DNA-binding domain of human c-Myc produced in Escherichia coli

1989 ◽  
Vol 9 (6) ◽  
pp. 2477-2486
Author(s):  
C V Dang ◽  
H van Dam ◽  
M Buckmire ◽  
W M Lee

We have identified the domain of the human c-myc protein (c-Myc) produced in Escherichia coli that is responsible for the ability of the protein to bind sequence-nonspecific DNA. Using analysis of binding of DNA by proteins transferred to nitrocellulose, DNA-cellulose chromatography, and a nitrocellulose filter binding assay, we examined the binding properties of c-Myc peptides generated by cyanogen bromide cleavage, of mutant c-Myc, and of proteins that fuse portions of c-Myc to staphylococcal protein A. The results of these analyses indicated that c-Myc amino acids 265 to 318 were responsible for DNA binding and that other regions of the protein (including a highly conserved basic region and a region containing the leucine zipper motif) were not required. Some mutant c-Mycs that did not bind DNA maintained rat embryo cell-cotransforming activity, which indicated that the c-Myc property of in vitro DNA binding was not essential for this activity. These mutants, however, were unable to transform established rat fibroblasts (Rat-1a cells) that were susceptible to transformation by wild-type c-Myc, although this lack of activity may not have been due to their inability to bind DNA.

1989 ◽  
Vol 9 (6) ◽  
pp. 2477-2486 ◽  
Author(s):  
C V Dang ◽  
H van Dam ◽  
M Buckmire ◽  
W M Lee

We have identified the domain of the human c-myc protein (c-Myc) produced in Escherichia coli that is responsible for the ability of the protein to bind sequence-nonspecific DNA. Using analysis of binding of DNA by proteins transferred to nitrocellulose, DNA-cellulose chromatography, and a nitrocellulose filter binding assay, we examined the binding properties of c-Myc peptides generated by cyanogen bromide cleavage, of mutant c-Myc, and of proteins that fuse portions of c-Myc to staphylococcal protein A. The results of these analyses indicated that c-Myc amino acids 265 to 318 were responsible for DNA binding and that other regions of the protein (including a highly conserved basic region and a region containing the leucine zipper motif) were not required. Some mutant c-Mycs that did not bind DNA maintained rat embryo cell-cotransforming activity, which indicated that the c-Myc property of in vitro DNA binding was not essential for this activity. These mutants, however, were unable to transform established rat fibroblasts (Rat-1a cells) that were susceptible to transformation by wild-type c-Myc, although this lack of activity may not have been due to their inability to bind DNA.


2020 ◽  
Author(s):  
Ichiro Inamoto ◽  
Inder Sheoran ◽  
Serban C. Popa ◽  
Montdher Hussain ◽  
Jumi A. Shin

ABSTRACTWe designed MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of transcription factors Max and Myc, which bind with high DNA sequence specificity and affinity to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. ME47, however, displays propensity for instability and misfolding. We therefore sought to improve ME47’s structural and functional features. We used phage-assisted continuous evolution (PACE) to uncover “nonrational” changes to complement our rational design. PACE mutated Arg12 that contacts the DNA phosphodiester backbone. We would not have rationally made such a change, but this mutation improved ME47’s stability with little change in DNA-binding function. We mutated Cys29 to Ser and Ala in ME47’s HLH to eliminate undesired disulfide formation; these mutations reduced E-box binding activity. To compensate, we fused the designed FosW leucine zipper to ME47 to increase the dimerization interface and improve protein stability and E-box targeting activity. This “franken-protein” MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper—plus mutations that arose during PACE and rational design—and is a tractable, reliable protein in vivo and in vitro. Compared with ME47, MEF gives three-fold stronger binding to E-box with four-fold increased specificity for E-box over nonspecific DNA. Generation of MEF demonstrates that combining rational design and continuous evolution can be a powerful tool for designing proteins with robust structure and strong DNA-binding function.


