Bisc 320, Molecular Biology lecture notes, Fall, 2007.
Some notes on:
Conservative site-specific recombination and transposons
See also, Watson, et al., chapter 11.
> 40% of severe hemophilia A is caused by an inversion in exon #22 in the 26 exon
factor VIII gene.
Leukemias: reciprocal exchange of exons between chromosomes.
Transposon terminal d.s. DNA sequences:
Inverted repeats (palindromes) allow inversions to occur via: IR--------IR
Direct repeats: deletions (excisions) and insertions occur via DR---------DR
Figs 11-1, 11-11-2, 11-3
DNA-protein synaptic complexes form at pairs of recombinant recognition sequences.
Conservative site-specific recombinases:
Table 11-1, Fig 11-5
cause d.s. breaks
; intermediate is a
structure having a free 3’OH on each d.s. DNA piece, with a monomeric serine protein
hooked to the 5’ end of the two DNA strands.
No ATP needed.
in each of the d.s. DNAs.
Four recombinase monomers are used in
recombination between two DNA duplexes.
Recombination is via swapping of left and
right s.s. overhangs of the four ends.
Salmonella Hin invertase can invert a segment of bacterial genomic DNA.
flip, in parenthesis:
(hixL hin P hixR)
flijB flijA, is in the “on” rightward-xcription
configuration, that allows flijA expression.
If there is a flip to the “off” configeration,
transcription from P is then to the left.
hixL and hixR are 60 BP each and palindromic to
actor for i
timulation) bends DNA.
4 Hin/2 Fis complex with
HU protein forms at hix sites.
(HU, unlike IHF is sequence independent.)
H2 flagellin; flijA encodes repressor of distant flagellin gene.
“On” allows only H2-type
of flagella; “off” causes H1 flagella to appear on bacterial surfaces.
This switch may
elude the mammalian immune system by changing the type of flagella exposed on
Fig 11-11, 11-12, 11-13
cause s.s breaks
; intermediate is a
structure with a protein
monomer hooked via tyrosine to the 3’ ends of nicks.
Rotation of structure produces
Four monomers are used in recombination between two DNA duplexes.
An acidic DDE (aspartate, aspartate, glutamate) motif is often found in tyrosine
recombinase proteins, such as MuA, TN5, and RSV integrase:
NH2---DNA binding site---DDE---protein-protein binding site—COOH
P1 bacteriophage Cre protein acts at pairs of lox
sites, creating a deletion of the lox
sequences and the intervening DNA:
Four subunits of Cre create a Holliday structure,
prior to the deletion event.
lysogenic state vs lytic growth after viral infection.
infection, linear d.s. lambda DNA circularizes via 12/12 s.s. DNA overlap. Integration of
the new lambda DNA circle is via a Holliday structure, with crossing over at:
PP’ X BB’