Note: Descriptions are shown in the official language in which they were submitted.
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TITLE: MINIMALIST BZIP PROTEINS AND USES THEREOF.
FIELD OF THE INVENTION
The invention relates to minimalist bZIP proteins and uses thereof.
Specifically, the minimalist bZIP proteins are made from the fusion of the
basic region of a bHLH protein to the leucine zipper dimerization domain of a
bZIP protein. These proteins are particularly useful in treating cancer.
BACKGROUND OF THE INVENTION
Nature's use of the protein a-helix for specific DNA recognition is ubiquitous
and maximally utilized by the basic region/leucine zipper motif (bZIP), which
comprises a pair of short a-helices that recognize the DNA major groove with
sequence-specificity and high affinity (Struhl, K., Trends Biochem. Sci. 1989,
14, 137-140; Landschulz, W. H. et al., Science 1988, 240, 1759-1764).
Crystal structures of the bZIP domain of GCN4 bound to two different DNA
sites (Konig, P. and Richmond, T. J., J. Mol. Biol. 1993, 233, 139-154;
Ellenberger, T. E. et al., Cell 1992, 71, 1223-1237; Keller, W. et al., J.
Mol.
Biol. 1995, 254, 657-667) and the Jun-Fos heterodimer bZIP-DNA crystal
(Glover, J. N. M. and Harrison, S. C., Nature 1995, 373, 257-261) show that a
continuous a-helix of -60 amino acids provides the basic-region interface for
binding to specific DNA sites, as well as the leucine zipper coiled-coil
dimerization structure. Remarkably, these crystal structures also demonstrate
astonishing conservation of protein backbone structure across species
between the two yeast GCN4 and avian Jun-Fos structures.
Myc, Max, and Mad Proteins
The basic-region/helix-loop-helix (bHLH) motif, including the subvariant basic-
region/helix-loop-helix/leucine-zipper (bHLHZ) motif, is very similar to the
bZIP
in that a dimer of a-helices binds specific sites in the DNA major groove;
protein dimerization is effected by the helix-loop-helix, a tetramer of a-
helices
in the bHLH, or by the helix-loop-helix/leucine-zipper in the bHLHZ, in which
dimerization is mediated by both the tetrameric HLH and adjacent leucine
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zipper (compare structures in Figure 1) (Murre, C. Cell, 1989, 56, 777-783).
The bHLH comprises bHLH proteins as well as subfamily variants: the
bHLHZ (such as Max and USF), and the bHLH/PAS (such as AhR and Arnt),
where the PAS domain assists in efficient protein dimerization. Unlike the
leucine zipper, the PAS structure is unknown. The PAS has been found in the
Per, Arnt, and Sim proteins-hence, "PAS"-as well as AhR and HIF-1a
(Gradin, K., et al., Mol. Cell. Biol. 1996, 16, 5221-5231). The PAS domain
comprises 200-300 amino acids and contains characteristic repeats termed
the "A" and "B" domains.
Like bZIP proteins, the bHLH protein family also regulates transcription. In
particular, the Myc, Max, and Mad transcription factor network comprises
widely expressed bHLHZ proteins critical for control of normal cell
proliferation
and differentiation (Amati, B. and Land, H., Curr. Opin. Gene. Dev. 1994, 4,
102-108; Orian, A. et al., Genes Dev., 2003, 17, 1101-1114). Myc is proto-
oncogenic; deregulated overexpression of myc genes leads to malignant
transformation, and myc genes are suspected of being among the most
frequently affected in human tumors and disease (Nesbit, C. D. et al.,
Oncogene 1999, 18, 3004-3016) including Burkitt's lymphoma (Taub, R. et al.,
Proc. Natl. Acad. Sci. USA 1982, 79, 7837-7841; Dalla-Favera, R. et al.. M.,
Proc. Natl. Acad. Sci. USA 1982, 79, 7824-7827), neuroblastomas (Schwab,
M. et al., Nature 1984, 308, 288-291), and small cell lung cancers (Nau, M. M.
et al., Nature 1985, 318, 69-73).
In contrast, Max is a stable, constitutively expressed dimerization partner
that
heterodimerizes with Myc, Mad, and Mxi, thereby controlling their DNA-
binding and gene-regulatory activities (Amati, B. and Land, H., Curr. Opin.
Gene. Dev. 1994, 4, 102-108; Orian, A. et al., Genes Dev., 2003, 17, 1101-
1114). Myc-Max is a transcriptional activator that binds the Enhancer box (E-
box) sequence 5'-CACGTG (Blackwood, E. M. et al., Science 1991, 251,
1211-1217; Blackwell, T. K. et al., Mol. Cell. Biol. 1993, 13, 5216-5224). Myc
does not homodimerize in vivo or at physiological concentrations, so its
activity is mediated by heterodimerization with Max. In contrast Max can
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homodimerize, although it preferentially heterodimerizes; Max homodimers
can bind the E-box, albeit with lower affinities than that of the heterodimers
(Blackwood, E. M. et al., Science 1991, 251, 1211-1217). Several promoters
contain the E-box sequence 5'-CACGTG, including that for p53 tumor
suppressor (Reisman, D. et al., Cell Growth Differ. 1993, 4, 57-65). Mad-Max
(Amati, B. et al., Cell 1993, 72, 233-245) and the related Mxi-Max (Zervos, A.
S. et al., Cell 1993, 72, 223-232) are transcriptional repressors that
antagonize Myc-Max by competing for the same E-box sequence.
The Max network is highly conserved in vertebrates and mammals and
ubiquitous; in Drosophila, for instance, a conservative estimate is that Max
network proteins interact with approximately 2000 genes (Orian, A. et al.,
Genes Dev., 2003, 17, 1101-1114). The transactivation domain mediating the
gene-regulatory activities of the Myc-Max heterodimer lies in the amino-
terminal region of Myc; Max's role is to allow Myc to bind DNA, thereby
mediating its cellular activities (Amati, B. and Land, H., Curr. Opin. Gene.
Dev. 1994, 4, 102-108). Therefore, mutant proteins that interfere with Myc-
Max recognition of the E-box site may also interfere with Myc's disease-
promoting activities.
AhR and Arnt Proteins
Not only interesting from a protein-design perspective, the AhR-Arnt system is
notable for its possible role in disease pathways. The AhR, also known as the
dioxin receptor, mediates signal transduction (Fisher, J. M., et al., Mol.
Carcinogen. 1989, 1, 216-221) by dioxins and related polycyclic aromatic
hydrocarbons, including benzo[a]yrenes found in cigarette smoke and smog,
heterocyclic amines in cooked meat, and polychlorinated biphenyls (PCBs).
In analogy to the glucocorticoid receptor, the latent AhR is found associated
with heat-shock protein hsp90 in the cytosol (Cadepond, F. et al., J. Biol.
Chem. 1991, 266, 5834-5841.). Ligand binding induces nuclear translocation
of the AhR (Pollenz, R. S. et al., Mol. Pharmacol. 1995, 45, 428-438), release
of hsp90, and dimerization with the nuclear protein Arnt (Reyes, H. et al.,
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Science 1992, 256, 1193-1195); this activated complex (Whitelaw, M. et al.,
Mol. Cell. Biol. 1993, 13, 2504-2514; Cuthill, S., et al., Mol. Cell. Biol.
1991,
11, 401-411) then binds specific xenobiotic response elements (XRE sites)
and activates gene transcription (Wu, L. and Whitlock, J. P. Nucl. Acid. Res.
1993, 21, 119-125; Fujisawa-Sehara, A. et al., Nucl. Acid. Res. 1987, 15,
4179-4191). The endogenous ligand, if any, for the dioxin receptor has yet to
be discovered. During evolution, plant flavones and later, certain combustion
products like dioxin, appear to have appropriated the AhR for stimulating
their
own metabolism.
AhR and Arnt are bHLH/PAS proteins; they differ from most other bHLH
transcription factors in that AhR-Arnt dimerization occurs only in the
presence
of ligand. The PAS domain is remote from the basic region, and importantly,
it does not affect DNA binding, as it is purely necessary for dimerization and
ligand binding; Poellinger and coworkers found that the minimal bHLH
domains of AhR and Arnt are solely capable of recognition of XRE sites and
dimerization (Pongratz, I., et al., Mol. Cell. Biol. 1998, 18, 4079-4088).
Previous work has shown that within the bZIP family, basic regions and
leucine zippers from different proteins can be exchanged with no resulting
change in a-helical structure or DNA-binding function (Agre, P. et al.,
Science
1989, 246, 922-926; Lajmi, A. R. et al., J. Am. Chem. Soc. 2000, 122, 5638-
5639; Sellers, J. W. et al., Nature 1989, 341, 74-76). Likewise, the
bHLH/bHLHZ is well conserved structurally and essentially identical among
bHLH/bHLHZ family members (Nair, S. K. and Burley, S. K., Cel12003, 112,
193-205). Protein-DNA crystal structures for bHLH proteins MyoD (Ma, P. C
et al., Cell 1994, 77, 451-459) and E47 (Ellenberger, T. et al., Genes Dev.
1994, 8, 970-980), and bHLHZ proteins Max (Ferre-D'Amare, A. R. et al.,
Nature 1993, 363, 38-45; Brownlie, P. et al., Structure 1997, 5, 509-520) and
USF (Ferre-D'Amare, A. R. et al., EMBO J. 1994, 13, 180-189) show closely
related structures and DNA-binding functions. Exchange of basic regions and
dimerization elements in the bHLHZ family also yields native-like proteins:
Prochownik and coworkers showed that the Max basic region could be fused
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to the USF HLHZ domain to generate hybrids that could homodimerize and
bind the E-box (Yin, X. et al., Oncogene 1998, 16, 2629-2637).
The crystal structures of bZIP and bHLH demonstrate that although they are
distinct protein structural families, they share the most similarity in
comparison
to other families of DNA-binding proteins: in particular, the a-helix DNA
recognition element is highly conserved in the two families (Konig, P. and
Richmond, T. J., J. Mol. Biol. 1993, 233, 139-154; Ellenberger, T. E. et al.,
Cell 1992, 71, 1223-1237; Keller, W. et al., J. Mol. Biol. 1995, 254, 657-667;
Glover, J. N. M. and Harrison, S. C., Nature 1995, 373, 257-26; Ma, P. C et
al., Cell 1994, 77, 451-459; Ellenberger, T. et al., Genes Dev. 1994, 8, 970-
980; Ferre-D'Amare, A. R. et al., Nature 1993, 363, 38-45; Brownlie, P. et
al.,
Structure 1997, 5, 509-520; Ferre-D'Amare, A. R. et al., EMBO J. 1994, 13,
180-189). In contrast, there are differences in the hinge angles which govern
positioning of the basic regions in the major grooves between bZIP and bHLH.
Additionally, the dimerization element in the bHLH is more complicated than
the smaller, simpler leucine zipper.
No simple code exists for protein-DNA recognition, and this fact has made
design of sequence-specific DNA-binding proteins a major challenge.
SUMMARY OF THE INVENTION
The invention relates to novel minimalist bZIP proteins that are small,
simplified molecular recognition scaffolds. These proteins are useful for
design of helical proteins that can target specific DNA ligands.
Accordingly, the invention provides a minimalist bZIP protein comprising:
a) a basic region of a basic helix-loop-helix protein (bHLH);
b) a hinge region; and
c) a leucine zipper domain of a bZIP protein,
wherein the minimalist bZIP protein binds a target DNA sequence.
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The bHLH proteins include bHLH subvariants, bHLHZ subvariants and
bHLH/PAS subvariants. In one embodiment, the target DNA sequence is an
E-box or XRE1 site.
