1
|
Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol 2018; 14:e1006290. [PMID: 29953437 PMCID: PMC6040777 DOI: 10.1371/journal.pcbi.1006290] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 07/11/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022] Open
Abstract
A major goal of cancer genomics is to identify somatic mutations that play a role in tumor initiation or progression. Somatic mutations within transcription factors are of particular interest, as gene expression dysregulation is widespread in cancers. The substantial gene expression variation evident across tumors suggests that numerous regulatory factors are likely to be involved and that somatic mutations within them may not occur at high frequencies across patient cohorts, thereby complicating efforts to uncover which ones are cancer-relevant. Here we analyze somatic mutations within the largest family of human transcription factors, namely those that bind DNA via Cys2His2 zinc finger domains. Specifically, to hone in on important mutations within these genes, we aggregated somatic mutations across all of them by their positions within Cys2His2 zinc finger domains. Remarkably, we found that for three classes of cancers profiled by The Cancer Genome Atlas (TCGA)-Uterine Corpus Endometrial Carcinoma, Colon and Rectal Adenocarcinomas, and Skin Cutaneous Melanoma-two specific, functionally important positions within zinc finger domains are mutated significantly more often than expected by chance, with alterations in 18%, 10% and 43% of tumors, respectively. Numerous zinc finger genes are affected, with those containing Krüppel-associated box (KRAB) repressor domains preferentially targeted by these mutations. Further, the genes with these mutations also have high overall missense mutation rates, are expressed at levels comparable to those of known cancer genes, and together have biological process annotations that are consistent with roles in cancers. Altogether, we introduce evidence broadly implicating mutations within a diverse set of zinc finger proteins as relevant for cancer, and propose that they contribute to the widespread transcriptional dysregulation observed in cancer cells.
Collapse
Affiliation(s)
- Daniel Munro
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Dario Ghersi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- * E-mail:
| |
Collapse
|
2
|
Rigard M, Bröms JE, Mosnier A, Hologne M, Martin A, Lindgren L, Punginelli C, Lays C, Walker O, Charbit A, Telouk P, Conlan W, Terradot L, Sjöstedt A, Henry T. Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence. PLoS Pathog 2016; 12:e1005821. [PMID: 27602570 PMCID: PMC5014421 DOI: 10.1371/journal.ppat.1005821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/20/2016] [Indexed: 12/12/2022] Open
Abstract
The virulence of Francisella tularensis, the etiological agent of tularemia, relies on an atypical type VI secretion system (T6SS) encoded by a genomic island termed the Francisella Pathogenicity Island (FPI). While the importance of the FPI in F. tularensis virulence is clearly established, the precise role of most of the FPI-encoded proteins remains to be deciphered. In this study, using highly virulent F. tularensis strains and the closely related species F. novicida, IglG was characterized as a protein featuring a unique α-helical N-terminal extension and a domain of unknown function (DUF4280), present in more than 250 bacterial species. Three dimensional modeling of IglG and of the DUF4280 consensus protein sequence indicates that these proteins adopt a PAAR-like fold, suggesting they could cap the T6SS in a similar way as the recently described PAAR proteins. The newly identified PAAR-like motif is characterized by four conserved cysteine residues, also present in IglG, which may bind a metal atom. We demonstrate that IglG binds metal ions and that each individual cysteine is required for T6SS-dependent secretion of IglG and of the Hcp homologue, IglC and for the F. novicida intracellular life cycle. In contrast, the Francisella-specific N-terminal α-helical extension is not required for IglG secretion, but is critical for F. novicida virulence and for the interaction of IglG with another FPI-encoded protein, IglF. Altogether, our data suggest that IglG is a PAAR-like protein acting as a bi-modal protein that may connect the tip of the Francisella T6SS with a putative T6SS effector, IglF. Francisella tularensis is a highly pathogenic bacterium causing tularemia. Its ability to cause disease is linked to its ability to replicate in the macrophage cytosol. The intracellular life cycle of Francisella is controlled by a type VI secretion system (T6SS), which is thought to inject effectors into the host cell to allow bacterial escape into the host cytosol. The molecular mechanisms behind this process are still largely unclear. In this work, we identify IglG as a protein with two important domains, one conserved in proteins from more than 250 bacterial species (DUF4280, renamed here as PAAR-like domain) and one specific for the Francisella genus. Using protein sequence analysis and three-dimensional structure predictions, comparative modeling and biochemistry approaches, our data demonstrate that IglG is a metal-binding protein that based on its PAAR-like domain might cap the VgrG spike of the T6SS and act as a membrane-puncturing protein. Furthermore, we identified that the Francisella-specific domain is directly involved in forming a protein complex with another virulence protein, IglF. This work, in addition to enhancing the molecular understanding of the Francisella T6SS, defines the features of the conserved DUF4280, a novel PAAR-like domain involved in type VI secretion (T6S) of many bacterial species.
