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Mikhailov N, Hämäläinen RH. Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases. Ann Biomed Eng 2024; 52:2627-2640. [PMID: 36001180 PMCID: PMC11329604 DOI: 10.1007/s10439-022-03051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/09/2022] [Indexed: 11/01/2022]
Abstract
Mitochondria, mainly known as energy factories of eukaryotic cells, also exert several additional signaling and metabolic functions and are today recognized as major cellular biosynthetic and signaling hubs. Mitochondria possess their own genome (mitochondrial DNA-mtDNA), that encodes proteins essential for oxidative phosphorylation, and mutations in it are an important contributor to human disease. The mtDNA mutations often exist in heteroplasmic conditions, with both healthy and mutant versions of the mtDNA residing in patients' cells and the level of mutant mtDNA may vary between different tissues and organs and affect the clinical outcome of the disease. Thus, shifting the ratio between healthy and mutant mtDNA in patients' cells provides an intriguing therapeutic option for mtDNA diseases. In this review we describe current strategies for modulating mitochondrial heteroplasmy levels with engineered endonucleases including mitochondrially targeted TALENs and Zinc finger nucleases (ZFNs) and discuss their therapeutic potential. These gene therapy tools could in the future provide therapeutic help both for patients with mitochondrial disease as well as in preventing the transfer of pathogenic mtDNA mutations from a mother to her offspring.
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Affiliation(s)
- Nikita Mikhailov
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Riikka H Hämäläinen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
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2
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Werner M, Brinkhofer J, Hammermüller L, Heim T, Pham TL, Huber J, Klein C, Thomas F. Peptide Boronic Acids by Late-Stage Hydroboration on the Solid Phase. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400640. [PMID: 38810019 PMCID: PMC11267286 DOI: 10.1002/advs.202400640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/15/2024] [Indexed: 05/31/2024]
Abstract
Organoboron compounds have a wide range of applications in numerous research fields, and methods to incorporate them in biomolecules are much sought after. Here, on-resin chemical syntheses of aliphatic and vinylogous peptide boronic acids are presented by transition metal-catalyzed late-stage hydroboration of alkene and alkyne groups in peptides and peptoids, for example on allyl- and propargylglycine residues, using readily available chemicals. These methods yield peptide boronic acids with much shorter linkers than previously reported on-resin methods. Furthermore, the methods are regio- and stereoselective, compatible with all canonical amino acid residues and can be applied to short, long, and in part even "difficult" peptide sequences. In a feasibility study, the protected peptide vinylboronic acids are further derivatized by the Petasis reaction using salicylaldehyde derivatives. The ability of the obtained peptide boronic acids to reversibly bind to carbohydrates is demonstrated in a catch-release model experiment using a fluorescently labeled peptide boronic acid on cross-linked dextran beads. In summary, this highlights the potential of the target compounds for drug discovery, glycan-specific target recognition, controlled release, and diagnostics.