1993 ◽  
Vol 13 (7) ◽  
pp. 3964-3974 ◽  
Author(s):  
B Stein ◽  
P C Cogswell ◽  
A S Baldwin

NF-kappa B and C/EBP represent distinct families of transcription factors that target unique DNA enhancer elements. The heterodimeric NF-kappa B complex is composed of two subunits, a 50- and a 65-kDa protein. All members of the NF-kappa B family, including the product of the proto-oncogene c-rel, are characterized by their highly homologous approximately 300-amino-acid N-terminal region. This Rel homology domain mediates DNA binding, dimerization, and nuclear targeting of these proteins. C/EBP contains the bZIP region, which is characterized by two motifs in the C-terminal half of the protein: a basic region involved in DNA binding and a leucine zipper motif involved in dimerization. The C/EBP family consist of several related proteins, C/EBP alpha, C/EBP beta, C/EBP gamma, and C/EBP delta, that form homodimers and that form heterodimers with each other. We now demonstrated the unexpected cross-coupling of members of the NF-kappa B family three members of the C/EBP family. NF-kappa B p65, p50, and Rel functionally synergize with C/EBP alpha, C/EBP beta, and C/EBP delta. This cross-coupling results in the inhibition of promoters with kappa B enhancer motifs and in the synergistic stimulation of promoters with C/EBP binding sites. These studies demonstrate that NF-kappa B augments gene expression mediated by a multimerized c-fos serum response element in the presence of C/EBP. We show a direct physical association of the bZIP region of C/EBP with the Rel homology domain of NF-kappa B. The cross-coupling of NF-kappa B with C/EBP highlights a mechanism of gene regulation involving an interaction between distinct transcription factor families.


2020 ◽  
Author(s):  
Jumi Shin ◽  
Ichiro Inamoto ◽  
Inder Sheoran ◽  
Serban Popa ◽  
Montdher Hussain

We designed MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of transcription factors Max and Myc, which bind with high DNA sequence specificity and affinity to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. ME47, however, displays propensity for instability and misfolding. We therefore sought to improve ME47's structural and functional features. We used phage-assisted continuous evolution (PACE) to uncover "nonrational" changes to complement our rational design. PACE mutated Arg12 that contacts the DNA phosphodiester backbone. We would not have rationally made such a change, but this mutation improved ME47's stability with little change in DNA-binding function. We mutated Cys29 to Ser and Ala in ME47's HLH to eliminate undesired disulfide formation; these mutations reduced E-box binding activity. To compensate, we fused the designed FosW leucine zipper to ME47 to increase the dimerization interface and improve protein stability and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper—plus mutations that arose during PACE and rational design—and is a tractable, reliable protein in vivo and in vitro. Compared with ME47, MEF gives three-fold stronger binding to Ebox with four-fold increased specificity for E-box over nonspecific DNA. Generation of MEF demonstrates that combining rational design and continuous evolution can be a powerful tool for designing proteins with robust structure and strong DNA-binding function. <br>


1991 ◽  
Vol 11 (10) ◽  
pp. 4918-4926 ◽  
Author(s):  
W T Pu ◽  
K Struhl

Yeast GCN4 and the Jun oncoprotein are transcriptional activators that bind DNA via a bZIP domain consisting of a leucine zipper dimerization element and an adjacent basic region that directly contacts DNA. Two highly conserved alanines (Ala-238 and Ala-239 in GCN4) and an invariant asparagine (Asn-235) in the basic region have been proposed to play important roles in DNA sequence recognition by bZIP proteins. Surprisingly, these conserved residues can be functionally replaced in GCN4 and in a derivative containing the Jun basic region (Jun-GCN4). The ability of an amino acid to functionally substitute for Asn-235 does not correlate with its preference for assuming the N-cap position of an alpha helix. This finding argues against the proposal of the scissors grip model that the invariant asparagine forms an N cap that permits the basic region to bend sharply and wrap around the DNA. In contrast to a prediction of the induced fork model, the pattern of functional substitutions of the conserved alanines together with the results of uracil interference experiments suggests that Ala-238 and Ala-239 do not make base-specific DNA contacts. Finally, the Jun-GCN4 chimeric proteins appear much more active in vivo than expected from their DNA-binding properties in vitro. The mechanistic and evolutionary implications of these results are discussed.