Collapse
Affiliation(s)
- Mélanie Rigard
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeanette E. Bröms
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Amandine Mosnier
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Amandine Martin
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Lena Lindgren
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Claire Punginelli
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Claire Lays
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Alain Charbit
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France
- Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Philippe Telouk
- University of Lyon, Lyon, France
- Laboratoire de Geologie de Lyon; Ecole Normale Supérieure de Lyon, Lyon, France
| | - Wayne Conlan
- National Research Council Canada, Human Health Therapeutics Portfolio, Ottawa, Ontario, Canada
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
- * E-mail: (LT); (AS); (TH)
| | - Anders Sjöstedt
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- * E-mail: (LT); (AS); (TH)
| | - Thomas Henry
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (LT); (AS); (TH)
| |
Collapse
|
3
|
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 2014; 158:1431-1443. [PMID: 25215497 DOI: 10.1016/j.cell.2014.08.009] [Citation(s) in RCA: 1143] [Impact Index Per Article: 114.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/03/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
Abstract
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.
Collapse
Affiliation(s)
- Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Ally Yang
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Mihai Albu
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Atina G Cote
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Alejandro Montenegro-Montero
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Philipp Drewe
- Computational Biology Center, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Hamed S Najafabadi
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Ishminder Mann
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Kate Cook
- Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Hong Zheng
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Alejandra Goity
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Harm van Bakel
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada; Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jean-Claude Lozano
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7621, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Mary Galli
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mathew G Lewsey
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eryong Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tuhin Mukherjee
- Department of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Xiaoting Chen
- Department of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA
| | - John S Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - François-Yves Bouget
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7621, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Gunnar Ratsch
- Computational Biology Center, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Luis F Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Timothy R Hughes
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada.
| |
Collapse
|
4
|
Priyadarshini C. G. P, Savithri H. Kinetics of interaction of Cotton Leaf Curl Kokhran Virus-Dabawali (CLCuKV-Dab) coat protein and its mutants with ssDNA. Virology 2009; 386:427-37. [DOI: 10.1016/j.virol.2009.01.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 12/23/2008] [Accepted: 01/15/2009] [Indexed: 11/27/2022]
|
5
|
Kacherovsky N, Tachibana C, Amos E, Fox D, Young ET. Promoter binding by the Adr1 transcriptional activator may be regulated by phosphorylation in the DNA-binding region. PLoS One 2008; 3:e3213. [PMID: 18791642 PMCID: PMC2527678 DOI: 10.1371/journal.pone.0003213] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 08/25/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Post-translational modification regulates promoter-binding by Adr1, a Zn-finger transcriptional activator of glucose-regulated genes. Support for this model includes the activation of an Adr1-dependent gene in the absence of Adr1 protein synthesis, and a requirement for the kinase Snf1 for Adr1 DNA-binding. A fusion protein with the Adr1 DNA-binding domain and a heterologous activation domain is glucose-regulated, suggesting that the DNA binding region is the target of regulation. METHODOLOGY/PRINCIPAL FINDINGS Peptide mapping identified serine 98 adjacent to the Zn-fingers as a phosphorylation site. An antibody specific for phosphorylated serine 98 on Adr1 showed that the level of phosphorylated Adr1 relative to the level of total Adr1 decreased with glucose derepression, in a Snf1-dependent manner. Relative phosphorylation decreased in a PHO85 mutant, and this mutant constitutively expressed an Adr1-dependent reporter. Pho85 did not phosphorylate Adr1 in vitro, suggesting that it affects Adr1 indirectly. Mutation of serine 98 to the phosphomimetic amino acid aspartate reduced in vitro DNA-binding of the recombinant Adr1 DNA-binding domain. Mutation to aspartate or alanine affected activation of a reporter by full-length Adr1, and in vivo promoter binding. CONCLUSIONS/SIGNIFICANCE Mutation of Adr1 serine 98 affects in vitro and in vivo DNA binding, and phosphorylation of serine 98 in vivo correlates with glucose availability, suggesting that Adr1 promoter-binding is regulated in part by serine 98 phosphorylation.
