Preferences in a trait decision determined by transcription factor variants

AbstractIn Saccharomyces cerevisiae, the decision to mate or invade relies on environmental cues that converge on a shared transcription factor, Ste12. Specificity toward invasion occurs via Ste12 binding cooperatively with the co-factor Tec1. Here, we characterize the in vitro binding preferences of Ste12 to identify a defined spacing and orientation of dimeric sites, one that is common in pheromone-regulated genes. We find that single amino acid changes in the DNA-binding domain of Ste12 can shift the preference of yeast toward either mating or invasion. These mutations define two distinct regions of this domain, suggesting alternative modes of DNA binding for each trait. Some exceptional Ste12 mutants promote hyperinvasion in a Tec1-independent manner; these fail to bind cooperative sites with Tec1 and bind to unusual dimeric Ste12 sites that contain one highly degenerate half site. We propose a model for how activation of invasion genes could have evolved with Ste12 alone.

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Two domains of ISGF3 gamma that mediate protein-DNA and protein-protein interactions during transcription factor assembly contribute to DNA-binding specificity.

Molecular and Cellular Biology ◽

10.1128/mcb.13.1.196 ◽

1993 ◽

Vol 13 (1) ◽

pp. 196-206 ◽

Cited By ~ 86

Author(s):

S A Veals ◽

T Santa Maria ◽

D E Levy

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Dna Binding ◽

Protein Interaction ◽

Binding Specificity ◽

Binding Domain ◽

Dna Binding Domain ◽

Response Element ◽

Ifn Alpha ◽

Dna Binding Specificity

Alpha interferon (IFN-alpha) induces the transcription of a large set of genes through activation of multimeric transcription factor ISGF3. This factor can be dissociated into two protein components, termed ISGF3 gamma and ISGF3 alpha. ISGF3 gamma is a 48-kDa protein related at the amino terminus to members of the IFN-regulatory factor (IRF) and Myb families of DNA-binding proteins; ISGF3 alpha consists of three polypeptides of 84, 91, and 113 kDa that self-assemble to form an activated component in response to IFN-alpha. DNA-binding studies indicated that ISGF3 gamma binds DNA alone, recognizing the IFN-stimulated response element, while the ISGF3 alpha polypeptides alone display no specific interactions with DNA. A complex between ISGF3 gamma and activated ISGF3 alpha binds the IFN-stimulated response element with much greater affinity than does the 48-kDa ISGF3 gamma protein alone. The DNA-binding domain of ISGF3 gamma and regions responsible for protein-protein interaction with ISGF3 alpha were identified by using deleted forms of ISGF3 gamma expressed in vitro. The amino-terminal region of ISGF3 gamma homologous to the IRF and Myb proteins was sufficient for interaction with DNA and displayed the binding specificity of the intact protein; phosphorylation of this region was necessary for activity. A second region of 160 amino acids separated from the DNA-binding domain by over 100 amino acids contained a domain capable of associating with ISGF3 alpha and was sufficient to confer specific ISGF3 alpha interaction to a heterologous protein. Interaction of the ISGF3 alpha component with the protein interaction domain of ISGF3 gamma altered the DNA-binding specificity of the resulting complex, suggesting that one or more of the ISGF3 alpha polypeptides make base-specific contacts with DNA. This interaction defines a mechanism through which IRF-like proteins complexed with regulatory components can display novel DNA-binding specificities.

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DNA-Binding Specificity of PAR and C/EBP Leucine Zipper Proteins: A Single Amino Acid Substitution in the C/EBP DNA-Binding Domain Confers PAR-Like Specificity to C/EBP

Biological Chemistry Hoppe-Seyler ◽

10.1515/bchm3.1996.377.12.797 ◽

1996 ◽

Vol 377 (12) ◽

pp. 797-810 ◽

Cited By ~ 2

Author(s):

Falvey Eileen ◽

Marcacci Lysiane ◽

Schibler Ueli

Keyword(s):