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Affiliation(s)
- Marius Werner
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
- Medicinal ChemistryInstitute of Pharmacy and Molecular Biotechnology (IPMB)Heidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Julian Brinkhofer
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Leon Hammermüller
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Thomas Heim
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Truc Lam Pham
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Jonas Huber
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Christian Klein
- Medicinal ChemistryInstitute of Pharmacy and Molecular Biotechnology (IPMB)Heidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Franziska Thomas
- Institute of Organic ChemistryHeidelberg UniversityIm Neuenheimer Feld 27069120HeidelbergGermany
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3
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Chu M, Wang T, Li W, Liu Y, Bian Z, Mao J, Chen B. Genome-Wide Identification and Analysis of the Genes Encoding Q-Type C2H2 Zinc Finger Proteins in Grapevine. Int J Mol Sci 2023; 24:15180. [PMID: 37894862 PMCID: PMC10607507 DOI: 10.3390/ijms242015180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Q-type C2H2 zinc finger proteins (ZFPs), the largest family of transcription factors, have been extensively studied in plant genomes. However, the genes encoding this transcription factor family have not been explored in grapevine genomes. Therefore, in this study, we conducted a genome-wide identification of ZFP genes in three species of grapevine, namely Vitis vinifera, Vitis riparia, and Vitis amurensis, based on the sequence databases and phylogenetic and their conserved domains. We identified 52, 54, and 55 members of Q-type C2H2 ZFPs in V. vinifera, V. riparia, and V. amurensis, respectively. The physical and chemical properties of VvZFPs, VrZFPs, and VaZFPs were examined. The results showed that these proteins exhibited differences in the physical and chemical properties and that they all were hydrophobic proteins; the instability index showed that the four proteins were stable. The subcellular location of the ZFPs in the grapevine was predicted mainly in the nucleus. The phylogenetic tree analysis of the amino acid sequences of VvZFP, VaZFP, VrZFP, and AtZFP proteins showed that they were closely related and were divided into six subgroups. Chromosome mapping analysis showed that VvZFPs, VrZFPs, and VaZFPs were unevenly distributed on different chromosomes. The clustered gene analysis showed that the motif distribution was similar and the sequence of genes was highly conserved. Exon and intron structure analysis showed that 118 genes of ZFPs were intron deletion types, and the remaining genes had variable numbers of introns, ranging from 2 to 15. Cis-element analysis showed that the promoter of VvZFPs contained multiple cis-elements related to plant hormone response, stress resistance, and growth, among which the stress resistance elements were the predominant elements. Finally, the expression of VvZFP genes was determined using real-time quantitative PCR, which confirmed that the identified genes were involved in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), and low-temperature (4 °C) stress. VvZFP10-GFP and VvZFP46-GFP fusion proteins were localized in the nucleus of tobacco cells, and VvZFP10 is the most responsive gene among all VvZFPs with the highest relative expression level to MeJA, ABA, SA and low-temperature (4 °C) stress. The present study provides a theoretical basis for exploring the mechanism of response to exogenous hormones and low-temperature tolerance in grapes and its molecular breeding in the future.
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Affiliation(s)
| | | | | | | | | | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (M.C.)
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (M.C.)
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4
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Hajdu B, Hunyadi-Gulyás É, Kato K, Kawaguchi A, Nagata K, Gyurcsik B. Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA. J Biol Inorg Chem 2023; 28:301-315. [PMID: 36820987 PMCID: PMC10036435 DOI: 10.1007/s00775-023-01988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
Zinc finger proteins specifically recognize DNA sequences and, therefore, play a crucial role in living organisms. In this study the Zn(II)-, and DNA-binding of 1MEY#, an artificial zinc finger protein consisting of three finger units was characterized by multiple methods. Fluorimetric, circular dichroism and isothermal calorimetric titrations were applied to determine the accurate stability constant of a zinc finger protein. Assuming that all three zinc finger subunits behave identically, the obtained thermodynamic data for the Zn(II) binding were ΔHbinding site = - (23.5 - 28.0) kcal/mol (depending on the applied protonation state of the cysteines) and logβ'pH 7.4 = 12.2 ± 0.1, being similar to those of the CP1 consensus zinc finger peptide. The specific DNA binding of the protein can be characterized by logβ'pH 7.4 = 8.20 ± 0.08, which is comparable to the affinity of the natural zinc finger proteins (Sp1, WT1, TFIIIA) toward DNA. This value is ~ 1.9 logβ' unit higher than those determined for semi- or nonspecific DNA binding. Competitive circular dichroism and electrophoretic mobility shift measurements revealed that the conditional stability constant characteristic for Zn(II) binding of 1MEY# protein increased by 3.4 orders of magnitude in the presence of its target DNA sequence.
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Affiliation(s)
- Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary.
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Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding. INORGANICS 2023. [DOI: 10.3390/inorganics11020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.