Collapse
Affiliation(s)
- Nataly Kacherovsky
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Christine Tachibana
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Emily Amos
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - David Fox
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Elton T. Young
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
6
|
Mendiratta G, Eriksson PR, Shen CH, Clark DJ. The DNA-binding domain of the yeast Spt10p activator includes a zinc finger that is homologous to foamy virus integrase. J Biol Chem 2006; 281:7040-8. [PMID: 16415340 DOI: 10.1074/jbc.m511416200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast SPT10 gene encodes a putative histone acetyltransferase that binds specifically to pairs of upstream activating sequence (UAS) elements found only in the histone gene promoters. Here, we demonstrate that the DNA-binding domain of Spt10p is located between residues 283 and 396 and includes a His(2)-Cys(2) zinc finger. The binding of Spt10p to the histone UAS is zinc-dependent and is disabled by a zinc finger mutation (C388S). The isolated DNA-binding domain binds to single histone UAS elements with high affinity. In contrast, full-length Spt10p binds with high affinity only to pairs of UAS elements with very strong positive cooperativity and is unable to bind to a single UAS element. This implies the presence of a "blocking" domain in full-length Spt10p, which forces it to search for a pair of UAS elements. Chromatin immunoprecipitation experiments indicate that, unlike wild-type Spt10p, the C388S protein does not bind to the promoter of the gene encoding histone H2A (HTA1) in vivo. The C388S mutant has a phenotype similar to that of the spt10Delta mutant: poor growth and global aberrations in gene expression. Thus, the C388S mutation disables the DNA-binding function of Spt10p in vitro and in vivo. The zinc finger of Spt10p is homologous to that of foamy virus integrase, perhaps suggesting that this integrase is also a sequence-specific DNA-binding protein.
Collapse
Affiliation(s)
- Geetu Mendiratta
- Laboratory of Molecular Growth Regulation, NICHD/National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-2426, USA
| | | | | | | |
Collapse
|
7
|
Abstract
Transcriptional transactivators are important proteins which in addition to controlling the cell regulatory circuitries, can be manipulated for various biotechnological processes. The latter is of great interest for non-conventional yeasts used for industrial purposes. To facilitate the identification of these transactivators, we have reanalyzed the "Génolevures" data (FEBS Lett. 487 (2000); http://cbi.labri.u-bordeaux.fr/Genolevures/) for the presence of zinc finger (Zf) proteins. After analysis of 239 RST ("random sequence tag") sequences, we describe in this paper 161 homologs of the Saccharomyces cerevisiae Zf proteins present in one or several of 13 different hemiascomyceteous yeasts. These partial sequences have been evaluated on different criteria such as percentage of identity of the proteins, synteny, detailed analysis of the Zf motif and flanking regions, and iterative BLASTs. They can be used to fetch the corresponding gene.
Collapse
Affiliation(s)
- Francoise Bussereau
- Institut de Génétique et Microbiologie (CNRS UMR 8621), Bâtiment 400, Université Paris-Sud, 91405 Orsay Cedex, France
| | | | | |
Collapse
|
8
|
Simpson RJY, Cram ED, Czolij R, Matthews JM, Crossley M, Mackay JP. CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions. J Biol Chem 2003; 278:28011-8. [PMID: 12736264 DOI: 10.1074/jbc.m211146200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Classical (CCHH) zinc fingers are among the most common protein domains found in eukaryotes. They function as molecular recognition elements that mediate specific contact with DNA, RNA, or other proteins and are composed of a betabetaalpha fold surrounding a single zinc ion that is ligated by two cysteine and two histidine residues. In a number of variant zinc fingers, the final histidine is not conserved, and in other unrelated zinc binding domains, residues such as aspartate can function as zinc ligands. To test whether the final histidine is required for normal folding and the DNA-binding function of classical zinc fingers, we focused on finger 3 of basic Krüppel-like factor. The structure of this domain was determined using NMR spectroscopy and found to constitute a typical classical zinc finger. We generated a panel of substitution mutants at the final histidine in this finger and found that several of the mutants retained some ability to fold in the presence of zinc. Consistent with this result, we showed that mutation of the final histidine had only a modest effect on DNA binding in the context of the full three-finger DNA-binding domain of basic Krüppel-like factor. Further, the zinc binding ability of one of the point mutants was tested and found to be indistinguishable from the wild-type domain. These results suggest that the final zinc chelating histidine is not an essential feature of classical zinc fingers and have implications for zinc finger evolution, regulation, and the design of experiments testing the functional roles of these domains.
