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Transposone And Retrotransposone


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  • 1.  
  • 2.
    • Transposone
    Presented by: Salar Bakhtiyari
  • 3. They are discrete sequence in the genome that are mobile they are able to transport themselves to other location. Other names:
    • Jumping genes
    • Selfish DNAs
    • Molecular parasites
    • Controlling elements
    TEs are present in the genome all species of three domains Transposable Elements
  • 4. What do we want to know about mobile genetics elements?
    • 1 – The history of mobile genetic elements
    • 2 – The classification of TEs
    • 3 – The structure of TEs
    • 4 – The mechanism of transposition
    • 5 – The effects of TEs on gene and genome
    • 6 – The use of TEs as molecular tools
  • 5. Why study mobile genetic elements?
    • They are the major forces driving evolution
    • They can cause genome rearrangement (mutation , deletion and insertion )
    • They have wide range of application potentials
  • 6. The discovery of mobile genetic elements
    • Transposable elements
    • Phage
    • Plasmid DNA
  • 7. The discovery of transposable elements
    • Barbara Mc Clintock discovered TEs in maize (1983)
    • Her work on chromosome breakage began by investigating genetic instability (1983)
    • Observing variegated patterns of pigmentation in maize plant and kernels
    • New kinds of genetic instability
    • She spent the next tree decades for this genetic elements
    • Controlling elements (1956)
  • 8. Barbara Mc Clintock 1902  1980 ( noble in 1984)
  • 9. Plasmid , phage
    • Cell to cell conjugation
    • Bactriophage mediated transduction
    • Bill Hayes ( 1952 )
    • Ellin Wollman and Francois Jancob , 1961
    • Alan Campbell
  • 10. Classification of transposable elements
    • DNA transposons
    • Retrotransposons
  • 11. Autonomous and non autonomous elements
    • Both class are subdivided into distinct superfamilies and families
    • Structure feature , internal organization , the size of target site duplication , sequence similarities at the DNA and protein levels
    • Autonomous : they have the ability to excise and transpose
    • non autonomous elements
    • They don’t transpose
    • They become unstable only when an autonomous member of same family is present elsewhere in the genome
    • They are derived from autonomous elements
    • A family consists of single type of autonomous element accompanied by many varieties of non autonomous elements
  • 12.  
  • 13. DNA based elements
    • Insertion sequence (IS)
    • The simplest (smallest) transposons are called IS
    • The IS elements are normal constituents of bacterial chromosome and plasmids
    • Spontaneous mutation of the lac and gal operons
    • They are autonomous units ,each of which codes only transposase
  • 14. Structure of IS
  • 15. Composite transposone
    • One class of large transposons are called Composite transposons
    • They carring the druge marker is flanked on either side by arms that consist of IS elements
    IS modules - identical (both functional: Tn9; Tn903) or closely related (differ in functional ability: Tn10; Tn5) 1. A functional IS module can transpose either itself or the entire transposon
  • 16. Mechanism of transposition
    • The stugger between the cuts determines the length of the direct repeats.
    • The target repeat is characteristic of each transposon; reflects the geometry of the cutting enzyme
    Direct repeats are generated by introduction of staggered cuts whose protruding ends are linked to the transposon .
  • 17. Mechanism of transposition 1- Replicative transpositon
    • Replicative :
    • Transposon is duplicated ; a copy of the original element is made at a recipient site(TnA); donor keeps original copy
    • Transposition- an increase in the number of Tn copies
    • ENZs: transposase (acts on the ends of original Tn) and resolvase (acts on the duplicated copies)
  • 18. Mechanism of transposition 2 - Nonreplicative
    • Nonreplicative :
    • Transposon moves from one site to another and is conserved; breaks in donor repaired
    • b) IS and Tn10 and Tn5 use this mechanism; no Tn copy increase
    • c) ENZs: only transposase
  • 19.
    • The first stages of Both replicative and non-replicative transpositio are semilar
    • IS elements, prokaryotic eukaryotic transposons, and bacteriophage Mu .
    Donor cut 1. Synapsis stage - two ends of transposon are brought together 3. . Nicked ends joine crosswise;covalent connection between the transposon the target 2. Transposon nicked at both ends; target nicked at both strands
  • 20. cuts in trans transfers in trans 22 bp Mu integrates by nonreplicative transposition; during lytic cycle- number of copies amplified by replicative transposition - MuA binds to ends as tetramer forming a synapsis . - MuA subunits act in trans to cut next to R1 and L1 (coordinately; two active sites to manipulate DNA). - MuA acts in trans to cut the target site DNA and mediate in trans strand transfer
  • 21. The chemistry of Donor and target cut The 3’-ends ends groups released from flanking DNA by donor cut reaction They are nuclophile that attack phosphodiester bonds in target DNA
    • Cutting of both ends
    3 ‘ OH 3 ‘ OH 3 ‘ OH 3 ‘ OH
    • Cutting of 3 ‘ end only
  • 22.