In a particular embodiment, the invention provides a minimalist bZIP protein
comprising:
a) a basic region from Max;
b) a hinge region; and
c) a leucine zipper region from C/EBP,
wherein the minimalist bZIP protein binds an E-box target DNA sequence.
In another particular embodiment, the invention provides a minimalist bZIP
protein comprising:
a) a basic region from Arnt;
b) a hinge region; and
c) a leucine zipper region from C/EBP,
wherein the minimalist bZIP protein binds an XRE1 target DNA sequence or
an E-box target DNA sequence. .
In yet another particular embodiment, the invention provides for a first and
second minimalist bZIP protein comprising a leucine zipper region in the first
minimalist bZIP protein and a leucine zipper region in the second minimalist
bZIP protein capable of forming a heterodimer. In a specific embodiment, the
leucine zipper region in the first minimalist bZIP protein is from Jun and the
leucine zipper region in the second minimalist bZIP protein is from Fos.
The invention also provides for the use of the minimalist bZIP proteins of the
invention for repressing myc-related transcriptional activation. The invention
further provides the use of the minimalist bZIP proteins able to bind to an E-
box target DNA sequence for treating cancer. The invention also provides for
a method of treating cancer comprising administering an effective amount of a
minimalist bZIP protein able to bind to an E-box target DNA sequence to a
mammal in need thereof. In one embodiment, the cancer is selected from the
group consisting of breast cancer, colon cancer, gynecological cancer,
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hepatocellular carcinomas, hematological tumors, Burkitt lymphoma,
neuroblastoma and small cell lung cancer
In another embodiment, the invention provides for the use of the minimalist
bZIP proteins able to bind to an XRE1 target DNA sequence for treating
cancer. The invention also provides for a method of treating cancer
comprising administering an effective amount of a minimalist bZIP protein
able to bind to an XRE1 target DNA sequence to a mammal in need thereof.
In one embodiment, the cancer is a soft tissue carcinoma or respiratory
cancer.
The invention also provides minimalist bZIP proteins further fused to an
activation domain, a repressor domain or a drug and uses thereof.
The invention also provides pharmaceutical compositions comprising the
minimalist bZIP proteins of the invention and a pharmaceutically acceptable
carrier, diluent or excipient, and uses thereof.
Other features and advantages of the present invention will become apparent
from the following detailed description. It should be understood, however,
that
the detailed description and the specific examples while indicating preferred
embodiments of the invention are given by way of illustration only, since
various changes and modifications within the spirit and scope of the invention
will become apparent to those skilled in the art from this detailed
description.
BRIEF DESCRIPTION OF THE DRAWINGS
The invention will now be described in relation to the drawings in which:
Figure 1 shows the protein-DNA crystal structure of protein bound to DNA
Left. GCN4 bZIP in complex with the AP-1 DNA site, 5'-TGACTCA
(Ellenberger, T. E., et al. Cell, 1992, 71, 1223-1237) DNA is the dark double
helix at the bottom of the figure, and the bZIP is the a-helical dimer above
(left). The leucine zipper dimerizes into the coiled-coil, which then smoothly
forks to either side of the DNA, allowing the basic region dimer to bind
opposite sides of the DNA major groove. Right. Max bHLH/ZIP in complex
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with the E-box DNA site, 5'-CACGTG (Ferre-D'Amare, A. R., et al. Nature,
1993, 363, 38-45) Note that the basic region and helix 1 are contiguous, and
that helix 2 and the leucine zipper are contiguous.
Figure 2 shows Arntl-C/EBP binding E-box. Plates were grown at 30 deg C
for 6 days. (A) Arntl-C-EBP inserted into vector pGAD424 and grown on SD-
His/-Leu plates with 10 mM 3-AT. (B) Control of vector alone also grown on
SD-His/-Leu plates with 10 mM 3-AT.
Figure 3 shows a schematic diagram of the Yeast One Hybrid system used to
evolve the minimalist bZIP proteins of the invention.
Figure 4 shows binding between MM3 and E-box. Plates were incubated four
days, 30 C. a. Max/C-EBP plated on SD/-His/-Leu plus 10 mM 3-AT.
Binding undetectable (some bubbles arise from sorbitol in plate medium). b.
MM3 plated on SD/-His/-Leu plus 10 mM 3-AT. c. MM3 plated on SD/-His/-
Leu plus 20 mM 3-AT. d. MM3 plated on SD/-His/-Leu plus 60 mM 3-AT.
DETAILED DESCRIPTION OF THE INVENTION
The a-helical bZIP motif serves as a manipulable scaffold for protein design.
The small, simple bZIP can be a very tractable scaffold for design of new
proteins with new DNA recognition properties. The present inventors have
examined heterodimeric and homodimeric bZIP motifs in which portions of
bHLH and bZIP proteins are fused to create novel hybrid proteins, thus
enlarging their binding capabilities. These small proteins still retain the
structure and function of native proteins, thus condensing these proteins to
minimal units of functionality.
(a) Novel Minimalist bZIP Proteins:
The invention relates to the creation of novel minimalist bZIP proteins based
on fusion of the DNA-binding domain from a bHLH protein and the leucine
zipper dimerization domain originating from a bZIP protein.
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Accordingly, in one embodiment, the invention provides a minimalist bZIP
protein comprising a) a basic region of a basic helix-loop-helix protein
(bHLH);
b) a hinge region; and c) a leucine zipper domain of a bZIP protein, wherein
the minimalist bZIP protein binds a target DNA sequence.
In one embodiment, the minimalist bZIP protein of the invention is 30-100
amino acids in length. In a preferred embodiment, the minimalist bZIP protein
is 40-60 amino acids in length.
The hinge offers a large amount of flexibility in length and identity.
Technically, a hinge could have zero amino acids, as long as the lengths of
basic region and zipper compensate for the flexibility. Accordingly, in one
embodiment, the hinge region has 0-20 amino acids. In another embodiment
the hinge region has 3 amino acids. In a specific embodiment, the hinge
region comprises the amino acid sequence RIR or GIR. As the orientation of
the minimalist bZIP protein is significant for binding to DNA, each desired
minimalist bZIP protein is constructed in triplicate using an additional 1, 2
or 3
amino acids from the C-terminal end of helix 1 in order to select for the best
orientation for binding to DNA. One of skill in the art could readily
determine
which of the 3 hinge regions best orients the protein to the DNA. For example,
if the structure is known, this can be analysed by the crystal structure or
NMR
structure. Alternatively the modeling can be based on the high-resolution
structure of a protein known to be similar. Accordingly, in an embodiment of
the invention, the invention provides the minimalist bZIP proteins of the
invention having an additional 1, 2 or 3 amino acids from the C-terminal end
of helix I of the bHLH protein between the basic region and the hinge region.
A minimalist bZIP protein that does not provide an ideal orientation for DNA
binding may be used as a negative control.
The leucine zipper domain is derived from bZIP proteins selected from the
group consisting of C/EBP, Jun, Fos, GCN4 and CREB. Where it is desired
to construct minimalist bZIP proteins that homodimerize, the preferred leucine
zipper domain is derived from C/EBP. Where it is desired to construct
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minimalist bZIP proteins that heterodimerize, use of the leucine zipper
domains of Jun or Fos is preferred.
In one embodiment, the basic region is derived from a bHLH protein selected
from the group consisting of a bHLH subvariant, bHLHZ subvariant or
bHLH/PAS subvariant. The bHLH subvariant may be selected from the group
consisting of MyoD, Myc, E2A, E47, E12, TALL, Id proteins, GL3 and EGL3,
TFEB, PIF1, PIL6, ATH, NGN and HAND1. The bHLHZ subvariant may be
selected from the group consisting of Mad, Mxi, Max, Myc, Spzl, USF, Mash,
BMP, TFE3 and AP4. The bHLH/PAS subvariant may be selected from the
group consisting of AhR, Arnt (also known as HIF-1(3), HIF-1a, HIF-2a, HIF-
3a, Per and Sim.
In a particular embodiment, the bHLHZ subvariant is Max. In another
particular embodiment, the bHLH/PAS subvariant is Arnt.
In one embodiment, the minimalist bZIP protein comprises a) a basic region
from Max; b) a hinge region; and c) a leucine zipper region from C/EBP,
wherein the minimalist bZIP protein binds an E-box target DNA sequence.
In a particular embodiment, the minimalist bZIP protein comprises the amino
acid sequence as shown in Table 1(SEQ ID NOs 1-6), differing only in the
number of amino acids in the hinge region.
In another embodiment, the invention provides a minimalist bZIP protein
comprising a) a basic region from Arnt; b) a hinge region; and c) a leucine
zipper region from C/EBP, wherein the minimalist bZIP protein binds an XRE1
target DNA sequence or an E-box target DNA sequence.
In a particular embodiment, the minimalist bZIP protein comprises the amino
acid sequence as shown in Table 2 (SEQ ID NOs 7-12), differing only in the
number of amino acids in the hinge region.
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In another particular embodiment, the invention provides a minimalist bZIP
protein comprising the amino acid sequence as shown in SEQ ID NOs 14-22,
52, 53 or 54.
In yet another particular embodiment, the invention provides for a first and
second minimalist bZIP protein comprising a leucine zipper region in the first
minimalist bZIP protein and a leucine zipper region in the second minimalist
bZIP protein capable of forming a heterodimer. In a specific embodiment, the
leucine zipper region in the first minimalist bZIP protein is from Jun and the
leucine zipper region in the second minimalist bZIP protein is from Fos.
The minimalist bZIP proteins of the invention are able to bind target DNA
sequences. In one embodiment, the minimalist bZIP proteins bind to the
homodimeric E-box DNA sequence 5'-CAG-CTG-3' (Class A proteins) and 5'-
CAC-GTG-3' (Class B proteins). In another embodiment, the minimalist bZIP
proteins of the invention bind to the heterodimeric XRE1 site 5'-TTGC-GTG-3'
(Class C proteins). Class A proteins include MyoD, E47, AP4, E12, Tall and
have the consensus as shown in Table 6. Class B proteins include Max, Myc,
USF, TFE3, TFEB, Arnt and have the consensus as shown in Table 6 of
grant. Class C proteins include AhR and Sim and recognize half sites 5'-
T(CfT)GC-3' or 5'-GT(A/G)C-3'. Finally, the minimalist proteins may be
generated to heterodimerize with a protein fused to a basic region of a bZIP
protein, such as GCN4 which binds to the half site: 5'-TGAC.
The different combinations of basic regions and leucine zipper regions
generates a large variety of binding repertoires. The ability to bind to a
particular target DNA sequence may depend on the spacing of the target DNA
sequences and the flanking sequences found in an endogenous DNA
promoter. A person skilled in the art would readily be able to test a
minimalist
bZIP protein to determine its ability to bind to particular target DNA
sequences.
For example, the structure and function of the proteins of the invention can
be
quantitatively characterized using techniques known in the art, such as by
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DNase I footprinting; chemical footprinting; circular dichroism;
thermodynamics by fluorescence anisotropy and calorimetry; and high-
resolution x-ray crystallography and molecular modeling. DNAse I footprinting
is used to demonstrate the binding of a protein to a specific DNA sequence.
When a protein binds the specific DNA sequence, clear footprints can be
seen. A wild type bHLH protein that is expected to bind the sequence can be
used as a positive control. Electrophoretic mobility shift assay (EMSA) is a
gel
assay in which one can detect whether the DNA sequence is bound by the
particular protein. If protein binds to the DNA, the DNA's mobility through
the
gel is retarded, and therefore, the band corresponding to DNA shifts. One
can also measure free energies of protein-DNA binding by titrating different
concentrations of protein with DNA and measuring the shift. Capillary
electrophoresis and other chromatography variants are similar to EMSA gel
assay in that free DNA would move through the column matrix differently from
DNA bound by protein. Therefore, these assays can measure where free
DNA elutes from the matrix; if protein binds DNA, there is a change in
mobility
of DNA. Normally, protein-bound DNA mobility would be slower. Alternatively,
the Yeast two-hybrid or Yeast one-hybrid system can be used to detect DNA-
protein interactions as described in the examples section below.