Amino Acid ◽

Dna Binding ◽

Amino Acid Substitution ◽

Leucine Zipper ◽

Binding Specificity ◽

Binding Domain ◽

Single Amino Acid Substitution ◽

Single Amino Acid ◽

Dna Binding Domain ◽

Dna Binding Specificity

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Two domains of ISGF3 gamma that mediate protein-DNA and protein-protein interactions during transcription factor assembly contribute to DNA-binding specificity

Molecular and Cellular Biology ◽

10.1128/mcb.13.1.196-206.1993 ◽

1993 ◽

Vol 13 (1) ◽

pp. 196-206

Author(s):

S A Veals ◽

T Santa Maria ◽

D E Levy

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Dna Binding ◽

Protein Interaction ◽

Binding Specificity ◽

Binding Domain ◽

Dna Binding Domain ◽

Response Element ◽

Ifn Alpha ◽

Dna Binding Specificity

Alpha interferon (IFN-alpha) induces the transcription of a large set of genes through activation of multimeric transcription factor ISGF3. This factor can be dissociated into two protein components, termed ISGF3 gamma and ISGF3 alpha. ISGF3 gamma is a 48-kDa protein related at the amino terminus to members of the IFN-regulatory factor (IRF) and Myb families of DNA-binding proteins; ISGF3 alpha consists of three polypeptides of 84, 91, and 113 kDa that self-assemble to form an activated component in response to IFN-alpha. DNA-binding studies indicated that ISGF3 gamma binds DNA alone, recognizing the IFN-stimulated response element, while the ISGF3 alpha polypeptides alone display no specific interactions with DNA. A complex between ISGF3 gamma and activated ISGF3 alpha binds the IFN-stimulated response element with much greater affinity than does the 48-kDa ISGF3 gamma protein alone. The DNA-binding domain of ISGF3 gamma and regions responsible for protein-protein interaction with ISGF3 alpha were identified by using deleted forms of ISGF3 gamma expressed in vitro. The amino-terminal region of ISGF3 gamma homologous to the IRF and Myb proteins was sufficient for interaction with DNA and displayed the binding specificity of the intact protein; phosphorylation of this region was necessary for activity. A second region of 160 amino acids separated from the DNA-binding domain by over 100 amino acids contained a domain capable of associating with ISGF3 alpha and was sufficient to confer specific ISGF3 alpha interaction to a heterologous protein. Interaction of the ISGF3 alpha component with the protein interaction domain of ISGF3 gamma altered the DNA-binding specificity of the resulting complex, suggesting that one or more of the ISGF3 alpha polypeptides make base-specific contacts with DNA. This interaction defines a mechanism through which IRF-like proteins complexed with regulatory components can display novel DNA-binding specificities.

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NMR Structure of Transcription Factor Sp1 DNA Binding Domain†,‡

Biochemistry ◽

10.1021/bi048438p ◽

2004 ◽

Vol 43 (51) ◽

pp. 16027-16035 ◽

Cited By ~ 54

Author(s):

Shinichiro Oka ◽

Yasuhisa Shiraishi ◽

Takuya Yoshida ◽

Tadayasu Ohkubo ◽

Yukio Sugiura ◽

...

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Binding Domain ◽

Nmr Structure ◽

Dna Binding Domain ◽

Transcription Factor Sp1

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Solution Structure of the DNA-Binding Domain of the Tomato Heat-Stress Transcription Factor HSF24

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1996.00911.x ◽

1996 ◽

Vol 236 (3) ◽

pp. 911-921 ◽

Cited By ~ 41

Author(s):

Jurgen Schultheiss ◽

Olaf Kunert ◽

Uwe Gase ◽

Klaus-Dieter Scharf ◽

Lutz Nover ◽

...

Keyword(s):

Transcription Factor ◽

Heat Stress ◽

Dna Binding ◽

Solution Structure ◽

Binding Domain ◽

Dna Binding Domain

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The C6 zinc finger and adjacent amino acids determine DNA-binding specificity and affinity in the yeast activator proteins LAC9 and PPR1.