Collapse
Affiliation(s)
- Raina J Y Simpson
- School of Molecular and Microbial Biosciences, G08, University of Sydney, New South Wales 2006, Australia
| | | | | | | | | | | |
Collapse
|
9
|
Wolfe SA, Nekludova L, Pabo CO. DNA recognition by Cys2His2 zinc finger proteins. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 29:183-212. [PMID: 10940247 DOI: 10.1146/annurev.biophys.29.1.183] [Citation(s) in RCA: 732] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cys2His2 zinc fingers are one of the most common DNA-binding motifs found in eukaryotic transcription factors. These proteins typically contain several fingers that make tandem contacts along the DNA. Each finger has a conserved beta beta alpha structure, and amino acids on the surface of the alpha-helix contact bases in the major groove. This simple, modular structure of zinc finger proteins, and the wide variety of DNA sequences they can recognize, make them an attractive framework for attempts to design novel DNA-binding proteins. Several studies have selected fingers with new specificities, and there clearly are recurring patterns in the observed side chain-base interactions. However, the structural details of recognition are intricate enough that there are no general rules (a "recognition code") that would allow the design of an optimal protein for any desired target site. Construction of multifinger proteins is also complicated by interactions between neighboring fingers and the effect of the intervening linker. This review analyzes DNA recognition by Cys2His2 zinc fingers and summarizes progress in generating proteins with novel specificities from fingers selected by phage display.
Collapse
Affiliation(s)
- S A Wolfe
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
| | | | | |
Collapse
|
10
|
Wolfe SA, Ramm EI, Pabo CO. Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers. Structure 2000; 8:739-50. [PMID: 10903945 DOI: 10.1016/s0969-2126(00)00161-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Several strategies have been reported for the design and selection of novel DNA-binding proteins. Most of these studies have used Cys(2)His(2) zinc finger proteins as a framework, and have focused on constructs that bind DNA in a manner similar to Zif268, with neighboring fingers connected by a canonical (Krüppel-type) linker. This linker does not seem ideal for larger constructs because only modest improvements in affinity are observed when more than three fingers are connected in this manner. Two strategies have been described that allow the productive assembly of more than three canonically linked fingers on a DNA site: connecting sets of fingers using linkers (covalent), or assembling sets of fingers using dimerization domains (non-covalent). RESULTS Using a combination of structure-based design and phage display, we have developed a new dimerization system for Cys(2)His(2) zinc fingers that allows the assembly of more than three fingers on a desired target site. Zinc finger constructs employing this new dimerization system have high affinity and good specificity for their target sites both in vitro and in vivo. Constructs that recognize an asymmetric binding site as heterodimers can be obtained through substitutions in the zinc finger and dimerization regions. CONCLUSIONS Our modular zinc finger dimerization system allows more than three Cys(2)His(2) zinc fingers to be productively assembled on a DNA-binding site. Dimerization may offer certain advantages over covalent linkage for the recognition of large DNA sequences. Our results also illustrate the power of combining structure-based design with phage display in a strategy that assimilates the best features of each method.