Circular Dichroism is an excellent method for characterizing the structure of
bZIP proteins, as the a-helix displays distinctive minima at 208 nm and 222
nm. Fluorescence anisotropy measures the tumbling motion of molecules
containing a fluorophore; nanosecond lifetimes of most fluorophores are
comparable to the time necessary for rotation of a molecule or complex of
molecular weight less than 105 D, the range of many protein-DNA complexes
(the excited state fluorescence lifetime for fluorescein is -4 ns) (Lakowicz,
J.R. Principles of Fluorescence Spectroscopy; 2nd Edition ed.; Plenum Press:
New York, 1999). Large complexes tumble slowly relative to the lifetime of
fluorophore and exhibit only slight depolarization of emission with respect to
polarized excitation, and a higher anisotropy than small complexes that
tumble rapidiy (Hill, J.J. and Royer, C.A. "Fluorescence Approaches to Study
of Protein-Nucleic Acid Complexation." Meth. Enzymol. 1997, 278, 390-416).
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Thus, the anisotropy of free, short DNA duplexes should be significantly less
than that for the same DNA bound by a protein such as a minimalist bZIP
protein of the invention. High-resolution NMR and/or X-ray crystallography for
structural characterization would also be useful for characterizing the novel
bZIP proteins of the present invention. One can obtain detailed pictures of
molecules showing positions of atoms, bond lengths, and distances,
producing high-resolution detail of atomic interactions. Calorimetry can also
be used for characterization of thermodynamics of complexation. One can
measure enthalpies and free energies (and can then calculate entropies) as
well as heat capacities. These thermodynamic parameters provide
information about how strong the complexation is, how stable it is, how
factors
like temperature or a mutation or salts can affect the binding strength and
stability. Other fluorescence experiments besides anisotropy, including
fluorescence resonance energy transfer (FRET) and fluorescence
homoquenching can also be used. With FRET and homoquenching, one can
label the protein and DNA with fluorophores whose properties are distance-
dependent. Therefore, if the fluorophores are close to each other, which
would occur when the protein and DNA bind, one would see fluorescence in
FRET or would see quenching of fluorescence in homoquenching. Thus, this
is useful for detecting binding of the minimalist bZIP protein of the
invention
with specific target DNA sequences. Mass spectrometry (MS) can be used to
determine the molecular weight of the molecule and can even detect
molecular complexes, like a protein-DNA complex.
Insertion of alanine residues into the basic region of bZIP has been shown to
retain the helical structure and DNA binding of the native protein (Lajmi et
al.
JACS, 2000, 122, 5638-5639). Accordingly, the minimalist bZIP proteins may
be further refined and/or simplified by generating Ala-rich basic regions. The
minimalist bZIP proteins may also be strung together such that the helical
units can generate multimeric proteins capable of binding longer sequences.
In a further embodiment, the sequences encoding the minimalist bZIP
proteins are mutagenized and then the protein products are selected for better
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binding to the DNA. Accordingly, in one embodiment, the minimalist bZIP
proteins are minimalist bZIP proteins of the invention that have been further
evolved by mutagenesis and selection. In a particular embodiment, the
mutagenesis and the selection occurs in a yeast one-hybrid or yeast two-
hybrid system.
In another embodiment, the minimalist bZIP proteins of the invention are
fused to an activation domain or a repressor domain. The activation domain
may be derived from the proteins Ga14, Myc, Mad (Mxi), and VP16, and HIF-
3a. An actual transcriptional repressor is not always necessary for repression
of gene expression because if the minimalist bZIP protein sits on a gene or
promoter, it may be enough to block or repress the transcription of the gene.
However, a repressor may be fused to the minimalist bZIP proteins of the
invention. A repressor domain may be derived from Id, Mad (Mxi), and HIF-
3a.
The minimalist bZIP proteins of the invention may also contain or be used to
obtain or design "peptide mimetics". "Peptide mimetics" are structures which
serve as substitutes for peptides in interactions between molecules (See
Morgan et al (1989), Ann. Reports Med. Chem. 24:243-252 for a review).
Peptide mimetics include synthetic structures which may or may not contain
amino acids and/or peptide bonds but retain the structural and functional
features of the proteins of the invention, including biological activity and a
reduced propensity to activate human T cells. Peptide mimetics also include
peptoids and oligopeptoids (Simon et al (1972) Proc. Natl. Acad, Sci USA
89:9367).
Peptide mimetics may be designed based on information obtained by
systematic replacement of L-amino acids by D-amino acids, replacement of
side chains with groups having different electronic properties, and by
systematic replacement of peptide bonds with amide bond replacements.
Local conformational constraints can also be introduced to determine
conformational requirements for activity of a candidate peptide mimetic. The
mimetics may include isosteric amide bonds, or D-amino acids to stabilize or
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promote reverse turn conformations and to help stabilize the molecule. Cyclic
amino acid analogues may be used to constrain amino acid residues to
particular conformational states. The mimetics can also include mimics of the
secondary structures of the proteins of the invention. These structures can
model the 3-dimensional orientation of amino acid residues into the known
secondary conformations of proteins. Peptoids may also be used which are
oligomers of N-substituted amino acids and can be used as motifs for the
generation of chemically diverse libraries of novel molecules.
The molecules of this invention can be prepared in any of several ways but it
is most preferably conducted exploiting routine recombinant methods. It is a
relatively straightforward procedure to use the protein sequences and
information provided herein to deduce a polynucleotide (DNA) encoding any
of the preferred protein sequences. This can be achieved for example using
computer software tools such as the DNSstar software suite [DNAstar Inc,
Madison, WI, USA] or similar. Any such DNA sequence with the capability of
encoding the preferred polypeptides of the present or significant homologues
thereof, should be considered as embodiments of this invention.
As a general scheme, genes encoding any of the preferred minimalist bZIP
protein sequences can be made using gene synthesis and cloned into a
suitable expression vector. In turn the expression vector is introduced into a
host cell and cells selected and cultured. The proteins of the invention are
purified from the culture medium and formulated into a preparation for
therapeutic administration.
Methods for purifying and manipulating recombinant proteins including fusion
proteins are well known in the art. Necessary techniques are explained fully
in the literature, such as, "Molecular Cloning: A Laboratory Manual", second
edition (Sambrook et al., 1989); "Oligonucleotide Synthesis" (M. J. Gait, ed.,
1984); "Animal Cell Culture" (R. I. Freshney, ed., 1987); "Methods in
Enzymology" (Academic Press, Inc.); "Handbook of Experimental
Immunology" (D. M. Weir & C. C. Blackwell, eds.); "Gene Transfer Vectors for
Mammalian Cells" (J. M. Miller & M. P. Calos, eds., 1987); "Current Protocols
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in Molecular Biology" (F. M. Ausubel et al., eds., 1987); "PCR: The
Polymerase Chain Reaction", (Mullis et al., eds., 1994); "Current Protocols in
Immunology" (J. E. Coligan et al., eds., 1991).
The proteins of the invention can be prepared using recombinant DNA
methods. The proteins of the invention may also be prepared by chemical
synthesis using techniques well known in the chemistry of proteins such as
solid phase synthesis (Merrifield, 1964, J. Am. Chem. Assoc. 85:2149-
2154) or synthesis in homogenous solution (Houbenweyl, 1987, Methods of
Organic Chemistry, ed. E. Wansch, Vol. 15 I and II, Thieme, Stuttgart).
The present invention also provides a purified and isolated nucleic acid
molecule comprising a sequence encoding the minimalist bZIP proteins of the
invention, preferably a sequence encoding the protein described herein as
shown in SEQ ID NOs. 1-12, 14-22, 52, 53 or 54.
The term "isolated and purified" as used herein refers to a nucleic acid
substantially free of cellular material or culture medium when produced by
recombinant DNA techniques, or chemical precursors, or other chemicals
when chemically synthesized. An "isolated and purified" nucleic acid is also
substantially free of sequences which naturally flank the nucleic acid (i.e.
sequences located at the 5' and 3' ends of the nucleic acid) from which the
nucleic acid is derived.
The term "nucleic acid" as used herein refers to a sequence of nucleotide or
nucleoside monomers consisting of naturally occurring bases, sugars and
intersugar (backbone) linkages. The term also includes modified or
substituted sequences comprising non-naturally occurring monomers or
portions thereof, which function similarly. The nucleic acid sequences of the
present invention may be ribonucleic (RNA) or deoxyribonucleic acids (DNA)
and may contain naturally occurring bases including adenine, guanine,
cytosine, thymidine and uracil. The sequences may also contain modified
bases such as xanthine, hypoxanthine, 2-aminoadenine, 6-methyl, 2-propyl,
and other alkyl adenines, 5-halo uracil, 5-halo cytosine, 6-aza uracil, 6-aza
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cytosine and 6-aza thymine, pseudo uracil, 4-thiouracil, 8-halo adenine, 8-
amino adenine, 8-thiol adenine, 8-thio-alkyl adenines, 8-hydroxyl adenine and
other 8-substituted adenines, 8-halo guanines, 8-amino guanine, 8-thiol
guanine, 8-thioalkyl guanines, 8-hydroxyl guanine and other 8-substituted
guanines, other aza and deaza uracils, thymidines, cytosines, adenines, or
guanines, 5-trifluoromethyl uracil and 5-trifluoro cytosine.
In one embodiment, the purified and isolated nucleic acid molecule
comprises:
(a) a nucleic acid sequence encoding the amino acid sequences of the
proteins of the invention, preferably as shown in SEQ ID NOs. 1-12,
14-22, 52, 53 or 54;
(b) nucleic acid sequences complementary to (a);
(c) nucleic acid sequences which are homologous to (a) or (b);
(d) a fragment of (a) to (c) that is at least 15 bases, preferably 20 to 30
bases, and which will hybridize to (a) to (c) under stringent
hybridization conditions; or
(e) a nucleic acid molecule differing from any of the nucleic acids of (a)
to (c) in codon sequences due to the degeneracy of the genetic
code.
Further, it will be appreciated that the invention includes nucleic acid
molecules comprising nucleic acid sequences having substantial sequence
homology with the nucleic acid sequences encoding the proteins and peptides
of the invention, and fragments thereof. The term "sequences having
substantial sequence homology" means those nucleic acid sequences which
have slight or inconsequential sequence variations from these sequences,
i.e., the sequences function in substantially the same manner to produce
functionally equivalent proteins. The variations may be attributable to local
mutations or structural modifications.
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Nucleic acid sequences having substantial homology include nucleic acid
sequences having at least 80%, preferably 90% identity with the nucleic acid
sequence encoding the proteins of the invention.
Another aspect of the invention provides a nucleic acid molecule, and
fragments thereof having at least 15 bases, which hybridize to nucleic acid
molecules of the invention under hybridization conditions, preferably
stringent
hybridization conditions. Appropriate stringency conditions which promote
DNA hybridization are known to those skilled in the art, or may be found in
Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989),
6.3.1-6.3.6. For example, the following may be employed: 6.0 x sodium
chloride/sodium citrate (SSC) at about 45 C, followed by a wash of 2.0 x SSC
at 50 C. The stringency may be selected based on the conditions used in the
wash step. For example, the salt concentration in the wash step can be
selected from a high stringency of about 0.2 x SSC at 50 C. In addition, the
temperature in the wash step can be at high stringency conditions, at about
65 C.
Accordingly, nucleic acid molecules of the present invention having a
sequence which encodes a protein of the invention may be incorporated
according to procedures known in the art into an appropriate expression
vector which ensures good expression of the protein. Possible expression
vectors include but are not limited to cosmids, plasmids, or modified viruses
(e.g., replication defective retroviruses, adenoviruses and adeno associated
viruses), so long as the vector is compatible with the host cell used. The
expression "vectors suitable for transformation of a host cell", means that
the
expression vectors contain a nucleic acid molecule of the invention and
regulatory sequences, selected on the basis of the host cells to be used for
expression, which are operatively linked to the nucleic acid molecule.