    • The product of these reaction is strand transfer complex
    • In strand transfer complex transposon is connected to the target site through one strand at each end
    • Next step differs and determines the type of transposition:
    • Strand transfer complex can be target for replication (replicative transposition) or for repair (nonreplicative transposition; breakage & reunion )
    transposon target Strand transfer complex
  • 23. Molecular mechanism of transposition (I) Replicative transposition Replicative transposition proceeds through a cointegrate . Transposition may fuse a donor and recipient replicon into a cointegrate. Resolution releases two replicons-each has copy of the transposon
  • 24. Replicative transposition Ligation to target ends 3. 3’-ends prime replication The crossover structure contains a single stranded region at each of the staggered ends= pseudoreplication forks that provide template for DNA synthesis Donor and target cut cointegrate .
  • 25. Non-replicative Replicative additional nicking common structure Breakage & reunion
  • 26. Retrotransposon ( retroposons )
    • Use of an RNA Intermediate
      • element is transcribed
      • reverse transcriptase produces a double-stranded DNA copy for insertion at another site
      • they as other elements generating short direct repeat
  • 27. Types of Retrotransposons
    • 1 – viral superfamily (autonomousretrotransposon)
          • retrovirus
          • LTR- retrotransposon
          • LINES
    • 2 – nonviral superfamily
    • (non autonomous retransposons)
    • SINES
    non LTR- retrotransposon
  • 28. retrovirus RNA reverstranscriptase Liner DNA Integration provirus Transcription RNA
  • 29. LTR - retrotrasposon pol Reverse transcriptase (RT) Integrase (IN) Ribonuclease H (RH) gag env ?
  • 30. mechanism of transposition Integrase acts on both the retrotransposon line DNA and target DNA
    • The integrase bring the ends
    • of the linear DNA together
    • Generate 2 base recessed 3’ -ends
    • and staggered end in target DNA
    3’-ends 5’-ends
  • 31. Non – LTR retrovirus
    • LINES = long interspersed elements
    • SINES = short interspersed elements
    • don’t terminate in the LTRs
    • they are significant part of relatively short sequence of mammalian genomes .
  • 32. Effect of transposabli elements on gene and genome
    • TEs cause a varity of change in the genome of their hosts
    • this ability to induce mutation depend on their of capability of transposing
    • some arrangement can be beneficial they can advantageous for adaptation to new environment
    • play important role in evolution .
    • they have the ability to rearrange genomic information in several ways
    • 1 – Modification of gene expression
    • 2 – Alternation gene sequence
    • 3 – Chromosomal structural changes
  • 33. Modification of gene expression
    • insertion of a TE within or adjacent to a gene
    • the element blocks or alters the pattern of transcription .
    • i nsertion of Fot1 in a intron of niad ( F . oxysporum )
    • different mutant transcripts all were shorter
    • They result from:
    • - presence of termination signal
    • - presence of an alternative promotor
  • 34. Alternation gene sequence
    • cut and pate mechanism often produce variation when they excise .
    • the excision process may result in addition of a few base pair ( footprint ) at donor site .
    • these footprint cause diversification of nucleotide sequence and new functional alleles
    • Example : Fot1 and Impala generally leave 4 bp – ( 108 ) or 5 – ( 63 ) foot prints
    • excision of the Asco - 1 transposon in A .immersus
    • Deletions of a a few to up to 1713 nucleotide in b2 gene
    • larger deletion led to variety of phenotypes in spore coloration
  • 35. Chromosomal structural changes
    • TEs can produce a series of genome rearrangment through ectopic recombination
    • deletion , duplication , inversion and translucation mediate by TEs ( Drosophila , Yeast , human )
    • karyoptypic variation in natural isolate in fungai
    • high level of chromosome – length polymorphism ( Magnoporthe grisea , F. oxysporum )
    • translocation tox1 of Cochliobolus heterostrophus
    • appearance of new virulence alleles in M . grisea
  • 36. Use as strain specific diagnostic tools
    • TEs are often restricted to specific strains
    • identify specific pathogen in plant pathology
    • Fot1 ( F. oxysporum f sp. albedians ) provide PCR targets
    • a sensitive detection thechnique to prevent the introduction of pathogenic form
    • - race of F. oxysporum responsible of carnation wilt
    • - date palm pathogen
    Use of TEs as molecular tools
  • 37. Use of TEs as molecular tools
    • MGR 586 ( Magneporthe grisea )
    • oryza : 30 – 50 wheat and other ( 1 – 2 )
    • they have used to distinguish genetically divergent population
    • fingerprinting of isolates pathogenic to oil palm tree. ( F. oxysporum , palm )
    Tools for the analysis of population structure
  • 38. Gene tagging with transposable elements
    • arise mutant phenotype
    • Disrupt target gene
    Use of TEs as molecular tools
    • jumping into coding region
    Target gene can easily determined by PCR methods
  • 39. Thanks for attention