Molecular and Cellular Biology ◽

10.1128/mcb.10.10.5128 ◽

1990 ◽

Vol 10 (10) ◽

pp. 5128-5137 ◽

Cited By ~ 10

Author(s):

M M Witte ◽

R C Dickson

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Dna Binding ◽

Zinc Finger ◽

Binding Specificity ◽

Binding Domain ◽

Dna Binding Domain ◽

Transcription Activator ◽

Activator Proteins ◽

Dna Binding Specificity

LAC9 is a DNA-binding protein that regulates transcription of the lactose-galactose regulon in Kluyveromyces lactis. The DNA-binding domain is composed of a zinc finger and nearby amino acids (M. M. Witte and R. C. Dickson, Mol. Cell. Biol. 8:3726-3733, 1988). The single zinc finger appears to be structurally related to the zinc finger of many other fungal transcription activator proteins that contain positively charged residues and six conserved cysteines with the general form Cys-Xaa2-Cys-Xaa6-Cys-Xaa6-9-Cys-Xaa2-Cys-Xaa 6-Cys, where Xaan indicates a stretch of the indicated number of any amino acids (R. M. Evans and S. M. Hollenberg, Cell 52:1-3, 1988). The function(s) of the zinc finger and other amino acids in DNA-binding remains unclear. To determine which portion of the LAC9 DNA-binding domain mediates sequence recognition, we replaced the C6 zinc finger, amino acids adjacent to the carboxyl side of the zinc finger, or both with the analogous region from the Saccharomyces cerevisiae PPR1 or LEU3 protein. A chimeric LAC9 protein, LAC9(PPR1 34-61), carrying only the PPR1 zinc finger, retained the DNA-binding specificity of LAC9. However, LAC9(PPR1 34-75), carrying the PPR1 zinc finger and 14 amino acids on the carboxyl side of the zinc finger, gained the DNA-binding specificity of PPR1, indicating that these 14 amino acids are necessary for specific DNA binding. Our data show that C6 fingers can substitute for each other and allow DNA binding, but binding affinity is reduced. Thus, in a qualitative sense C6 fingers perform a similar function(s). However, the high-affinity binding required by natural C6 finger proteins demands a unique C6 finger with a specific amino acid sequence. This requirement may reflect conformational constraints, including interactions between the C6 finger and the carboxyl-adjacent amino acids; alternatively or in addition, it may indicate that unique, nonconserved amino acid residues in zinc fingers make sequence-specifying or stabilizing contacts with DNA.

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Adaptive evolution of transcription factor binding affinities

10.1101/118455 ◽

2017 ◽

Author(s):

Jungeui Hong ◽

Nathan Brandt ◽

Ally Yang ◽

Tim Hughes ◽

David Gresham

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Dna Binding ◽

Adaptive Evolution ◽

Consensus Sequence ◽

Binding Domain ◽

Dna Binding Domain ◽

Missense Mutations ◽

Binding Affinities ◽

Synonymous Mutations

Understanding the molecular basis of gene expression evolution is a central problem in evolutionary biology. However, connecting changes in gene expression to increased fitness, and identifying the functional basis of those changes, remains challenging. To study adaptive evolution of gene expression in real time, we performed long term experimental evolution (LTEE) of Saccharomyces cerevisiae (budding yeast) in ammonium-limited chemostats. Following several hundred generations of continuous selection we found significant divergence of nitrogen-responsive gene expression in lineages with increased fitness. In multiple independent lineages we found repeated selection for non-synonymous mutations in the zinc finger DNA binding domain of the activating transcription factor (TF), GAT1, that operates within incoherent feedforward loops to control expression of the nitrogen catabolite repression (NCR) regulon. Missense mutations in the DNA binding domain of GAT1 reduce its binding affinity for the GATAA consensus sequence in a promoter-specific manner, resulting in increased expression of ammonium permease genes via both direct and indirect effects, thereby conferring increased fitness. We find that altered transcriptional output of the NCR regulon results in antagonistic pleiotropy in alternate environments and that the DNA binding domain of GAT1 is subject to purifying selection in natural populations. Our study shows that adaptive evolution of gene expression can entail tuning expression output by quantitative changes in TF binding affinities while maintaining the overall topology of a gene regulatory network.

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