"Operatively linked" is intended to mean that the nucleic acid is linked to
regulatory sequences in a manner which allows expression of the nucleic
acid.
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The invention therefore contemplates a recombinant expression vector of the
invention containing a nucleic acid molecule of the invention, or a fragment
thereof, and the necessary regulatory sequences for the transcription and
translation of the inserted protein-sequence. Suitable regulatory sequences
may be derived from a variety of sources, including bacterial, fungal, or
viral
genes (For example, see the regulatory sequences described in Goeddel,
Gene Expression Technology: Methods in Enzymology 185, Academic Press,
San Diego, CA (1990)). Selection of appropriate regulatory sequences is
dependent on the host cell chosen, and may be readily accomplished by one
of ordinary skill in the art. Examples of such regulatory sequences include: a
transcriptional promoter and enhancer or RNA polymerase binding sequence,
a ribosomal binding sequence, including a translation initiation signal.
Additionally, depending on the host cell chosen and the vector employed,
other sequences, such as an origin of replication, additional DNA restriction
sites, enhancers, and sequences conferring inducibility of transcription may
be incorporated into the expression vector. It will also be appreciated that
the
necessary regulatory sequences may be supplied by the native protein and/or
its flanking regions.
The recombinant expression vectors of the invention may also contain a
selectable marker gene which facilitates the selection of host cells
transformed or transfected with a recombinant molecule of the invention.
Examples of selectable marker genes are genes encoding a protein such as
G418 and hygromycin which confer resistance to certain drugs, 11-
galactosidase, chloramphenicol acetyltransferase, or firefly luciferase.
Transcription of the selectable marker gene is monitored by changes in the
concentration of the selectable marker protein such as 13-galactosidase,
chloramphenicol acetyltransferase, or firefly luciferase. If the selectable
marker gene encodes a protein conferring antibiotic resistance such as
neomycin resistance transformant cells can be selected with G418. Cells that
have incorporated the selectable marker gene will survive, while the other
cells die. This makes it possible to visualize and assay for expression of
recombinant expression vectors of the invention and in particular to determine
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the effect of a mutation on expression and phenotype. It will be appreciated
that selectable markers can be introduced on a separate vector from the
nucleic acid of interest.
The recombinant expression vectors may also contain genes which encode a
fusion moiety which provides increased expression of the recombinant
protein; increased solubility of the recombinant protein; and aid in the
purification of a target recombinant protein by acting as a ligand in affinity
purification. For example, a proteolytic cleavage site may be added to the
target recombinant protein to allow separation of the recombinant protein from
the fusion moiety subsequent to purification of the fusion protein.
Recombinant expression vectors can be introduced into host cells to produce
a transformed host cell. The term "transformed host cell" is intended to
include prokaryotic and eukaryotic cells which have been transformed or
transfected with a recombinant expression vector of the invention. The terms
"transformed with", "transfected with", "transformation" and "transfection"
are
intended to encompass introduction of nucleic acid (e.g. a vector) into a cell
by one of many possible techniques known in the art. Prokaryotic cells can
be transformed with nucleic acid by, for example, electroporation or calcium-
chloride mediated transformation. Nucleic acid can be introduced into
mammalian cells via conventional techniques such as calcium phosphate or
calcium chloride co-precipitation, DEAE-dextran mediated transfection,
lipofectin, electroporation or microinjection. Suitable methods for
transforming
and transfecting host cells can be found in Sambrook et al. (Molecular
Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory
press (1989)), and other such laboratory textbooks.
Suitable host cells include a wide variety of prokaryotic and eukaryotic host
cells. For example, the proteins of the invention may be expressed in
bacterial cells such as E. coli, insect cells (using baculovirus), yeast cells
or
mammalian cells. Other suitable host cells can be found in Goeddel, Gene
Expression Technology: Methods in Enzymology 185, Academic Press, San
Diego, CA (1991).
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The nucleic acid molecules of the invention may also be chemically
synthesized using standard techniques. Various methods of chemically
synthesizing polydeoxynucleotides are known, including solid-phase synthesis
which, like peptide synthesis, has been fully automated in commercially
available DNA synthesizers (See e.g., Itakura et al. U.S. Patent No.
4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura U.S.
Patent Nos. 4,401,796 and 4,373,071).
The invention also provides nucleic acids encoding fusion proteins comprising
a novel protein of the invention and a selected protein, or a selectable
marker
protein.
Another aspect of the present invention is a cultured cell comprising at least
one of the above-mentioned vectors.
A further aspect of the present invention is a method for preparing a
minimalist bZIP protein comprising culturing the above mentioned cell under
conditions permitting expression of the minimalist bZIP protein from the
expression vector and purifying the minimalist bZIP protein from the cell.
Uses of the Minimalist bZIP proteins of the Invention:
Mutant proteins that interfere with Myc-Max recognition of the E-box may
interfere with Myc's disease promoting activities. Accordingly, the invention
provides a use of the minimalist bZIP proteins of the invention able to bind
to
an E-box target DNA sequence for repressing myc-related transcriptional
activation.
Myc is an oncoprotein known to be overexpressed in a wide variety of human
diseases, including 80% breast, 70% colon, and 90% gynecological cancers,
50% hepatocellular carcinomas and a variety of hematological tumors
(Gardner, L. et al., Encyclopedia of Cancer, Bertino, J. R. Ed., 2002,
Academic Press).
Accordingly, in one embodiment, the invention provides the use of the
minimalist bZIP proteins able to bind to an E-box target DNA sequence for
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treating cancer. In antoher embodiment, the invention provides a method of
treating cancer comprising administering an effective amount of a minimalist
bZIP protein able to bind to an E-box target DNA sequence to a mammal in
need thereof. In one embodiment, the cancer is selected from the group
consisting of breast cancer, colon cancer, gynecological cancer,
hepatocellular carcinomas, hematological tumors, Burkitt lymphoma,
neuroblastoma and small cell lung cancer. In another embodiment, the
mammal is human.
As discussed above, the minimalist bZIP protein may also be fused to a
repressor of transcription. Accordingly, the invention provides the use of a
minimalist bZIP protein able to bind to an E-box target DNA sequence fused
to a repressor for repressing myc-related transcriptional activation and/or
for
treating cancer. In another embodiment, the invention provides a method of
treating cancer comprising administering an effective amount of a minimalist
bZIP protein able to bind to an E-box target DNA sequence fused to a
repressor to a mammal in need thereof.
The Myc, Max and Mad transcription factor network are critical for control of
normal cell proliferation and differentiation. Accordingly, the invention also
provides the use of the minimalist bZIP proteins able to bind to an E-box
target DNA sequence for controlling cell proliferation and/or differentiation.
In
another embodiment, the invention provides the use of a minimalist bZIP
protein able to bind to an E-box target DNA sequence fused to an activation
domain for activating cell proliferation and/or differentiation. In yet
another
embodiment, the invention provides the use of a minimalist bZIP protein able
to target an E-box target DNA sequence fused to a repressor for repressing
cell proliferation and/or differentiation.
In another embodiment, the invention provides for a method of regulating a
desired gene by inserting at least one E-box sequence upstream of the
desired gene and introducing a minimalist bZIP protein capable of recognizing
the inserted E-box sequence, wherein the minimalist bZIP protein then acts to
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regulate the expression of the gene. The minimalist bZIP protein used in the
method can be further fused to an activation or repressor domain.
The Ahr/Arnt system is notable for its possible role in disease pathways given
its role in mediating signal transduction by dioxins and related polycyclic
aromatic hydrocarbons. Given that the endogenous ligand for the dioxin
receptor is not yet known, the minimalist bZIP proteins of the invention that
target the XRE1 site are useful for regulating the dioxin pathway.
2,3,7,8-tetrachlorodibenzo-p-dioxin, commonly referred to as TCDD or dioxin,
produces a variety of highly toxic effects, including chloracne,
teratogenesis,
tumor promotion, and immunotoxicity (Whitelaw, M. et al., Mol. Cell Biol.
1993, 13, 2504-2514; Poland, A. and Knutson, J. C., Ann. Rev. Pharmacol.
Toxicol. 1982, 22, 517). Dioxin is an industrial byproduct produced during
herbicide manufacture, the bleaching of paper pulp, and combustion of
chlorinated organic materials. Dioxin can accumulate in the environment;
although it decomposes rapidly in organic solution under artificial or natural
light, no photodecomposition occurs in aqueous environments or on wet or
dry soil (Crosby, D. G., et al., Science, 1971, 173, 748-749). The resistance
of dioxin to metabolic degradation and the stability of the dioxin-receptor
complex may account for its persistence and toxicity (Johnson, E. F., Science,
1991, 252, 924).
Animal studies have proven this ubiquitous pollutant to be extremely lethal,
perhaps the most powerful carcinogen tested (Roberts, L., Science, 1991,
251, 624-626; Gray, L. E. Jr. and Ostby, J. S., Toxicol. Appl. Pharmacol.,
1995, 133, 285-294]. Human effects, however, have been subject to wide
controversy, especially in studies concerning dioxin-tainted Agent Orange
used by the United States during the Vietnam War as a defoliant.
In 1991, the National Institute of Occupational Safety and Health published an
exhaustive examination of 5172 male chemical workers exposed to dioxin on
the job from 1942 to 1982 (Fingerhut, M. A., et al., N. Engi. J. Med., 1991,
324, 212-218). The low exposure cohort worked for less than one year in a
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dioxin-tainted occupation, the high exposure cohort for at least a year; the
latency period for cancer occurrence was at least twenty years (Roberts, L.,
Science, 1991, 251, 624-626). The low-exposure group showed no increased
risk in cancer, despite exposure to dioxin at levels 90 times higher than that
for the general population. The high exposure group, however, was estimated
to be exposed to dioxin levels 500 times higher than that for the general
population and had nearly a 50% increase in cancer mortality, mostly in soft
tissue sarcomas and, unexpectedly, respiratory cancer.
Dioxin's disease/cancerous effects can be mediated by aryl hydrocarbon
receptor. This receptor must first bind the ligand to initiate its detrimental
effects. A receptor-binding model for dioxin may explain the result that the
low-exposure cohort in the NIOSH study discussed above exhibited no
increase in cancer risk. Response to dioxin increases slowly at low dioxin
concentrations but elevates rapidly after reaching a critical concentration
(dissociation constant, Kd). Thus, instead of a linear model for dioxin
toxicity,
the binding curve would be sigmoidal, and there may exist a practical
threshold below which dioxin concentrations may be deemed to be "safe."
This receptor-mediated mechanism for dioxin action provides a target for
monitoring levels of ligand.
The AhR mediates signal transduction by dioxins and related polycyclic
aromatic hydrocarbons (PAHs), including benzo[a]pyrenes found in cigarette
smoke and smog, heterocyclic amines found in cooked meat, and
polychlorinated biphenyis (PCBs) (Fisher, J. M. et al., Mol. Carcinogen.,
1989,
1, 216-221). In analogy to the glucocorticoid receptor, the latent dioxin
receptor is found associated with heat-shock protein hsp90 in the cytosol
(Cadepond, F., et al., J. Biol. Chem. 1991, 266, 5834-5831). Ligand binding
induces release of hsp90, nuclear translocation of the AhR (Pollenz, R. S., et
al., Mol. Pharmacol., 1995, 45, 428-438), and dimerization with the nuclear
protein Arnt (Reyes, H., et al., Science, 1992, 256, 1193-1195); this
activated
complex then binds specific DNA sites (xenobiotic response elements or
XREs) and activates gene transcription (Wu, L. and Whitlock, J. P. Nucl.