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6
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Kluska K, Chorążewska A, Peris-Díaz MD, Adamczyk J, Krężel A. Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains. Int J Mol Sci 2022; 23:ijms232314602. [PMID: 36498928 PMCID: PMC9735795 DOI: 10.3390/ijms232314602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability.
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7
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Kluska K, Veronesi G, Deniaud A, Hajdu B, Gyurcsik B, Bal W, Krężel A. Structures of Silver Fingers and a Pathway to Their Genotoxicity. Angew Chem Int Ed Engl 2022; 61:e202116621. [PMID: 35041243 PMCID: PMC9303758 DOI: 10.1002/anie.202116621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Recently, we demonstrated that AgI can directly replace ZnII in zinc fingers (ZFs). The cooperative binding of AgI to ZFs leads to a thermodynamically irreversible formation of silver clusters destroying the native ZF structure. Thus, a reported loss of biological function of ZF proteins is a likely consequence of such replacement. Here, we report an X-ray absorption spectroscopy (XAS) study of Agn Sn clusters formed in ZFs to probe their structural features. Selective probing of the local environment around AgI by XAS showed the predominance of digonal AgI coordination to two sulfur donors, coordinated with an average Ag-S distance at 2.41 Å. No Ag-N bonds were present. A mixed AgS2 /AgS3 geometry was found solely in the CCCH AgI -ZF. We also show that cooperative replacement of ZnII ions with the studied Ag2 S2 clusters occurred in a three-ZF transcription factor protein 1MEY#, leading to a dissociation of 1MEY# from the complex with its cognate DNA.
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Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Giulia Veronesi
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 38000, Grenoble, France
| | - Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 38000, Grenoble, France
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Informatics, University of Szeged, Dóm tér 7, 6720, Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Informatics, University of Szeged, Dóm tér 7, 6720, Szeged, Hungary
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383, Wrocław, Poland
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8
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Kluska K, Veronesi G, Deniaud A, Hajdu B, Gyurcsik B, Bal W, Krezel A. Structures of Silver Fingers and a Pathway to Their Genotoxicity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Katarzyna Kluska
- University of Wroclaw: Uniwersytet Wroclawski Faculty of Biotechnology, Department of Chemical Biology 50-383 Wrocław POLAND
| | - Giulia Veronesi
- Université Grenoble Alpes: Universite Grenoble Alpes Laboratoire de Chimie et Biologie des Metaux F-38000 Grenoble FRANCE
| | - Aurelien Deniaud
- Université de Grenoble I: Universite Grenoble Alpes Laboratoire de Chimie at Biologie des Metaux F-38000 Grenoble FRANCE
| | - Balint Hajdu
- University of Szeged: Szegedi Tudomanyegyetem Department of Inorganic Analytical Chemistry H-6720 Szeged HUNGARY
| | - Bela Gyurcsik
- University of Szeged: Szegedi Tudomanyegyetem Depertment of Inorganic Analytical Chemistry H-6720 Szeged HUNGARY
| | - Wojciech Bal
- Polish Academy of Sciences: Polska Akademia Nauk Institute of Biochemistry and Biophysics 02-106 Warsaw POLAND
| | - Artur Krezel
- University of Wroclaw Department of Chemical Biology, Faculty of Biotechnology F. Joliot-Curie 14A 50-383 Wrocław POLAND
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9
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Kuang C, Xiao Y, Hondmann D. Cleavage-free human genome editing. Mol Ther 2022; 30:268-282. [PMID: 34864205 PMCID: PMC8753458 DOI: 10.1016/j.ymthe.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/17/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
Most gene editing technologies introduce breaks or nicks into DNA, leading to the generation of mutagenic insertions and deletions by non-homologous end-joining repair. Here, we report a new, cleavage-free gene editing approach based on replication interrupted template-driven DNA modification (RITDM). The RITDM system makes use of sequence-specific DLR fusion molecules that are specifically designed to enable localized, temporary blockage of DNA replication fork progression, thereby exposing single-stranded DNA that can be bound by DNA sequence modification templates for precise editing. We evaluate the use of zinc-finger arrays for sequence recognition. We demonstrate that RITDM can be used for gene editing at endogenous genomic loci in human cells and highlight its safety profile of low indel frequencies and undetectable off-target side effects in RITDM-edited clones and pools of cells.
