Site-Specific Recombination and Transposition of DNA

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Chapter 11 

Site-Specific Specific Recombination 

and 

Transposition of DNA 

生物学基地班 

200431060005 李湘



Site-Specific Specific Recombination and 

Transposition of DNA 

• Conservation Site-Specific Specific Recombination 

• Biological Roles of Site-Specific Specific Recombination 

• Transposition 

• Examples of Transposable Elements and Their 

Regulation 

• V(D)J Recombination



CSSR 

Transposition



Conservation Site-Specific Specific Recombination Occurs at 

specific DNA Sequences in the Target DNA 

Recombination: A segment carries specific short sequence 

and will be moved



Three types of the DNA rearrangements 

Insertion , Deletion and Inversion

Structures involved inCSSR 


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Site-Specific 

Specific Recombinases Cleave and Rejoin DNA 

Serine family and Tyrosine family



Serine Recombinases Introduce DSB in 

DNA and Promote Recombination



Tyrosine Recombinases Break and Rejoin 

one Pair of DNA Strand at a Time



Structure of tytosine recombinases bound to DNA 

reveal the mechanism of DNA reveal the 

mechanism of DNA exchange 

Cre recombinase is a beautiful Example 

Cre is an enzyme encoded by phage P1,which 

functions to circularize the linear phage genome 

during infection. 

The combination sites on the DNA ,where Cre 

acts,are called lox sites. 

Only Cre protein and the los sites are needed for 

complete recombination

The subunits 

colored in green 

are in the active 

conformation 





Bilogical roles of site-specific 

specific 

recombination 

• many phage insert their DNA into the host 

chromosome during infection 

• Alter fene expression 

• used to help maintain the structural integrity of 

circular DNA molecules during cycles 

recombination and cell division

Recombination sites 

involved in λ 

integration and 

excision showing the 

important sequence 

elements 





DNA inversion by the Hin 

reconbinase of salmonella



Hin recombination requires a DNA 

Enhancer 

Complexes formed 

during Hin-catalyzed 

recombination



Circular DNA molecules can form 

multimers



Regulation of chromosome 

segregation by Ftsk



Transposition



Transposition of a mobile genetic element to a 

new site in the host DNA



Three Principal classes of 

Transposable Elements 

1.DNA transposons 

2. Viral-like 

like retrotransposons including the 

retrovirus, which are also called LTR 

retrotransposons 

3. Poly-A retrotransposons, , also called nonviral 

retrotransposons



Genetic organization of the three 

classes of transposable elements

Occurrence and distribution 





Transposons exist both Autonomous 

and Nonautonomous Elements 

• Autonomous transposons: carry a pair of 

terminal inverted repeats and a transposase gene; 

function independently 

• Nonautonomous transposons: carry only the 

terminal inverted repeats; need the transposase 

encoded by autonomous transposons to enable 

transposition



CUT and PASTE



Three mechanisms for cleaving 

the nontransferred srand



Replicative Transposition



DNA Transposases and Retroviral Integrases 

• They carry a catalytic domain that has a 

common three-dimensional 

shap. 

• The domain contains three evolutionarily 

invariant acidic aa.: two aspartates (D) and a 

glutamate (E) 

• The aa’s formed the active site and coordinate 

divalent metal ions (Mg 2+ ,Mn 

2+ )



Similarities of catalytic domains of transposases and integrases



The mechanism of poly-A Retrotransposons



Examples of transposable elements and their 

regulation 

• Two types of regulation appear as recurring 

themes: 

1. Trnasposons control the number of their copies 

present in a given cell. 

2. Trnasposons control target site choice.



IS4-family 

transposons are compact elements with 

multiple mechanisms for copy number control 

• Tn10 transposes via the cut-and paste mechanism, 

using the DNA hairpin strategy to cleave the 

nontransfered strands 

• Tn10 limits its copy number in any given cell by 

strategies that restrict its transposition frequency. One 

mechanism is the use of an antisense RNA to control 

the expression of the transposase gene 

• By this mechanism, cells that carry more copes of Tn10 

will transcribe more of the antisense RNA, which in 

turn will limit expression of the transposase gene. The 

transposition frequencywill, , therefore, be very low in 

such a strain



Genetic organization of bacterial transposon Tn10



Antisense 

Regulation 

of Tn10 

Expression



Tn10 Transposition is coupled to cellular 

DNA replication 

• Bacteria methylate their DNA at GATC sites and 

GATC sites, this sites are hemimethylated for a few 

minutes. 

• It is during the brief period—when the Tn10 DNA is 

hemimethylated—that that transposition is more likely to 

occur 

• Both RNA polymerase and transposase bind more 

tightly to the hemimethylated sequences than to their 

fully methylated versions. As a result, when the DNA is 

hemimethylated, , the transposase gene is most 

efficiently expressed, and the transposaseprotein binds 

most efficiently to the DNA



Transposition of 

Tn10 after 

passage of a 

Replication fork



Overview of the early steps of Mu 

transposition



The interplay between 

MuA and MuB 

leads to the 

development of an 

immune target DNA



V(D)J recombination 

The principal mechanism cells use to 

generate antibodies and T cell receptors 

with such diversity relies on a specialized 

set of DNA rearrangement reactions



Structure of an antibody molecule



Overview of 

the process of 

V(D)J 

Recombination



The early events in V(D)J recombination occur by 

a mechanism similar to transposon excision 

• Recombination sequences, called recombination 

signal sequences, flank the gene segments that 

are assembled by V(D)J recombination 

• Recombination always occurs between a pair of 

recombination signal sequences which are 

organized as inverted repeats flanking the DNA 

segments that are destined to be joined



Recombination signal sequence 

recognized in V(D)J recombination



The V(D)J 

recombination 

pathway : 

Cleavages occur 

by a mechanism 

similar to 

transposon 

excision

Site-Specific Recombination and Transposition of DNA

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