2020 ◽  
Author(s):  
Jumi Shin ◽  
Ichiro Inamoto ◽  
Inder Sheoran ◽  
Serban Popa ◽  
Montdher Hussain

We designed MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of transcription factors Max and Myc, which bind with high DNA sequence specificity and affinity to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. ME47, however, displays propensity for instability and misfolding. We therefore sought to improve ME47's structural and functional features. We used phage-assisted continuous evolution (PACE) to uncover "nonrational" changes to complement our rational design. PACE mutated Arg12 that contacts the DNA phosphodiester backbone. We would not have rationally made such a change, but this mutation improved ME47's stability with little change in DNA-binding function. We mutated Cys29 to Ser and Ala in ME47's HLH to eliminate undesired disulfide formation; these mutations reduced E-box binding activity. To compensate, we fused the designed FosW leucine zipper to ME47 to increase the dimerization interface and improve protein stability and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper—plus mutations that arose during PACE and rational design—and is a tractable, reliable protein in vivo and in vitro. Compared with ME47, MEF gives three-fold stronger binding to Ebox with four-fold increased specificity for E-box over nonspecific DNA. Generation of MEF demonstrates that combining rational design and continuous evolution can be a powerful tool for designing proteins with robust structure and strong DNA-binding function. <br>


1991 ◽  
Vol 11 (10) ◽  
pp. 4918-4926
Author(s):  
W T Pu ◽  
K Struhl

Yeast GCN4 and the Jun oncoprotein are transcriptional activators that bind DNA via a bZIP domain consisting of a leucine zipper dimerization element and an adjacent basic region that directly contacts DNA. Two highly conserved alanines (Ala-238 and Ala-239 in GCN4) and an invariant asparagine (Asn-235) in the basic region have been proposed to play important roles in DNA sequence recognition by bZIP proteins. Surprisingly, these conserved residues can be functionally replaced in GCN4 and in a derivative containing the Jun basic region (Jun-GCN4). The ability of an amino acid to functionally substitute for Asn-235 does not correlate with its preference for assuming the N-cap position of an alpha helix. This finding argues against the proposal of the scissors grip model that the invariant asparagine forms an N cap that permits the basic region to bend sharply and wrap around the DNA. In contrast to a prediction of the induced fork model, the pattern of functional substitutions of the conserved alanines together with the results of uracil interference experiments suggests that Ala-238 and Ala-239 do not make base-specific DNA contacts. Finally, the Jun-GCN4 chimeric proteins appear much more active in vivo than expected from their DNA-binding properties in vitro. The mechanistic and evolutionary implications of these results are discussed.


1993 ◽  
Vol 13 (7) ◽  
pp. 3964-3974 ◽  
Author(s):  
B Stein ◽  
P C Cogswell ◽  
A S Baldwin

NF-kappa B and C/EBP represent distinct families of transcription factors that target unique DNA enhancer elements. The heterodimeric NF-kappa B complex is composed of two subunits, a 50- and a 65-kDa protein. All members of the NF-kappa B family, including the product of the proto-oncogene c-rel, are characterized by their highly homologous approximately 300-amino-acid N-terminal region. This Rel homology domain mediates DNA binding, dimerization, and nuclear targeting of these proteins. C/EBP contains the bZIP region, which is characterized by two motifs in the C-terminal half of the protein: a basic region involved in DNA binding and a leucine zipper motif involved in dimerization. The C/EBP family consist of several related proteins, C/EBP alpha, C/EBP beta, C/EBP gamma, and C/EBP delta, that form homodimers and that form heterodimers with each other. We now demonstrated the unexpected cross-coupling of members of the NF-kappa B family three members of the C/EBP family. NF-kappa B p65, p50, and Rel functionally synergize with C/EBP alpha, C/EBP beta, and C/EBP delta. This cross-coupling results in the inhibition of promoters with kappa B enhancer motifs and in the synergistic stimulation of promoters with C/EBP binding sites. These studies demonstrate that NF-kappa B augments gene expression mediated by a multimerized c-fos serum response element in the presence of C/EBP. We show a direct physical association of the bZIP region of C/EBP with the Rel homology domain of NF-kappa B. The cross-coupling of NF-kappa B with C/EBP highlights a mechanism of gene regulation involving an interaction between distinct transcription factor families.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2992-2992
Author(s):  
Ido Paz-Priel ◽  
Dong Hong Cai ◽  
Dehua Wang ◽  
Jeanne Kowalski ◽  
Amanda Blackford ◽  
...  