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Acid. Res. 1993, 21, 119-125; Fujisawa-Sehara, A. et al., Nucl. Acid. Res.
1987, 95, 4179-4191). Dioxins are very potent inducers of transcription target
genes, including cytochrome P4501A1, which codes for aryl hydrocarbon
hydroxylase, a catalyst for oxygenation of polycyclic hydrocarbons to phenois
and epoxides, some of which are mutagenic and carcinogenic (Whitelaw, M.
et al., Mol. Ce118io1. 1993, 13, 2504-2514).
Accordingly, the invention also provides the use of a minimalist bZIP protein
able to bind to an XRE1 target DNA sequence for treating cancer. In another
embodiment, the invention provides a method of treating cancer comprising
administering an effective amount of a minimalist bZIP protein able to bind to
an XRE1 target DNA sequence to a mammal in need thereof. In another
embodiment, the invention provides the use of a minimalist bZIP protein able
to bind to an XRE1 target DNA sequence fused to a repressor domain for
treating cancer. In yet another embodiment, the invention provides a method
of treating cancer comprising administering an effective amount of a
minimalist bZIP protein able to bind to an XRE1 target DNA sequence fused
to a repressor domain to a mammal in need thereof. In one embodiment, the
cancer is a soft tissue carcinoma or respiratory cancer. In another
embodiment, the mammal is human.
Since the minimalist bZIP proteins of the invention bind to specific DNA
sequences, the proteins may be used as targeting agents. In another
embodiment, the minimalist bZIP proteins are fused to a drug. For example,
the drug may be an anti-cancer agent. In another embodiment, the invention
provides a method of treating cancer comprising administering an effective
amount of a minimalist bZIP protein fused to a drug to a mammal in need
thereof.
Additionally, these a-helical, bZIP/bHLH hybrids have agricultural and
biological (nonhuman) applications. For example, the plant G-box is 5'-
CACGTG, the same sequence as the mammalian E-box; the G-box refers
specifically to plants. The G-box is bound by bZIP proteins; however, the
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bZIP/bHLH hybrids of the present invention also bind the G-box, as it is
identical to the E-box. Plants use bZIP proteins ubiquitously; Arabidopsis
thaliana has four times as many bZIP proteins as do humans and yeast
(Jakoby, M. et al., Trends Plant Sci., 2002, 7, 106-111). In Arabidopsis, many
G-box regulated genes are linked to ultraviolet and blue light signal
transduction and regulation of light-sensitive promoters, and there is
evidence
that some GBF-like proteins (G-box binding factor), including ROM1 and
ROM1, may regulate storage protein expression, and therefore, play a role in
seed maturation. Control of storage protein expression may achieve
healthier, more vigorous, larger plants and crops. In addition, the E-box/G-
box can be cloned upstream of a gene that one wishes to control: hence, a
genetically modified plant. By extension, the genetically modified organism
does not have to be a plant, but it could be an animal; these proteins can
also
have veterinary applications in cases of genes that fortuitously possess an E-
box (or E-box-related) or XRE1 (or XRE1-related) sequence in the promoter.
This plant could then be engineered to express a bHLH/bZIP hybrid that
would then target the cloned E-box/G-box, thereby, regulating the desired
gene. Numerous other plant applications are contemplated by the use of
minimalist bZIP proteins including controlled regulation of proteins to either
enhance or decrease the growth of specific plant organs and tissues by
reducing the expression or effectiveness of endogenous growth-associated
proteins. The regulation of gene expression by the use of minimalist bZIP
proteins and insertions of E-box sequences can result in the modification of
various traits, such as durability, size, succulence, texture, and longevity.
It is
envisioned that both monocotyledonous and dicotyledonous plants can be
used, as well as stem and leaf vegetables (e.g., broccoli, lettuce, spinach,
cabbage), fruit and seed vegetables (e.g., tomato), fiber crops and cereals
(e.g., corn, oats, wheat), and forest and ornamental crops (e.g., cotton). For
example, regulation of grape growth in the wine industry in order to provide
the ability to fight common grape afflictions, such as phylloxera, or to
regulate
leaf, root, stem or petiole growth for improved cabbage, spinach, celery,
beets, soybeans, sugarcane, flower stalks can be envisioned.
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The invention also provides a pharmaceutical composition for treating a
mammal with cancer comprising a minimalist bZIP protein of the invention and
a pharmaceutically acceptable carrier, diluent or excipient. In a preferred
embodiment, the mammal is human. In one embodiment, the minimalist bZIP
protein recognizes an E-box/G-box DNA sequence. In a specific embodiment,
the cancer is selected from the group consisting of breast cancer, colon
cancer, gynecological cancer, hepatocellular carcinomas, hematological
tumors, Burkitt lymphoma, neuroblastoma and small cell lung cancer. In
another embodiment, the minimalist bZIP protein recognizes an XRE site. In a
specific embodiment, the cancer is a soft tissue carcinoma or respiratory
cancer. In a further embodiment, the minimalist bZIP protein of the
pharmaceutical composition is fused to a repressor.
The proteins of the invention may be formulated into pharmaceutical
compositions for administration to subjects in a biologically compatible form
suitable for administration in vivo. By "biologically compatible form suitable
for administration in vivo" is meant a form of the substance to be
administered
in which any toxic effects are outweighed by the therapeutic effects. The
substances may be administered to living organisms including humans and
animals. Administration of a therapeutically active amount of the
pharmaceutical compositions of the present invention is defined as an amount
effective, at dosages and for periods of time necessary to achieve the desired
result. For example, a therapeutically active amount of a substance may vary
according to factors such as the disease state, age, sex, and weight of the
individual, and the ability of protein to elicit a desired response in the
individual. Dosage regime may be adjusted to provide the optimum
therapeutic response. For example, several divided doses may be
administered daily or the dose may be proportionally reduced as indicated by
the exigencies of the therapeutic situation.
The active substance may be administered in a convenient manner such as
by injection (subcutaneous, intravenous, intramuscular, etc.), oral
administration, inhalation, transdermal administration (such as topical cream
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or ointment, etc.), or suppository applications. Depending on the route of
administration, the active substance may be coated in a material to protect
the
compound from the action of enzymes, acids and other natural conditions
which may inactivate the compound.
The compositions described herein can be prepared by per se known
methods for the preparation of pharmaceutically acceptable compositions
which can be administered to subjects, such that an effective quantity of the
active substance is combined in a mixture with a pharmaceutically acceptable
vehicle. Suitable vehicles are described, for example, in Remington's
Pharmaceutical Sciences (Remington's Pharmaceutical Sciences (2000 - 20th
edition) Mack Publishing Company). On this basis, the compositions include,
albeit not exclusively, solutions of the substances in association with one or
more pharmaceutically acceptable vehicles or diluents, and contained in
buffered solutions with a suitable pH and iso-osmotic with the physiological
fluids.
Methods of Evolving Better DNA Binding Minimalist bZIP Proteins
In order to examine the binding activities of the minimalist bZIP proteins in
vivo, a useful strategy based on the yeast one-hybrid system was used.
Examination of in vivo binding was chosen, rather than in vitro, in order to
mimic the native cellular environment. Additionally, the system allows for in
vivo directed evolution of proteins targeting specific DNA sites:
particularly,
bZIP-like homodimers that bind the E-box.
An excellent assay for monitoring in vivo interactions between proteins and
DNA is provided by the yeast one-hybrid system (Kumar, R. et al., J. Biol.
Chem., 1996, 271, 29612-29618; Chen, X. et al., Nature, 1996, 383, 691-
696). The basis for the yeast one-hybrid assay is the useful fact that
eukaryotic transcriptional activators comprise physically and functionally
independent DNA-binding domains and activation domains. Therefore, a
hybrid protein can be constructed that comprises a DNA-binding domain
fused to a suitable transcriptional activator domain. This hybrid can then be
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assayed for binding to a specific DNA target, because successful protein-DNA
complexation results in transcription of one or more reporter genes. Thus, the
yeast one-hybrid assay is particularly useful for isolating proteins that bind
a
specific DNA target; for instance, this system can be used to map the DNA-
binding domains of previously known proteins as well as discovery of new
proteins capable of recognizing a desired target site.
Because the yeast one-hybrid assay is an in vivo system, it offers the
advantage of examination of protein-DNA recognition in the native eukaryotic
environment, in contrast to other in vitro surface display technologies
(Benhar,
I., Biotech. Adv., 2001, 19, 1-33). Both in vivo and in vitro binding assays,
such as the yeast one- and two-hybrid assays and phage display, enable
monitoring of specific protein-DNA and protein-protein interactions. The main
application of such systems is their use for selection of individual targets
from
large libraries of different clones. Diversity in these libraries can be
generated
by various means, such as using degenerate oligonucleotides for
randomization of large sections of a gene's coding sequence (Wang, B. S.
and Pabo, C. 0., Proc. Natl. Acad. Sci. USA, 1999, 96, 9568-9573) or
mutagenic PCR protocols to generate small numbers of random mutations in
genes (Cherry, J. R. et al., Nat. Biotech, 1999, 17, 379-384). Similarly, a
directed evolution process, in which molecules with desired traits can be
evolved and isolated, can be achieved by starting with large, diverse
libraries
of mutants followed by an appropriate selection procedure. Multiple rounds of
directed evolution can be performed to give improvement in the desired
molecular function.
Creating large libraries of mutant clones can be a tedious and difficult task.
This is partially due to the low efficiency of transformation obtained with
ligated plasmid vectors-typically one to three orders of magnitude lower
transformation efficiency than that obtained with supercoiled plasmids
(Tobias, A. V. in Directed Evolution Library Creation, Arnold, F. H. and
Georgiou, G., Eds, 2003, Humana Press, Totowa, NJ). An excellent
alternative to classical cloning methods involving ligated vectors is cloning
by
CA 02525255 2005-11-03
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use of homologous recombination (Aylon, Y. and Kupiec, M., Mut. Res., 2004,
566, 231-248). Whereas this method is not applicable in bacteria, due to low
frequency of recombination, it is very useful in yeast. In yeast, homologous
recombination can substitute for ligation in order to give very high
transformation frequencies (Butler, T. and Alcalde, M., in Directed Evolution
Library Creation, Arnold, F. H. and Georgiou, G., Eds, 2003, Humana Press,
Totowa, NJ). In homologous recombination, mutant gene inserts are
cotransformed with linearized plasmid; the end sequences on the inserts and
linearized plasmid are homologous. Yeast can then perform homologous
recombination on the inserts and plasmids to form closed circular plasmids.
Another advantage is that the homologous recombination procedure also
allows the mutated linear PCR products to recombine amongst themselves
prior to creation of circular plasmid (Swers, J. S., et al., Nucl. Acids.
Res.,
2004, 32, 36-44). This process drives shuffling of acquired mutations within
the PCR products. Thus, successive rounds of directed evolution using
homologous recombination and appropriate selection steps leads to loss of
unwanted mutations and accumulation of positive ones-this procedure
resembles the natural evolution process.
Accordingly, the minimalist bZIP proteins of the invention can be evolved by:
(a) linearizing DNA duplexes carrying a minimalist bZIP protein sequence;
(b) subjecting the DNA in step (a) to mutagenic PCR to create a mutated
minimalist bZIP library;
(c) linearizing an appropriate yeast vector that has anchors homologous with
the genes encoded in the minimalize bZIP library in (b);
(d) cotransforming the products of step (c) with the linearized vector into
yeast
with a genome integrated with target DNA sites; and
(e) plating on selective medium;
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wherein the colonies that grow in the selective medium have evolved
minimalist bZIP proteins that bind to the target DNA site.