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Affiliation(s)
- Chenzhong Kuang
- Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA
| | - Yan Xiao
- Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA
| | - Dirk Hondmann
- Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA,Corresponding author: Dirk Hondmann, Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA.
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10
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Yu S, Li Y, Gao L, Zhao P, Wang L, Li L, Lin YW. A highly selective and sensitive Zn 2+ fluorescent sensor based on zinc finger-like peptide and its application in cell imaging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 261:120042. [PMID: 34116420 DOI: 10.1016/j.saa.2021.120042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/14/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Developing new chemosensors for detection of Zn2+ has attracted great attentions because of the important roles of Zn2+ in biological systems, and it will produce toxic effects with an excessive intake of zinc ion. Metalloproteins are often used as an effective template for the design and development of peptide-based fluorescent sensors. In this study, we designed a new and simple ratiometric fluorescent sensor for Zn2+, which was based on a zinc finger-like peptide and labeled with a dansyl group, i.e., Dansyl-His-Gln-Arg-Thr-His-Trp-NH2 (D-P6), by using solid phase peptide synthesis (SPPS). The dimeric peptide has a high affinity for Zn2+ overothermetalions, as indicated by spectroscopic studies, as well as molecular modeling. Remarkably, the sensor exhibited a highly selective and sensitive ratiometric fluorescent response to Zn2+ by fluorescent resonance energy transfer effect between tryptophan residue and fluorophore dansyl group, with a very low detection limit of 33 nM in aqueous solution. Furthermore, the sensor displayed a very low biotoxicity, which allows successful detection of Zn2+ in living HeLa cells. We believe that the new sensor may have potential applications in biological science.
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Affiliation(s)
- Shuaibing Yu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yan Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Lei Gao
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital Affiliated to Shandong University, Liaocheng, China
| | - Peiran Zhao
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital Affiliated to Shandong University, Liaocheng, China
| | - Lei Wang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China.
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China.
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11
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Woolfson DN. A Brief History of De Novo Protein Design: Minimal, Rational, and Computational. J Mol Biol 2021; 433:167160. [PMID: 34298061 DOI: 10.1016/j.jmb.2021.167160] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
Abstract
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the primary motivation for de novo protein design was to test our understanding of the informational aspect of the protein-folding problem; i.e., how does protein sequence determine protein structure and function? This necessitated minimal and rational design approaches whereby the placement of each residue in a design was reasoned using chemical principles and/or biochemical knowledge. At that time, though with some notable exceptions, the use of computers to aid design was not widespread. Over the past two decades, the tables have turned and computational protein design is firmly established. Here, I illustrate this progress through a timeline of de novo protein structures that have been solved to atomic resolution and deposited in the Protein Data Bank. From this, it is clear that the impact of rational and computational design has been considerable: More-complex and more-sophisticated designs are being targeted with many being resolved to atomic resolution. Furthermore, our ability to generate and manipulate synthetic proteins has advanced to a point where they are providing realistic alternatives to natural protein functions for applications both in vitro and in cells. Also, and increasingly, computational protein design is becoming accessible to non-specialists. This all begs the questions: Is there still a place for minimal and rational design approaches? And, what challenges lie ahead for the burgeoning field of de novo protein design as a whole?