Collapse
Affiliation(s)
- S A Wolfe
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | |
Collapse
|
11
|
Bai Y, Salvadore C, Chiang YC, Collart MA, Liu HY, Denis CL. The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5. Mol Cell Biol 1999; 19:6642-51. [PMID: 10490603 PMCID: PMC84645 DOI: 10.1128/mcb.19.10.6642] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The CCR4-NOT complex (1 mDa in size), consisting of the proteins CCR4, CAF1, and NOT1 to NOT5, regulates gene expression both positively and negatively and is distinct from other large transcriptional complexes in Saccharomyces cerevisiae such as SNF/SWI, TFIID, SAGA, and RNA polymerase II holoenzyme. The physical and genetic interactions between the components of the CCR4-NOT complex were investigated in order to gain insight into how this complex affects the expression of diverse genes and processes. The CAF1 protein was found to be absolutely required for CCR4 association with the NOT proteins, and CCR4 and CAF1, in turn, physically interacted with NOT1 through its central amino acid region from positions 667 to 1152. The NOT3, NOT4, and NOT5 proteins had no significant effect on the association of CCR4, CAF1, and NOT1 with each other. In contrast, the NOT2, NOT4, and NOT5 interacted with the C-terminal region (residues 1490 to 2108) of NOT1 in which NOT2 and NOT5 physically associated in the absence of CAF1, NOT3, and NOT4. These and other data indicate that the physical ordering of these proteins in the complex is CCR4-CAF1-NOT1-(NOT2, NOT5), with NOT4 and NOT3 more peripheral to NOT2 and NOT5. The physical separation of CCR4 and CAF1 from other components of the CCR4-NOT complex correlated with genetic analysis indicating partially separate functions for these two groups of proteins. ccr4 or caf1 deletion suppressed the increased 3-aminotriazole resistance phenotype conferred by not mutations, resulted in opposite effects on gene expression as compared to several not mutations, and resulted in a number of synthetic phenotypes in combination with not mutations. These results define the CCR4-NOT complex as consisting of at least two physically and functionally separated groups of proteins.
Collapse
Affiliation(s)
- Y Bai
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
| | | | | | | | | | | |
Collapse
|
12
|
Avram D, Leid M, Bakalinsky AT. Fzf1p of Saccharomyces cerevisiae is a positive regulator of SSU1 transcription and its first zinc finger region is required for DNA binding. Yeast 1999; 15:473-80. [PMID: 10234785 DOI: 10.1002/(sici)1097-0061(199904)15:6<473::aid-yea388>3.0.co;2-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The FZF1 gene of Saccharomyces cerevisiae encodes a five-zinc-finger transcription factor involved in sulphite tolerance. Previous work based on multicopy suppression analysis placed FZF1 upstream of SSU1, which encodes a plasma membrane protein and putative transporter also implicated in sulphite detoxification. Consistent with this analysis, Fzf1p was found to be a positive regulator of SSU1 transcription. The SSU1 promoter region involved in activation by FZF1 was defined, and the FZF1 protein was shown to bind to it directly in vitro. Deletion of a single, amino-terminal zinc finger of Fzf1p resulted in loss of DNA binding, while the fourth and fifth zinc fingers were found to be dispensable.
Collapse
Affiliation(s)
- D Avram
- Laboratory of Molecular Pharmacology, Oregon State University, Corvallis 97331-6602, USA
| | | | | |
Collapse
|
13
|
Komarnitsky PB, Klebanow ER, Weil PA, Denis CL. ADR1-mediated transcriptional activation requires the presence of an intact TFIID complex. Mol Cell Biol 1998; 18:5861-7. [PMID: 9742103 PMCID: PMC109172 DOI: 10.1128/mcb.18.10.5861] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/1998] [Accepted: 06/25/1998] [Indexed: 11/20/2022] Open
Abstract
The yeast transcriptional activator ADR1, which is required for ADH2 and other genes' expression, contains four transactivation domains (TADs). While previous studies have shown that these TADs act through GCN5 and ADA2, and presumably TFIIB, other factors are likely to be involved in ADR1 function. In this study, we addressed the question of whether TFIID is also required for ADR1 action. In vitro binding studies indicated that TADI of ADR1 was able to retain TAFII90 from yeast extracts and TADII could retain TBP and TAFII130/145. TADIV, however, was capable of retaining multiple TAFIIs, suggesting that TADIV was binding TFIID from yeast whole-cell extracts. The ability of TADIV truncation derivatives to interact with TFIID correlated with their transcription activation potential in vivo. In addition, the ability of LexA-ADR1-TADIV to activate transcription in vivo was compromised by a mutation in TAFII130/145. ADR1 was found to associate in vivo with TFIID in that immunoprecipitation of either TAFII90 or TBP from yeast whole-cell extracts specifically coimmunoprecipitated ADR1. Most importantly, depletion of TAFII90 from yeast cells dramatically reduced ADH2 derepression. These results indicate that ADR1 physically associates with TFIID and that its ability to activate transcription requires an intact TFIID complex.