The above method can further comprise repeating steps (a) to (e) with the
sequence encoding the evolved minimalist bZIP protein.
The following non-limiting examples are illustrative of the present invention:
EXAMPLES
Generation of Max-C/EBP bZIP minimalist proteins:
The basic region of Max was fused to the leucine zipper of C/EBP. Three
different fusion proteins were constructed Max-1, -2, -3 which differ by one
amino acid in order to leave some flexibility in the hinge region-where the
zipper is fused to the basic region, which splays out to straddle DNA. Table I
shows the sequences of Max-1, -2 and -3-C/EBP with two different hinge
regions, RIR and GIR, which are expected to have different helical
capabilities. A BamH I site was used for joining the basic regions to the
zipper regions. Because there are -3.5 amino acids per turn in an a-helix,
Max-1, -2, and -3 should be sufficient for generating a protein capable of
targeting the E-box site. Indeed, the Max-1-C/EBP has been evolved into
MM3 which binds to the E-box.
Generation of Arnt-C/EBP bZIP minimalist proteins:
Arnt is a bHLH protein (no leucine zipper). Arnt basic region binds 5'-GTG,
half of the canonical E-box. Native Arnt preferentially heterodimerizes, but
does homodimerize. Three different fusion proteins were constructed Arnt-1, -
2, -3 which differ by one amino acid in order to leave some flexibility in the
hinge region-where the zipper is fused to the basic region, which splays out
to straddle DNA. Table 2 shows the sequences of Arnt-1, -2 and -3-C/EBP
with two different hinge regions, RIR and GIR, which are expected to have
different helical capabilities.
Desi_gn of Protein Heterodimers that Target Asymmetric DNA Site.
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The xenobiotic response element 1(XRE1) resides in the 5' flanking region of
the CYP9A1 (cytochrome P450) gene. The XRE1 sequence is 5'-
TTGC=GTG. Arnt binds to 5'-GTG, which is half of the E-box sequence 5'-
CAC=GTG. AhR binds to 5'-TTGC. Fortuitously, well-characterized bHLH
and bZIP proteins bind to these same half sites. The bHLH protein Max binds
to 5'-CAC=GTG; the bZIP protein C/EBP binds 5'-TTGC=GCAA (Agre, P. et
al., Science 1989, 246, 922-926; Landschulz, W. H. et al., Science 1988, 240,
1759-1764). A heterodimer comprising the Max and C/EBP basic regions
may therefore recognize 5'-TTGC=GTG, same as the AhR-Arnt heterodimer.
Because of the wealth of information on C/EBP and Max, including Max
bHLH-DNA crystal structures (Ferre-D'Amare, A. R. et al., Nature 1993, 363,
38-45; Ellenberger, T. et al., Genes Dev. 1994, 8, 970-980), these proteins
were a sound first-generation choice.
We use the leucine zippers from bZIP proteins Jun and Fos to ensure
heterodimerization. In the crystal structure (Glover, J. N. M. and Harrison,
S.
C., Nature 1995, 373, 257-261), the Fos-Jun heterodimer is oriented on the
AP-1 DNA site (5'-TGACTCA) such that the Fos basic region binds to 5'-
TGAC and Jun binds 5'-CTCA. Therefore, the C/EBP basic region is fused to
the Fos zipper, whereas the Max basic is fused to the Jun zipper (Table 3).
These fusions should maintain proper orientation for heterodimerization such
that binding will occur at 5'-TTGC=GTG, rather than 5'-GTG=TTGC.
Incidentally, although Jun and Fos preferentially heterodimerize, Jun can
homodimerize, whereas Fos does not. Both Max and Arnt can homodimerize,
so the Max-Jun and Arnt-Jun homodimers that may occur will be reflective of
the natural system.
Second Generation Hybrids: AhR or Amt basic region, Fos or Jun
leucine zipper
The AhR bHLH is promiscuous in dimerization partners; the AhR bHLH/PAS
construct, however, specifically heterodimerizes with only the Arnt bHLH/PAS,
and therefore, the PAS domain confers dimerization specificity. The proteins
CA 02525255 2005-11-03
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of the invention do not contain the PAS domain, but do use the Jun and Fos
leucine zippers to promote heterodimerization.
Hybrids are constructed comprising the basic regions of human AhR
(Dolwick, K. M. et al., Mol. Pharm., 1993, 44, 911-917) and human Arnt
(Hoffman, E. C., et al., Science, 1991, 252, 954) with the leucine zippers of
Fos and Jun, respectively (Table 4). The same flexibility in the fusion
junction
is explored in these hybrids as well. Thus, portions of Helix 1 in the AhR and
Arnt sequences are used to lengthen the hinge between the basic region and
zipper. This junction may not be as straightforward as for the well-
characterized bHLH proteins used in the first-generation studies, as AhR and
Arnt are bHLH/PAS proteins (Hogenesch, J. B. et al., J. Biol. Chem., 1997,
272, 8581-8593; Lindebro, M. C. et al., EMBO J., 1995, 14, 3528-3539),
which are closely related, but not identical, to the bHLH and bHLHZ motifs.
The reference sequences are shown in Table 5.
Comparison of protein-DNA interactions: bHLH bZIP and the unknown
AhR
Arnt is believed to form a complex with the 5'-GTG site resembling that of
Max, E47, USF, and MyoD-these are all bHLH or bHLHZ proteins that use
the same basic-region residues to contact the E-box (Swanson, H. I. and
Yang, J.-H., J. Biol. Chem., 1996, 271, 31657-35661). The AhR complex with
5'-TTGC likely represents a unique variant of the bHLH motif; AhR's basic
region is unlikely to be strongly helical, as it contains four prolines and
one
glycine, residues known to be helix breakers (Luque, I. et al., Biochemistry,
1996, 35, 13681-13688). The AhR basic may also not display the
characteristic transition from disordered to stable a-helix upon binding to
specific DNA, as do other known bHLH proteins (Ferre-D'Amare, A. R. et al.,
EMBO J. 1994, 13, 180-189).
That the AhR basic may employ a different mechanism from known bHLH
proteins for DNA recognition expands the present invention's ability to
recognize diverse sequences. Most bZIP and bHLH heterodimers bind half
CA 02525255 2005-11-03
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sites that are palindromic or pseudopalindromic. The AhR-Arnt heterodimer
binds two distinct, unrelated half sites (Rowlands, J. C. and Gustafsson, J.
A.,
Crit. Rev. Toxicol., 1997, 27, 109-134; Bacsi, S. C. et al., Mol. Pharmacol.,
1995, 47, 432-438). Thus, a pair of basic a-helices (or new motifs that AhR
represents) is capable of tremendous molecular diversity in ligand-binding.
= The Max bHLHZ Structure. The structures of bHLH and bHLHZ proteins
in complex with E-box sites show a high level of conservation of specific
protein-DNA interactions. The Max bHLH/ZIP complex with the Class B E-
box shows three highly conserved specific contacts (Table III): His2$ makes a
hydrogen bond to N7 of G3', GIu32 accepts hydrogen bonds from N4 of C3
and N6 of A2, and Arg36 makes a hydrogen bond to N7 of G1' at the dyad
axis. The intact Max structure also shows the same specific contacts
(Brownlie, P. et al., Structure 1997, 5, 509-520), and the USF bHLH/ZIP
complex displays these specific contacts and makes equivalent backbone
contacts to phosphodiester groups with Asn29, Arg33, and Arg35 as does Max
(Ferre-D'Amare, A. R. et al., EMBO J. 1994, 13, 180-189). Both MyoD and
E47 are bHLH proteins that bind the Class A E-box. For MyoD, the contacts
to the outer base pairs are similar to those of Max: GIu32 accepts hydrogen
bonds from N4 of C3 and N6 of A2 (weak, 3.5-3.8 A distance) (Ma, P. C et al.,
Cell 1994, 77, 451-459). This essential glutamic acid is absolutely conserved
in both Class A and B proteins, and the bifurcated interaction with the CA
step
is conserved in all structures discussed. E47 makes this same contact with
GIu32, plus its side chain methylenes make van der Waals contact with the
C5 methyl group on T2' (Ellenberger, T. et al., Genes Dev. 1994, 8, 970-980).
= The MyoD bHLH Structure. The other specific contacts that MyoD bHLH
makes are not identical to Max bHLH/ZIP: Arg25 makes a hydrogen bond to
N7 of G10' and a water-mediated contact to 06 of G10'; Thr29 makes a van
der Waals interaction with T2'-the corresponding amino acids in Max and
USF do not make specific DNA contacts. Notably, Arg25 is buried in the
major groove in MyoD, but in Max, it swings away from the major groove and
makes a phosphodiester contact; in its stead, the highly conserved His28 of
CA 02525255 2005-11-03
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Max (one helical turn from Arg25) contacts N7 of G3' and displaces the Arg25
side chain. Arg3l of MyoD makes electrostatic contacts with phosphodiesters
flanking the E-box and maybe a weak interaction with a flanking adenine; in
Class B proteins Max and USF, the corresponding amino acid is hydrophobic
and makes no contact at all to DNA. Finally, position 36 is critical for
discrimination between the Class A and B E-box sequences. In Class B
proteins Max and USF, Arg36 specifically contacts N7 of G1' at the dyad axis.
In Class A proteins MyoD and E47, position 36 is occupied by Leu and Val,
respectively. Curiously, the MyoD cocrystal structure, shows no contact of
Leu36 whatsover with DNA. When Leu36 is mutated to Arg, MyoD now binds
to the Class B site. So this position is critical for discrimination of the
central
base pairs (Blackwell, T. K. et al., Mol. Cell. Biol. 1993, 13, 5216-5224).
= Comparison of AhR and Arnt with Known Structures: Swanson and
Yang performed extensive mutation and deletion analyses on both the AhR
and Arnt basic regions; they show that Arnt behaves similarly to Class B
proteins Max and USF (Swanson, H. I. and Yang, J.-H., J. Biol. Chem., 1996,
271, 31657-35661). For Arnt, they found that GIu32, Arg35, and Arg36 were
critical for recognition of 5'-GTG, same as Max. They do not discuss His28.
When the Glu32 side chain is shortened by mutation to Asp, or when Arg35
and Arg36 are mutated to Gln, DNA binding is abolished, but
heterodimerization to AhR is unaffected. When Arg33 and Arg34 are mutated
to Gin, DNA-binding is reduced somewhat, so it is likely that these residues
are involved in nonspecific phosphodiester interactions, same as for the
corresponding amino acids in Max, MyoD, and USF.
Unlike Arnt, AhR does not display classic bHLH behavior. When AhR Pro3l
and Ser32 are substituted with Leu and Glu to give a Max-like sequence,
binding is abolished. Replacements at Arg34 and Arg36 also virtually
abolished DNA-binding. When the two prolines in the AhR sequence KPIPAE
(see Table 6) are replaced with alanines, -70% binding is retained, so these
Pro's are not involved in critical interactions. Critical residues for
specific DNA
binding are Pro3l, Ser32, Lys33, Arg34, His35, and Arg36 (Swanson, H. I.
CA 02525255 2005-11-03
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and Yang, J.-H., J. Biol. Chem., 1996, 271, 31657-35661). Although AhR is
similar to other bHLH and bHLHZ proteins in that it uses the same stretch of
amino acids to contact DNA (Table 6), given the four prolines and glycine in
its basic region, AhR must be using a nonhelical DNA-binding structure.