Abstract The CEBPA gene is mutated in 10% of acute myeloid leukemia (AML) cases, and wild-type CEBPA levels are reduced in additional AMLs, e.g. as a result of AML1-ETO or flt3ITD mediated inhibition of transcription or bcr-abl mediated inhibition of translation. One consequence of diminished C/EBPα activity or expression is likely inhibition of myeloid differentiation. We now find, via analysis of data from two published microarray studies, that CEBPA and Bcl-2 RNA levels correlate highly in low risk human AMLs (P = 0.003 and 0.001), suggesting that inhibition of apoptosis via induction of bcl-2 by C/EBPα or its mutant variants also contributes to transformation. Lack of correlation in other risk groups may reflect the presence of additional mutations that inhibit apoptosis. Among the low-risk patients, those with AML1-ETO had the lowest, CBFβ-SMMHC intermediate, and PML-RARα the highest levels of CEBPA (P &lt; 0.05). Patients with CEBPA mutations were mainly in the intermediate-risk, normal karyotype group, and within this group the average CEBPA level was higher than those having wild-type alleles (P = 0.0002), suggesting a selective advantage to enable dominant-inhibition of remaining wild-type C/EBPs and/or induction of bcl-2. The two categories of C/EBPα mutant alleles associated with AML are C/EBPα p30, lacking an N-terminal transactivation domain, and C/EBPα LZ, carrying in-frame mutations in the leucine zipper (LZ) that prevent DNA-binding. Each of this oncoproteins induced bcl-2 in hematopoietic cell lines, and wild-type C/EBPα also induced bcl-2 when transduced into normal murine myeloid progenitors or in the splenocytes of H2K-C/EBPalpha]-Eμ transgenic mice. Remarkably, C/EBPα LZ oncoproteins activated the bcl-2 P2 promoter despite lack of DNA-binding, and C/EBPα p30 also activated the promoter. C/EBPα and the C/EBPα oncoproteins cooperated with NF-κB p50, but not p65, to induce bcl-2 promoter transcription. Endogenous C/EBPα preferentially coimmunoprecipitated with p50, versus p65, in myeloid cell extracts. Mutation of residues 297–302 in the C/EBPα basic region (BR) prevented induction of endogenous bcl-2 or the bcl-2 promoter and interaction with p50 but not p65 when co-expressed in 293T cells, whereas C/EBPα p30 or a C/EBPα LZ oncoprotein retain the ability to co-ip with p50. These findings offer an explanation for preferential in-frame rather than out-of-frame mutation of the LZ with sparing of the BR in the C/EBPα LZ oncoproteins that constitute one-third of CEBPA mutations in AML. C/EBPα or its mutant variants may tether to a subset of NF-κB targets genes, including Bcl-2, via p50 to facilitate gene activation. Targeting interaction between the C/EBPα basic region and NF-κB p50 may contribute to the therapy of AMLs expressing either mutant or residual wild-type C/EBPα , by increasing susceptibility to apoptosis. Targetting this interaction may also be relevant to the therapy of other malignancies expressing C/EBPs, not only via down-regulation of bcl-2 but also by preventing their cooperative activation of genes mediating inflammation and angiogenesis, which have recently been shown to contribute to the pathogenesis of several solid tumors in animal models.


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