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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12
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Hussey BJ, McMillen DR. Programmable T7-based synthetic transcription factors. Nucleic Acids Res 2019; 46:9842-9854. [PMID: 30169636 PMCID: PMC6182181 DOI: 10.1093/nar/gky785] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
Despite recent progress on synthetic transcription factor generation in eukaryotes, there remains a need for high-activity bacterial versions of these systems. In synthetic biology applications, it is useful for transcription factors to have two key features: they should be orthogonal (influencing only their own targets, with minimal off-target effects), and programmable (able to be directed to a wide range of user-specified transcriptional start sites). The RNA polymerase of the bacteriophage T7 has a number of appealing properties for synthetic biological designs: it can produce high transcription rates; it is a compact, single-subunit polymerase that has been functionally expressed in a variety of organisms; and its viral origin reduces the connection between its activity and that of its host's transcriptional machinery. We have created a system where a T7 RNA polymerase is recruited to transcriptional start sites by DNA binding proteins, either directly or bridged through protein–protein interactions, yielding a modular and programmable system for strong transcriptional activation of multiple orthogonal synthetic transcription factor variants in Escherichia coli. To our knowledge this is the first exogenous, programmable activator system in bacteria.
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Affiliation(s)
- Brendan J Hussey
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - David R McMillen
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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13
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Chabert V, Lebrun V, Lebrun C, Latour JM, Sénèque O. Model peptide for anti-sigma factor domain HHCC zinc fingers: high reactivity toward 1O 2 leads to domain unfolding. Chem Sci 2019; 10:3608-3615. [PMID: 30996953 PMCID: PMC6432622 DOI: 10.1039/c9sc00341j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/14/2019] [Indexed: 11/25/2022] Open
Abstract
All organisms have to cope with the deleterious effects of reactive oxygen species. Some of them are able to mount a transcriptional response to various oxidative stresses, which involves sensor proteins capable of assessing the redox status of the cell or to detect reactive oxygen species. In this article, we describe the design, synthesis and characterization of Zn·LASD(HHCC), a model for the Zn(Cys)2(His)2 zinc finger site of ChrR, a sensor protein involved in the bacterial defence against singlet oxygen that belongs to the family of zinc-binding anti-sigma factors possessing a characteristic H/C-X24/25-H-X3-C-X2-C motif. The 46-amino acid model peptide LASD(HHCC) was synthetized by solid phase peptide synthesis and its Zn2+-binding properties were investigated using electronic absorption, circular dichroism and NMR. LASD(HHCC) forms a 1 : 1 complex with Zn2+, namely Zn·LASD(HHCC), that adopts a well-defined conformation with the Zn2+ ion capping a 3-helix core that reproduces almost perfectly the fold of the ChrR in the vicinity of its zinc site. H2O2 reacts with Zn·LASD(HHCC) to yield a disulfide with a second order rate constant of 0.030 ± 0.002 M-1 s-1. Zn·LASD(HHCC) reacts rapidly with singlet oxygen to yield sulfinates and sulfonates. A lower limit of the chemical reaction rate constant between Zn·LASD(HHCC) and 1O2 was determined to be 3.9 × 106 M-1 s-1. Therefore, the Zn(Cys)2(His)2 site of Zn·LASD(HHCC) appears to be at least 5 times more reactive toward these two oxidants than that of a classical ββα zinc finger. Consequences for the activation mechanism of ChrR are discussed.
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Affiliation(s)
- Valentin Chabert
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Vincent Lebrun
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Colette Lebrun
- Univ. Grenoble Alpes , CEA , CNRS , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Olivier Sénèque
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
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14
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Belczyk-Ciesielska A, Csipak B, Hajdu B, Sparavier A, Asaka MN, Nagata K, Gyurcsik B, Bal W. Nickel(ii)-promoted specific hydrolysis of zinc finger proteins. Metallomics 2018; 10:1089-1098. [DOI: 10.1039/c8mt00098k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The (S/T)XH sequence in Cys2His2zinc fingers can be hydrolytically cleaved by Ni(ii) ions. This reaction can be applied for purification, inhibition or activation of designed zinc finger fusion proteins.