= How do AhR and Arnt Interact with DNA? The absolutely conserved
Asn235 of GCN4 spans the major groove to accept a hydrogen bond from N4
of C3' and donate a hydrogen bond to 04 of T4 (Table 6; Asn235 of GCN4 is
aligned with His28 of Max) (Ellenberger, T. E. et al., Cell 1992, 71, 1223-
1237). This crucial interaction requires that the basic region lie deep in the
major groove and specifies two of four base pairs in each half site. GCN4
Asn235 corresponds to Max His28, as far as comparisons between different
protein families can be made. Asn is capable of a bifurcated hydrogen bond
and can therefore dictate the identities of two base pairs, and this may
explain
how bZIP proteins bind a four bp half site, whereas bHLH proteins bind only
three bp. In GCN4, the methyl side chains of Ala238 and Ala239 make van der
Waals contacts with the C5 methyl groups on T4 and T2'. The highly
conserved GIu32 of Max corresponds in position with Ala239; Glu32 dictates the
outer CA step in Max, much as GCN4 Asn235 dictates the outer TG step.
Noteworthy is the van der Waals contact that the USF GIu32 side chain makes
to thymine, akin to that of Ala238 and Ala239 in GCN4. GCN4 Arg243 makes
bidentate contact with N7 and 06 of G1' in the AP-1 complex (Ellenberger, T.
E. et al., Cell 1992, 71, 1223-1237), and N7 of G1' and the phosphodiester
group of Cl with ATF/CREB (Konig, P. and Richmond, T. J., J. Mol. Biol.
1993). In bHLHZ proteins, the corresponding Arg36 makes a single contact
with N7 of the central G, and Leu36 in the MyoD bHLH makes no DNA
contact. Although the bHLH and bZIP are distinct protein families, their DNA-
binding domains display significant similarity in structure and alignment.
Because the bZIP, bHLH, and bHLHZ all use basic a-helical structures to bind
the major groove, the corresponding amino acids are similarly placed for
DNA-binding function (see alignment in Table 6). Therefore, as long as the
basic regions are properly situated in the major groove, a-helical structure
CA 02525255 2005-11-03
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and DNA-binding function will be retained. The caveat is to maintain proper
orientation for binding; the hinge region is responsible for orienting the
basic
regions, and therefore flexibility is designed into the hinge by generating
variants of each bHLH/bZIP hybrid differing by a single amino acid in the
hinge. Although the AhR basic region is unlikely to have substantial helical
structure, it is possible that the conserved Asn3l in AhR and Sim may also
make a bidentate interaction with DNA, thereby specifying the outer two base
pairs. In order to recognize the XRE1 5'-TTGC sequence, Asn3l needs to
span the major groove to contact 04 of T4 and N6 of A3' to specify the outer
TT step. The inner GC base pairs are recognized by the conserved
Lys/Arg34 and Arg37. Although the Class C protein AhR is unlikely to utilize a
helical structure to bind the major groove, its basic region contains several
conserved amino acids capable of making DNA contacts similar to those
discussed for the bHLH and bZIP.
Further Simplification of the Protein Scaffold with Alanine Mutagenesis
Alanine is substituted in the basic region of the minimalist bZIP proteins of
the
invention (Table 7). Because Arnt is similar to Max and USF, Ala
substitutions for Arnt is more straightforward than for AhR, which is not
helical, but Ala replacements in AhR should become so.
The Ala-mutants Max-13A, C/EBP-18A, Arnt-16A, and AhR-17A are designed
to maintain both specific and nonspecific protein-DNA interactions, akin to
the
GCN4 mutant 1 1A; even more heavily mutated proteins are designed wherein
only specific contacts are conserved, similar to 18A. In Table 7, specific
interactions are boldfaced, nonspecific phosphodiester contacts are
underlined, and proposed alanine substitutions are italicized; the Max
structure and mutagenesis work on AhR and Arnt are the basis for Table 7
(Ferre-D'Amare, A. R., et al. Nature 1993, 363, 38-45. Swanson, H. I. and
Yang, J.-H. J. Biol. Chem. 1996, 271, 31657-31665.) At the bottom of Table
7, the GCN4 sequence is shown as a reference; note that in C/EBP, the
highly conserved position 239 is occupied by Val rather than Ala; Va1239 is
conserved in C/EBP-18A. Most bZIP proteins have A1a239. Johnson has
CA 02525255 2005-11-03
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shown that Va1239 is an important determinant for C/EBP binding to the half
site 5'-TTGC (Johnson, P. F., Mol. Cell. Biol. 1993, 13, 6919-6930). Johnson
generated numerous GCN4-C/EBP hybrids wherein the fusion junctions of the
two proteins varied; Va1239 was critical for discrimination between GCN4 vs.
C/EBP sites. Therefore, another mutant would be C/EBP-19A, in which
Va1239 4 Ala.
Eniarging the DNA-Binding Repertoire: Determinants of Specificity in
bHLH and bHLH/ZIP Proteins
Class A proteins target 5'-CAG=CTG, whereas Class B proteins target 5'-
CAC=GTG. bHLH proteins MyoD and E47 have highly conserved Arg31 and
Leu/VaI36, in contrast to Class B bHLH/ZIP proteins, which contain the
absolutely conserved Arg36 and a hydrophobic amino acid at position 31 (Leu,
Ile, Val, Met-no contact with DNA). MyoD can be changed from Class A to B
specificity by mutating Leu36 to Arg ( Blackwell, T. K. et al., Mol. Cell.
Biol.
1993, 13, 5216-5224). If Max-13A is a functional Class B protein, then Max-
13A-RL may have Class A binding specificity. In this case, Arg31 from MyoD
is also retained, because it is highly conserved, and the MyoD crystal
structure shows that it makes nonspecific interactions with the DNA backbone
plus a weak specific contact in the major groove.
These Ala-based minimalist bZIP proteins and the mutants that switch binding
between C/EBP and GCN4 or Max and MyoD are tests of the protein-design
capabilities of the present invention (Table 8).
Yeast One-Hybrid Assay for Monitoring the In Vivo interactions between
Proteins and DNA
Construction of Reporter Strain
A reporter strain was constructed such that the E-box target, 5'-CACGTG,
resides upstream of the HIS3 reporter gene. The bHLH/bZIP hybrid was
fused to the GAL4 transcriptional activation domain so that if a hybrid binds
the E-box, the HIS3 protein will be expressed, thus allowing yeast to survive
CA 02525255 2005-11-03
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under conditions of histidine auxotrophy. Four tandem copies of the E-box
(as shown in Table 9) were cloned into the pHISi-1 integrating reporter vector
(Matchmaker One-Hybrid System, Clontech). After insertion of the E-box
insert, the pHISi-1 vector was linearized and incorporated into the yeast
genome by homologous recombination to generate Saccharomyces
cerevisiae YM4271[pHlSi-1/E-box]. To assess background due to the
reporter, 3-aminotriazole (3-AT) was used as a competitive inhibitor of the
HIS3 protein. Because it is possible that the reporter may be activated by
endogenous factors, YM4271 [pHISi-1/E-box] was subjected to titration with
varying amounts of 3-AT to measure the concentration of 3-AT sufficient for
suppression of background growth. Results demonstrate that 10 mM 3-AT
suppresses background expression.
The recombinant plasmid pGAD424 having the Arntl-C/EBP (SEQ ID NO. 7)
insertion was transformed into the reporter strain and plated on SD -His -Leu
with 10mM3-AT to test for binding activity (Figure 2A). The vector alone was
transformed as a negative control (Figure 2B). The results show that the
Arntl-C/EBP minimalist bZIP protein was able to bind to the E-box target DNA
sequence.
Evolution of the Minimalist bZIP proteins
The minimalist bZIP protein carrying the basic region of Max, a hinge region
and the leucine zipper domain of C/EBP was evolved into better binders of the
E-box DNA sequence by use of a modified yeast one-hybrid assay, in which
mutated PCR fragments were cloned via homologous recombination. A
schematic of the process is shown in Figure 3.
These resultant new protein constructs may compete efficiently with the Myc-
Max heterodimer for binding the E-box site and would be therefore able to
repress myc transcriptional activity and control the aberrant activity of myc
upon oncogenic transformation. Because these fusion proteins do not contain
the native Max HLHZ dimerization domain, as it has been replaced by the
C/EBP leucine zipper, they are unable to heterodimerize with Myc.
CA 02525255 2005-11-03
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MM3 Protein
Construction of Protein Library
The gene for Max-C/EBP served as the template for mutagenic PCR for
generation of the protein library. PCR reaction conditions were adjusted to
minimize mutational bias and to yield 1-3 mutations/gene. The mutated Max-
C/EBP genes were inserted into vector pGAD424, which carries a GAL4
activation domain and LEU2 selection marker (Matchmaker One-Hybrid
System, Clontech).
The original Max-C/EBP hybrid, as shown in Table 10, was tested in the
standard yeast one-hybrid assay using the reporter strain described above,
and the binding was undetectable. The binding was undetectable likely due
to the fact that the E-box used lacks flanking regions and also based on the
spacing between the tandem repeats. For example, two other E-box variants,
the Max E-box (favored target site for Max) and Arnt E-box (favored target
site
for Arnt) are also shown in Table 9. Although Max and Arnt both target the
core E-box (5'-CACGTG), they have flanking sequence preferences.
Additionally, the spacing between the four E-boxes as denoted by N(o, 2, 4, 8)
may play a role.
Therefore, the Matchmaker One-Hybrid System from Clontech was modified
in order to perform directed evolution. Vector pGAD424 was linearized and
cotransformed with an excess of mutagenized Max-C/EBP genes. These
mutant PCR products share a 48 base-pair homology with both 5' and 3' ends
of the linearized pGAD424 vector. Approximately 106 independent clones
were generated during one round of selection.
Library Screening
Transformation of the yeast cells was performed by electroporation.
Following electroporation, cells were plated on minimal selective medium
lacking leucine and histidine with the appropriate amount of 3-AT to suppress
CA 02525255 2005-11-03
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background. Plasmid pGAD424 was also transformed as a negative control;
the activation domain alone did not activate the reporter system.
Selection and Validation of Positive Clones
In order to confirm positive clones, that is, those clones expressing protein
that bind the DNA target site, a number of validation experiments were
performed. Positive colonies indicating potential protein-DNA recognition at
the E-box appeared after 4-6 days incubation. Colonies were considered
positive if their diameters exceeded 2 mm. Only one grew after replating.
Plasmid DNA from this positive clone was transformed into the control yeast
strain containing pHISi-1 plasmid YM4271[pHISi-1], with no integrated target
DNA, to test specific binding to E-box. This serves as a negative control to
confirm that the selected protein is unable to activate the HIS3 reporter in
the
absence of target DNA. After successfully passing these two validations,
plasmid DNA was sequenced. The sequence is shown in Table 10 as MM3
(mutant Max 3).
The sequence demonstrates that there has been a frameshift resulting in 8
different amino acids in the C-terminal end of the basic region compared to
the original Max1-C/EBP minimalist protein sequence. This change would
affect spacing and orientation. The changes make sense because they are
good alpha-helix formers, one basic residue (R) which is good for making an
electrostatic interaction with DNA (maybe far from DNA, but reasonable), and
two hydrophilic residues (S and T) that help solubility in water. The sequence
also optionally has a mutation in the leucine zipper domain as shown in Table
10.
To reconfirm that the plasmid is truly the source of protein that binds E-box
and activates reporter, the sequenced plasmid was again transformed into
YM4271[pHISi-1/E-box] and assayed for growth under library screening
conditions. Plasmid was extracted from colonies and sequenced a second
CA 02525255 2005-11-03
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timee The second sequence matched the first sequence for MM3, thereby
confirming the result.
A plasmid containing just the C/EBP leucine zipper was constructed to test
the indispensability of the basic region for DNA binding. Although the C/EBP
zipper is expected to play some role in aiding DNA binding, for the well-
structured, a-helical zipper helps to stabilize the more disordered basic
region, the zipper itself is not part of the DNA-binding domain of the bZIP.