Collapse
Affiliation(s)
- P B Komarnitsky
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
| | | | | | | |
Collapse
|
14
|
Corton JC, Moreno E, Johnston SA. Alterations in the GAL4 DNA-binding domain can affect transcriptional activation independent of DNA binding. J Biol Chem 1998; 273:13776-80. [PMID: 9593720 DOI: 10.1074/jbc.273.22.13776] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GAL4 protein belongs to a large class of fungal transcriptional activator proteins encoding within their DNA-binding domains (DBD) six cysteines that coordinate two atoms of zinc (the Zn2Cys6 domain). In an effort to characterize the interactions between the Zn2Cys6 class transcriptional activator proteins and their DNA-binding sites, we have replaced in the full-length GAL4 protein small regions of the Zn2Cys6 domain with the analogous regions of another Zn2Cys6 protein called PPR1 an activator of pyrimidine biosynthetic genes. Alterations between the first and third cysteines abolished binding to GAL4 (upstream activation sequence of GAL (UASG)) or PPR1 (upstream acitvation sequence of UAS) DNA-binding sites and severely reduced transcriptional activation in yeast. In contrast, alterations between the third and fourth cysteines had only minor effects on binding to UASG but led to substantial decreases in activation in both yeast and a mammalian cell line. In the crystal structure of the GAL4 DBD-UASG complex (Marmorstein, R., Carey, M., Ptashne, M., and Harrison, S. C. (1992) Nature 356, 408-414), this region is facing away from the DNA, making it likely that there exists within the GAL4 DBD an accessible domain important in activation.
Collapse
Affiliation(s)
- J C Corton
- Chemical Industry Institute of Toxicology, Research Triangle Park, North Carolina 27709-2137, USA.
| | | | | |
Collapse
|
15
|
Powers CA, Mathur M, Raaka BM, Ron D, Samuels HH. TLS (translocated-in-liposarcoma) is a high-affinity interactor for steroid, thyroid hormone, and retinoid receptors. Mol Endocrinol 1998; 12:4-18. [PMID: 9440806 DOI: 10.1210/mend.12.1.0043] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nuclear receptors for steroid hormones, thyroid hormone, retinoids, and vitamin D are thought to mediate their transcriptional effects in concert with coregulator proteins that modulate receptor interactions with components of the basal transcription complex. In an effort to identify potential coregulators, receptor fusions with glutathione-S-transferase were used to isolate proteins in nuclear extracts capable of binding nuclear hormone receptors. Glutathione-S-transferase fusions with mouse retinoid X receptor-alpha enabled the selective isolation of a 65-kDa protein (p65) from nuclear extracts of rat and human cells. Binding of p65 to mouse retinoid X receptor-alpha was centered around the DNA-binding domain. p65 also bound regions encompassing the DNA-binding domain in estrogen, thyroid hormone, and glucocorticoid receptors. p65 was identified as TLS (translocated-in-liposarcoma), a recently identified member of the RNP family of nuclear RNA-binding proteins whose members are thought to function in RNA processing. The N-terminal half of TLS bound to thyroid hormone receptor with high affinity while the receptor was bound to appropriate DNA target sites. Functional studies indicated that the N-terminal half of TLS can interact with thyroid hormone receptor in vivo. TLS was originally discovered as part of a fusion protein arising from a chromosomal translocation causing human myxoid liposarcomas. TLS contains a potent transactivation domain whose translocation-induced fusion with a DNA-binding protein (CHOP) yields a powerful transforming oncogene and transcription factor. The transactivation and RNA-binding properties of TLS and the nature of its interaction with nuclear receptors suggest a novel role in nuclear receptor function.
Collapse
Affiliation(s)
- C A Powers
- Division of Molecular Endocrinology, New York University Medical Center 10016, USA
| | | | | | | | | |
Collapse
|
16
|
Schmiedeskamp M, Rajagopal P, Klevit RE. NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1. Protein Sci 1997; 6:1835-48. [PMID: 9300483 PMCID: PMC2143792 DOI: 10.1002/pro.5560060904] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mutagenesis studies have revealed that the minimal DNA-binding domain of the yeast transcription factor ADR1 consists of two Cys2-His2 zinc fingers plus an additional 20 residues proximal and N-terminal to the fingers. We have assigned NMR 1H, 15N, and 13C chemical shifts for the entire minimal DNA-binding domain of ADR1 both free and bound to specific DNA. 1H chemical shift values suggest little structural difference between the zinc fingers in this construct and in single-finger constructs, and 13C alpha chemical shift index analysis indicates little change in finger structure upon DNA binding. 1H chemical shift perturbations upon DNA binding are observed, however, and these are mapped to define the protein-DNA interface. The two zinc fingers appear to bind DNA with different orientations, as the entire helix of finger 1 is perturbed, while only the extreme N-terminus of the finger 2 helix is affected. Furthermore, residues N-terminal to the first finger undergo large chemical shift changes upon DNA binding suggesting a role at the protein-DNA interface. A striking correspondence is observed between the protein-DNA interface mapped by chemical shift changes and that previously mapped by mutagenesis.
