Chromosome

1.Separation 1 Separation and Transmission (eukaryotes) 2. Separation and Transmission (Prokaryotes) (P k t ) 3.Organization and Structure 3O i ti d St t 4.Recombination 4 Recombination and Transposition

CHAPTER 17
RECOMBINATION AND TRANSPOSITION AT THE MOLECULAR LEVEL

Introduction
Genetic recombination:
involves chromosomes breaking and rejoining to form new combinations j g

There are three main types

1. Homologous recombination 2. Site-specific recombination p 3. Transposition

Sister chromatid exchange

Therefore, Therefore SCE is not considered a form of recombination

Homologous recombination

parental genotype

Also termed nonparental genotype

Mechanism for the recombination Holliday Model

Both chromatids are nicked at identical locations

Alignment of homologous chromosomes

Nicking

Strand invasion

Branch migration

Isomerization

Resolution

Animation
Holliday model
http://highered.mcgraw-hill.com/sites/0072835125/student_view0/index.html http://engels.genetics.wisc.edu/Holliday/index.html

http://engels.genetics.wisc.edu/Holliday/holliday3D.html http://engels genetics wisc edu/Holliday/holliday3D html

Double-stranded break model

Step 1. Doublestrand b k t d break formation
RecBCD R BCD 5 3 5 3

Step 2 Resection 2.

Displacement loop Step 3. First RecA strand invasion

RecG RuvAB

Step 4. Formation of a double Holliday junction and B h j ti d Brach migration

Step 5. Alternative resolution

RuvC

Homologous Recombination Leads to Gene Conversion

G Gene conversion i
Gene conversion occurs when a pair of different alleles is converted to a pair of identical alleles. For example, a pair of Bb alleles could be converted to BB or bb.

1. DNA gap repair synthesis 2. DNA mismatch repair p

Genes, Alleles and Chromosome

Dominant Recessive
The physical location of a gene on a chromosome is called its locus.

Gap repair synthesis

RecA promotes strand invasion and D loop D-loop formation

Both chromosomes carry the B allele

Mismatch DNA repair

Site-specific recombination

During this process, two DNA segments with little or no homology align themselves at specific sites
The sites are relatively short DNA sequences that provide a specific location for recombination The breakage and reunion of chromosome fragments is catalyzed by specialized enzymes

Site-specific recombination is used by

Certain viruses, to insert their DNA into host cell DNA Mammals, to generate a diverse array of antibodies

Integration of Viral Genomes by SiteSpecific Recombination

Certain bacteriophages can integrate their viral DNA into the bacterial chromosome, creating a prophage
This prophage can e ist in a latent or l sogenic state for exist latent, lysogenic, many generations

This process has been examined extensively for, which infects E. coli
The integration of DNA into the E. coli chromosome is outlined in Figure 17.8

Bacteriophage integration
Encoded by phage

Integrase Ligase Integrase I t excisionase

Antibody Diversity Is Produced by Site-Specific Site Specific Recombination

3 billion DNA base pairs containing an p g estimated 20,00025,000 genes.

RAG1 and RGA2

The fusion process is not entirely precise so that a few bases can be added or lost at the junction This further accentuates the diversity of antibody genes

Nonhomolog ous DNA end joining

Figure 17.9

Figure 17.9

Diversity Domain; Joining Domain

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 Overall, this process is called V(D)J recombination

(D) only occurs i th h l in the heavy-chain gene h i

V(D)J recombination produces an enormous ( ) p diversity in polypeptides

Light chain
300 (V domains) X 4 (J domains) = 1,200 possible combinations

Heavy chain
500 (V domains) X 12 (D domains) X 4 (J domains) = 24,000 possible combinations 24 000

Thus, the light chain-heavy chain combination yields

1,200 X 24,000 = 28,800,000 possible antibody molecules!!!

17-38

Animation
Antibody Diversity

http://www.youtube.com/watch?v=fed0Ka4EhX8 h // b / h? f d0K 4EhX8 http://www.youtube.com/watch?v=Y8eEMYqkwz0

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Mutations in the RAG1 gene or RAG2 g gene cause Omenn syndrome y

Infant with unique dermatitis that characterizes Omenn syndrome

27 Permission for these images pending from www.emedicine.com/ped/topic1640.htm

Transposition
Transposable elements (TEs)
(jumping genes)

Transposition Pathways T iti P th 1. 1 Simple transposition 2. Replicative transposition 3. Retrotransposition

Simple transposition

This mechanism is also called a cut and paste cut-and-paste It is widely found in bacteria and eukaryotes y y

Replication transposition

This mechanism involves replication of the TE and insertion of the copy into another chromosomal location It is relatively uncommon and only f i l ti l d l found i b t i d in bacteria

Retrotransposition

This mechanism is very common but only found in eukaryotes These types of elements are termed retroelements, retrotransposons, or retroposons

Retroelements Use Reverse Transcriptase and Integrase

Retroelement already found in the host genome

A single retroelement can be copied into many RNA transcripts Therefore, Therefore retroelements may accumulate rapidly within a genome

Transposable Elements Have Characteristic DNA Sequences

Direct repeats Found within the host DNA

Catalyzes the transposition event

Inverted repeats Length ranges from 9 to 40 bp

Simplest TEs

Inverted repeats are DNA sequences that are identical (or very similar) but run in opposite directions such as directions, 5 CTGACTCTT 3 3 3 GACTGAGAA 5 5
and

5 AAGAGTCAG 3 3 3 TTCTCAGTC 5 5

Animation
Simple transposition
http://highered.mcgraw-hill.com/sites/0072835125/student_view0/index.html http://engels.genetics.wisc.edu/Holliday/index.html htt // l ti i d /H llid /i d ht l

http://engels.genetics.wisc.edu/Holliday/holliday3D.html p // g g / y/ y

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Confers a selective advantage

Contain additional genes that are not necessary for transposition per se Only the two inverted repeats at the end of the transposon are involved in the transposition event

 Organi ation is similar to insertion seq ences Organization sequences Except that a resolvase gene is found between the inverted repeats p Both enzymes are needed to catalyze the transposition of these types of elements

Long terminal repeats Typically a few hundred nucleotides long

Transposase

Figure 17.14

They are in the same direction and are repeated at both ends of the element

Replicative Transposition Requires Both Transposase and Resolvase

1st step: Transposase

Figure 17.15

2nd step: Resolvase R l

Large circular g chromosome known as a cointegrant

Figure 17.15

Transposable Elements Influence on Mutation and Evolution

There are two schools of thought 1. TEs exist because they simply can! This has been termed the selfish DNA theory y 2. TEs exist because they offer some advantage Carry antibiotic-resistance genes Cause greater genetic variability Cause the insertion of exons into the coding sequences of structural genes f t t l This phenomenon, called exon shuffling, may lead g to the evolution of genes with more diverse functions

 One thing is clear:

Transposable elements can rapidly enter the genome of an organism and proliferate quickly Drosophila melanogaster A TE known as the P element was introduced into the species
in the 1950s Remarkably, in the last 50 years, the P element has expanded throughout D. melanogaster populations worldwide The only strains without the P element are lab stocks collected prior to 1950

Transposable elements have a variety of effects on chromosome structure and gene expression
17-78

Q4: Would you expect the Alu sequence to have become

so prevalent in the human genome if it had been a replicative transposon?

A4: Probably not. Retroelements like Alu are able to

make many copies at a time while replicative transposons tend to only make a single additional t t dt l k i l dditi l copy per transposition.

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