This control containing just the leucine zipper showed no colony growth as
expected.
The MM3 is a stronger binder of the E-box than Max-C/EBP (Figure 4) in this
assay; because the Yl H assay is not quantitative, it is not possible to say
how
strongly MM3 binds E-box. yeast cells expressing MM3 were plated on plates
containing 0-60 mM 3-AT to test the strength of binding between MM3 and E-
box. Since 3-AT inhibits HIS3 protein necessary for cell survival under
histidine auxotrophy, cell growth on higher concentrations of 3-AT
demonstrate strong binding of MM3 to E-box. Even at 60 mM 3-AT,
significant colony growth occurs after four days.
MM3 was discovered after only one round of evolution; further evolution may
uncover better E-box binding mutants.
While the present invention has been described with reference to what are
presently considered to be the preferred examples, it is to be understood that
the invention is not limited to the disclosed examples. To the contrary, the
invention is intended to cover various modifications and equivalent
arrangements included within the spirit and scope of the appended claims.
-43-
Table 1: Max basic repion, C/EBP leucine zipper (with RIRIGIR linker)
Maxl- ADKRAHHNALERKRRDHIKDSFHS-RIR-LEQKVLELTSDNDRLRKRVEQLSRELDTL SEQ ID No. 1
C/EBP R
Max2- ADKRAHHNALERKRRDHIKDSFHSL-RIR-LEQKVLELTSDNDRLRKRVEQLSRELDTL SEQ ID No. 2
C/EBP(R)
Max3- ADKRAHHNALERKRRDHIKDSFHSLR-RIR-LEQKVLELTSDNDRLRKRVEQLSRELDTL SEQ ID No.
3
C/EBP(R)
Maxl- ADKRAHHNALERKRRDHIKDSFHS-GIR-LEQKVLELTSDNDRLRKRVEQLSRELDTL SEQ ID No. 4
0
C/EBP G
cn
cn
Max2- ADKRAHHNALERKRRDHIKDSFHSL-GIR-LEQKVLELTSDNDRLRKRVEQLSRELDTL SEQ ID No. 5
N
N
C/EBP(G U'I
L"
Max3- ADKRAHHNALERKRRDHIKDSFHSLR-GIR-LEQKVLELTSDNDRLRKRVEQLSRELDTL SEQ ID No.
6
C/EBP(G) cn ~
Note: RIR/GIR spacer added for facile cloning (BamH / site for joining basics
and zippers).
w
-44-
Table 2: Arnt basic region, C/EBP leucine zipper (with R/R/GIR linker)
Arntl- KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITE-RIR- SEQ ID No. 7
C/EBP(R) LEQKVLELTSDNDRLRKRVEQLSRELDTL
Arnt2- KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITEL-RIR- SEQ ID No. 8
C/EBP R) LEQKVLELTSDNDRLRKRVEQLSRELDTL
Arnt3- KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITELS-RIR- SEQ ID No. 9
C/EBP(R) LEQKVLELTSDNDRLRKRVEQLSRELDTL
Arntl- KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITE-GIR- SEQ ID No. 10
C/EBP(G) LEQKVLELTSDNDRLRKRVEQLSRELDTL
Arnt2- KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITEL-GIR- SEQ ID No. 11
U9
C/EBP G LEQKVLELTSDNDRLRKRVEQLSRELDTL N
cn
N
Arnt3- KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITELS-GIR- SEQ ID No. 12
C/EBP(G LEQKVLELTSDNDRLRKRVEQLSRELDTL o
0
cn
r
r
i
0
w
-45-
Table 3: First Generation Fusion Proteins: C/EBP or Max basic region. Fos or
Jun leucine zipper.Dashes within protein sequences are place holders for
sequence alignment purposes. Highly
conserved amino acids are in bold. The putative basic helix-loop-helix is
marked. The basic regions
are aligned at highly conserved positions 32 and 36 using numbering for Max.
basic 32 36 ~ ZIP SEQ ID
No.
*C/EBP-Fos SNEYRVRRERNNIAVRKSRDKAKQRNVE---
LEAETDQLEDEKSALQTEIANLLKEKEKLEFILAAHRP 13
Maxl-Jun ADKRAHHNALERKRRDHIKDSFHS---LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVN 14
Max2-Jun ADKRAHHNALERKRRDHIKDSFHSL-LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVN 15
Max3-Jun ADKRAHHNALERKRRDHIKDSFHSLR-LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVN 16
*replace Q with E in the ZIP for cloning with Xho I enzyme.
O
U9
U9
U9
U9
O
O
U9
F'
F'
I
O
W
-46-
Table 4: Second Generation Fusion Proteins: AhR or Arnt basic region, Fos or
Jun leucine zipper.
Dashes within protein sequences are place holders for sequence alignment
purposes. Highly conserved
amino acids are in bold. The putative basic helix-loop-helix is marked. The
basic regions are aligned at
highly conserved positions 32 and 36 using numbering for Max.
basic 32 36 ~ ZIP SEQ
ID No.
AhR1- ASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDR---
LEAETDQLEDEKSALQTEIANLLKEKEKLEFILAAHRP 17
Fos
AhR2- ASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDRL--
LEAETDQLEDEKSALQTEIANLLKEKEKLEFILAAHRP 18
Fos
AhR3- ASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDRLA-
LEAETDQLEDEKSALQTEIANLLKEKEKLEFILAAHR 19
Fos
0
*replace Q with E in the ZIP for cloning with Xho I enzyme. N
cn
N
U9
U9
basic 32 36 / ZIP SEQ
ID No.
cn
Arntl KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITE---
LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNH 20
-Jun
Arnt2 KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITEL--
LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVN 21 ow
-Jun
Arnt3 KFLRCDDDQMSNDKERFARENHSEIERRRRNKMTAYITELS-
LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVN 22
-Jun
-47-
Table 5 Reference Sequences: Dashes within protein sequences are place holders
for sequence
alignment purposes. Highly conserved amino acids are in bold. The putative
basic helix-loop-helix is
marked.
basic ~ Helix I ~ loop ~ Helix II SEQ IDNO.
AhR ASRKRRKPVQKTVKPIPAEGIKSNPSKRHR-DRLNTELDRLASLLPF-PQDVINKLDKL-
SVLRLSVTYLRAKSFFDV 23
Arnt KFLRCDDDQMSNDKERFARENHSEIERRRR-NKMTAYITELSDMVPT-CSALARKPDKL-
TILRMAVSHMKSLRGTGNT 24
0
basic ~ ZIP SEQ ID NO.
cn
N
U9
Fos KRRIRRERNKMAAAKCRNRRRELTDT-LQAETDQLEDEKSALQTEIANLLKEKEKLEFILAAHRP 25
Jun KAERKRMRNRIAASKCRKRKLERIAR-LEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVN 26 "'
U9
F-'
F-'
-48-
Table 6: Sequence alignment of basic regions of bHLH, bHLHZ, and bZIP
proteins. Numbering is same as that for
Max (Ferre-D'Amare, A. R. et al., Nature 1993, 363, 38-45). Highly conserved
amino acids are in bold. Adapted
from (Swanson, H. I., et al., J. Biol. Chem., 1995, 270, 26292-26302).
Basic Regioas(PartiaZ) DNA binding sites
Class B 25 30 321 SEQ ID No.
Max ADKRAHHNALERKRR 5'-CAC=GTG 27
Myc NVKRRTHNVLERQRR 28
USF EKRRAQHNEVERRRR 29
TFE3 RQKKDNHNLIERRRR 30
TFEB RQKKDNHNLIERRRR 31
Arnt RFARENHSEIERRRR 32
CONSENSUS --BB--HN--ERRRR N
cn
Class A 321 SEQ ID No. Ln
MyoD ADRRKAATMRERRRL 5'-CAG=CTG 33 'n
E47 RERRMANNARERVRV 34
AP4 RIRREIANSNERRRM 35
E12 KERRVANNARERLRV 36 I Tall VVRRIFTNSRERWRQ 37
CONSENSUS --RR---N-RER-R-
w
Class C 4 3 21 SEQ ID No.
AhR KPIPAEGIKSNPSKRHRD 5'-T(C/T)GC half site 38
Sim MKEKSKNAARTRRE 5'-GT(A/G)C half site 39
CONSENSUS ------N--B--R-
bZZP 235 4321 SEQ ID NO.
GCN4 DPAALKRARNTEAARRSR 5'-TGAC half site 40
-49-
Table 7: Alanine-based mutants. Numbering is same as that for Max (Ferre-
D'Amare, A. R. et al., Nature
1993, 363, 38-45).
Basic Helix I
25 30 1
Max ADKRAHHNALERKRRDHIKDSFHS SEQ ID NO. 41
Max-13A AAKRAAHNAAERARRAAAAAAAAA SEQ ID NO. 42
Arnt KFLRCDDDQMSNDKERLARENHSEIERRRRNKMTAYITE SEQ ID NO. 43
Arnt-16A AAARAAHSAAERARRAAAAAAAAA SEQ ID NO. 44
AhR ASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDR SEQ ID NO. 45
AhR-17A AAAAAAAAAPSKRHRAAAAAAAAA SEQ ID NO. 46
U9
U9
bzlP Sequences 235 Ln
C/EBP SNEYRVRRERNNIAVRKSRDKAKQRNVE SEQ ID NO. 47 L'
C/EBP-18A AAAAAAARARNNAAVRKSRAAAAAAAAA SEQ ID NO. 48
- - - Ln
GCN4 DPAALKRARNTEAARRSRARKLQRMKQ SEQ ID NO. 49
- - ~
0
w
-50-
Table 8: Alanine-based mutants designed to switch between Class A and Class B
binding sites. Numbering is
same as that for Max
Basic Helix I
25 30 1
Max ADKRAHHNALERKRRDHIKDSFHS SEQ ID NO. 41
MyoD ADRRKAATMRERRRLSKVNEAFET SEQ ID NO. 50
Max-13A AAKRAAHNAAERARRAAAAAAAAA binds 5'-CAC=GTG SEQ ID NO. 42
Max-13A-RL AAKRAAHNARERARLAAAAAAAAA binds 5'-CAG=CTG SEQ ID NO. 51
~
O
U9
N
U9
N
U9
U9
O
O
U9
F'
F'
I
O
W
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Table 9: E-box Inserts
Four Tandem Copies of E-box Insert 5'- CACGTG 4-3'
Max E-box Insert 5'-[CCACGTGGN o 2 6]4-3'
Arnt E-box Insert 5'-[TCACGTGAN(o, 2, 6)]4-3'
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Table 10: Evolution of Minimalist bZIP Proteins: Sequence of original Max-
C/EBP comprising the basic region of Max, residues 22-47, an RIR linker
providing a BamH I site that facilitates cloning, and the C/EBP leucine
zipper,
residues 310-338. Sequence of MM3 that was evolved after one round of
directed evolution in the modified yeast one-hybrid system. Mutations are in
bold underline. In the Max basic region, a Leu is mutated to Ser; a frameshift
mutation occurs at the C-terminal end of the basic region and in the C/EBP
zipper, there is optionally an Asn mutated to Ser.
Max- ADKRAHHNALERKRRDHIKDSFHS-RIR- SEQ ID NO. 52
C/EBP LEQKVLELTSDNDRLRKRVEQLSRELDTL
MM3a ADKRAHHNASERKRRDTSRTLSTL-RIR- SEQ ID NO. 53
LEQKVLELTSDSDRLRKRVEQLSRELDTL
MM3b ADKRAHHNASERKRRDTSRTLSTL-RIR- SEQ ID NO. 54
LEQKVLELTSDNDRLRKRVEQLSRELDTL
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