Collapse
Affiliation(s)
- M Schmiedeskamp
- Biomolecular Structure Center, University of Washington, Seattle 98195, USA
| | | | | |
Collapse
|
17
|
Chiang YC, Komarnitsky P, Chase D, Denis CL. ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB. J Biol Chem 1996; 271:32359-65. [PMID: 8943299 DOI: 10.1074/jbc.271.50.32359] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The yeast transcriptional activator ADR1, which is required for ADH2 and peroxisomal gene expression, contains four separable and partially redundant activation domains (TADs). Mutations in ADA2 or GCN5, encoding components of the ADA coactivator complex involved in histone acetylation, severely reduced LexA-ADR1-TAD activation of a LexA-lacZ reporter gene. Similarly, the ability of the wild-type ADR1 gene to activate an ADH2-driven promoter was compromised in strains deleted for ADA2 or GCN5. In contrast, defects in other general transcription cofactors such as CCR4, CAF1/POP2, and SNF/SWI displayed much less or no effect on LexA-ADR1-TAD activation. Using an in vitro protein binding assay, ADA2 and GCN5 were found to specifically contact individual ADR1 TADs. ADA2 could bind TAD II, and GCN5 physically interacted with all four TADs. Both TADs I and IV were also shown to make specific contacts to the C-terminal segment of TFIIB. In contrast, no significant binding to TBP was observed. TAD IV deletion analysis indicated that its ability to bind GCN5 and TFIIB was directly correlated with its ability to activate transcription in vivo. ADR1 TADs appear to make several contacts, which may help explain both their partial redundancy and their varying requirements at different promoters. The contact to and dependence on GCN5, a histone acetyltransferase, suggests that rearrangement of nucleosomes may be one important means by which ADR1 activates transcription.
Collapse
Affiliation(s)
- Y C Chiang
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
| | | | | | | |
Collapse
|
18
|
Svetlov VV, Cooper TG. Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 1995; 11:1439-84. [PMID: 8750235 DOI: 10.1002/yea.320111502] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- V V Svetlov
- Department of Microbiology and Immunology, University of Tennessee, Memphis 36163, USA
| | | |
Collapse
|
19
|
Simon MM, Pavlik P, Hartig A, Binder M, Ruis H, Cook WJ, Denis CL, Schanz B. A C-terminal region of the Saccharomyces cerevisiae transcription factor ADR1 plays an important role in the regulation of peroxisome proliferation by fatty acids. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:289-96. [PMID: 7500953 DOI: 10.1007/bf00290529] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Saccharomyces cerevisiae transcriptional activator ADR1, which controls ADH2 gene expression, was shown to be involved in the regulation of peroxisome proliferation. To study the mode of action of ADR1, we compared strains carrying the adr1-1 mutation, high or low copy numbers of the ADR1 gene, the constitutive allele ADR1-5c, and 3'-deletions of ADR1. High ADR1 gene dosage increased the transcription of genes encoding peroxisomal proteins as compared to one copy of the ADR1 gene. Furthermore, overexpression of ADR1 under ethanol growth conditions induced the proliferation of peroxisomal structures. The organelles were observed to be localized in clusters, a typical feature of peroxisomes induced by oleic acid. In contrast, the ADR1-5c allele, which induces ADH2 expression to a level comparable to that of high ADR1 gene dosage was found to have only a small effect. An analysis of functional domains of the ADR1 protein revealed that the N-terminal 220 amino acids of ADR1 were sufficient for wild-type levels of transcription of the FOX2, FOX3, and PAS1 genes, but the entire ADR1 protein was required for complete induction of the CTA1 gene and for growth oleic acid medium. Our data suggest that a functional domain of the ADR1 protein localized between residues 643 and 1323 is required for the induction of peroxisomal structures and for the utilization of oleic acid.
Collapse
Affiliation(s)
- M M Simon
- Zentrum für Angewandte Genetik, BOKU Wien/Austria
| | | | | | | | | | | | | | | |
Collapse
|