The
Temperate Bacteriophage Repressor
David Marcey
and Stephanie Levi
© 2007
I.
Introduction
II. Operator Structure
III. Repressor Structure
IV.
Repressor-Operator Interactions
IV. References
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I.
Introduction
The
structure at left is a dimer of the amino terminal
domains of phage 434 repressor complexed with operator DNA.
Each temperate
(or lysogenic) bacteriophage (e.g. lambda, 434, P22) encodes its own
repressor protein. The repressor binds to 6 binding sites within the
phage genome. These sites can also be bound by a second transcriptional
repressor encoded by the phage, called Cro. The pattern of binding
of repressor and Cro to these sites determines whether the phage grows
lytically or
lysogenically.
The genetic switch
that underlies the choices between lytic and lysogenic growth in the
case of phage lambda are described in Chapter 16 of your text. If
you are unfamiliar with the mechanisms of the lambda genetic switch,
you may wish to study Figure 1
(Genetic Switch Overview). The phage 434 switch works in essentially
the same way, with the 434 repressor and Cro proteins binding to comparable
sites in the right and left operators of that phage.
Figure 2a,b (Operator DNA Sequences) shows the DNA sequences of
operator sites from lambda and 434.
In this tutorial
we look in detail at the binding of the repressor from phage 434 to
its operator sites. In Chapter 16 of your text we considered the binding
of lambda phage repressor to its sites, and so you can compare binding
in the two cases.
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II. Operator
Structure
The nucleotide sequences of operator
DNA to which repressor protein binds consists of fourteen
base pairs .
The outer four base pairs
at the ends of the operator
(A-T,C-G,A-T,A-T)
serve as key recognition sequences for repressor binding.
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III. Repressor
Structure
Repressor binds to operator
DNA as dimers.
Each monomer binds to an operator half
site. The amino-terminal
domains of repressor are responsible for DNA binding and the
carboxy-terminal domains (not shown) are primarily responsible for
dimerization of the repressor monomers.
The
amino-terminal domain of each monomer is composed of five alpha-helices
connected by short loops.
Helices
two and three
of each amino-terminal
domain form a helix-turn-helix motif
found in many prokaryotic transcription factors, and in a modified
form (the homeo domain) in some eukaryotic transcription factors.
This motif comprises ~20 residues. Helix three
inserts
into the major groove of operator DNA.
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IV. Repressor-Operator
Interactions
Helix
three of each repressor monomer
is primarily responsible for binding to the ACAA
recognition sequence in the major groove. As shown for one monomer,
glutamine 28 forms hydrogen bonds with
adenine one
of this sequence.
Hydrogen
bonds also link glutamine 29 of helix
three with guanine
2, as well as glutamine 33 with
thymine
4.
Packing
of the side chains of glutamine 29 and
threonine 27 forms a hydrophobic
pocket that accepts the methyl group from
thymine three.
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V. References
Aggarwal,
A. K., Rodgers, D. W., Drottar, M., Ptashne, M., Harrison, S. C.:
Recognition of a DNA operator by the repressor of phage 434: a view
at high resolution. Science 242: 899-907 (1988).
Shimon,
L. J., Harrison, S. C.: The phage 434 OR2/R1-69 complex at 2.5 A resolution.
J Mol Biol 232: 826-838 (1993).
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