V(D)J Recombination: Mechanism, Errors, and Fidelity

15. Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination

16. Programmed Genome Rearrangements in Tetrahymena

17. Programmed Rearrangement in Ciliates: Paramecium

18. Programmed Genome Rearrangements in the Ciliate Oxytricha

19. DNA Recombination Strategies During Antigenic Variation in the African Trypanosome

20. Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite Plasmodium falciparum

21. Mobile DNA in the Pathogenic Neisseria

22. vls Antigenic Variation Systems of Lyme Disease Borrelia: Eluding Host Immunity through both Random, Segmental Gene Conversion and Framework Heterogeneity

23. Mating-type Gene Switching in Saccharomyces cerevisiae

24. A Unique DNA Recombination Mechanism of the Mating/Cell-type Switching of Fission Yeasts: a Review

IV. Dna-Only Transposons

25. Mechanisms of DNA Transposition

26. Everyman’s Guide to Bacterial Insertion Sequences

27. Copy-out-Paste-in Transposition of IS911: A Major Transposition Pathway

28. The IS200/IS605 Family and “Peel and Paste” Single-strand Transposition Mechanism

29. Transposons Tn10 and Tn5

30. Tn7

31. Transposable Phage Mu

32. The Tn3-family of Replicative Transposons

33. P Transposable Elements in Drosophila and other Eukaryotic Organisms

34. Mariner and the ITm Superfamily of Transposons

V. LTR Retrotransposons

35. hAT Transposable Elements

36. Mutator and MULE Transposons

37. Adeno-associated Virus as a Mammalian DNA Vector

38. Sleeping Beauty Transposition

39. piggyBac Transposon

40. Helitrons, the Eukaryotic Rolling-circle Transposable Elements

41. Ty1 LTR-retrotransposon of Budding Yeast, Saccharomyces cerevisiae

42. Ty3, a Position-specific Retrotransposon in Budding Yeast

43. The Long Terminal Repeat Retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe

44. Retroviral Integrase Structure and DNA Recombination Mechanism

45. Host Factors in Retroviral Integration and Selection of Integration Target Sites

46. Reverse Transcription of Retroviruses and LTR Retrotransposons

47. Mammalian Endogenous Retroviruses

48. Retroviral DNA Transposition: Themes and Variations

VI. Non-LTR Retrotransposons

49. Integration, Regulation, and Long-Term Stability of R2 Retrotransposons

50. Site-Specific non-LTR retrotransponsons

51. The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

52. Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

53. Diversity-generating Retroelements in Phage and Bacterial Genomes

54. An Unexplored Diversity of Reverse Transcriptases in Bacteria

55. Tyrosine Recombinase Retrotransposons and Transposons

Index

About the Author

Nancy L. Craig, is an Investigator with the Howard Hughes Medical Institute and a Professor in the Department of Molecular Biology & Genetics at the Johns Hopkins University School of Medicine. Dr. Craig is a member of the National Academy of Sciences and a Fellow of the American Association for the Advancement of Science, American Academy of Microbiology, and the American Academy of Arts and Sciences.

Reviews

"Mobile DNA III provides a one-stop-shop for anyone wanting to keep abreast of current understanding of the activity of these elements and the enzymes that they encode. It should will be an invaluable resource for some time to come." -David Finnegan, Institute of Cell Biology, University of Edinburgh, King's Buildings.