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Affiliation(s)
| | - Brigitta Csipak
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | | | - Masamitsu N. Asaka
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Kyosuke Nagata
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- Warsaw
- Poland
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15
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Chemical Approach to Biological Safety: Molecular-Level Control of an Integrated Zinc Finger Nuclease. Chembiochem 2017; 19:66-75. [DOI: 10.1002/cbic.201700420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Indexed: 01/20/2023]
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16
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Patel A, Zhang X, Blumenthal RM, Cheng X. Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. J Biol Chem 2017; 292:15994-16002. [PMID: 28801461 DOI: 10.1074/jbc.m117.805754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/31/2017] [Indexed: 11/06/2022] Open
Abstract
PRDM9 is the only mammalian gene that has been associated with speciation. The PR/SET domain 9 (PRDM9) protein is a major determinant of meiotic recombination hot spots and acts through sequence-specific DNA binding via its C2H2 zinc finger (ZF) tandem array, which is highly polymorphic within and between species. The most common human variant, PRDM9 allele A (PRDM9a), contains 13 fingers (ZF1-13). Allele C (PRDM9c) is the second-most common among African populations and differs from PRDM9a by an arginine-to-serine change (R764S) in ZF9 and by replacement of ZF11 with two other fingers, yielding 14 fingers in PRDM9c. Here we co-crystallized the six-finger fragment ZF8-13 of PRDM9c, in complex with an oligonucleotide representing a known PRDM9c-specific hot spot sequence, and compared the structure with that of a characterized PRDM9a-specific complex. There are three major differences. First, Ser764 in ZF9 allows PRDM9c to accommodate a variable base, whereas PRDM9a Arg764 recognizes a conserved guanine. Second, the two-finger expansion of ZF11 allows PRDM9c to recognize three-base-pair-longer sequences. A tryptophan in the additional ZF interacts with a conserved thymine methyl group. Third, an Arg-Asp dipeptide immediately preceding the ZF helix, conserved in two PRDM9a fingers and three PRDM9c fingers, permits adaptability to variations from a C:G base pair (G-Arg interaction) to a G:C base pair (C-Asp interaction). This Arg-Asp conformational switch allows identical ZF modules to recognize different sequences. Our findings illuminate the molecular mechanisms for flexible and conserved binding of human PRDM9 alleles to their cognate DNA sequences.
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Affiliation(s)
- Anamika Patel
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Xing Zhang
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.,the Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and
| | - Robert M Blumenthal
- the Department of Medical Microbiology and Immunology and Program in Bioinformatics, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - Xiaodong Cheng
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, .,the Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and
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17
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Kauzlaric A, Ecco G, Cassano M, Duc J, Imbeault M, Trono D. The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units. PLoS One 2017; 12:e0173746. [PMID: 28334004 PMCID: PMC5363842 DOI: 10.1371/journal.pone.0173746] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/24/2017] [Indexed: 12/13/2022] Open
Abstract
KRAB-containing poly-zinc finger proteins (KZFPs) constitute the largest family of transcription factors encoded by mammalian genomes, and growing evidence indicates that they fulfill functions critical to both embryonic development and maintenance of adult homeostasis. KZFP genes underwent broad and independent waves of expansion in many higher vertebrates lineages, yet comprehensive studies of members harbored by a given species are scarce. Here we present a thorough analysis of KZFP genes and related units in the murine genome. We first identified about twice as many elements than previously annotated as either KZFP genes or pseudogenes, notably by assigning to this family an entity formerly considered as a large group of Satellite repeats. We then could delineate an organization in clusters distributed throughout the genome, with signs of recombination, translocation, duplication and seeding of new sites by retrotransposition of KZFP genes and related genetic units (KZFP/rGUs). Moreover, we harvested evidence indicating that closely related paralogs had evolved through both drifting and shifting of sequences encoding for zinc finger arrays. Finally, we could demonstrate that the KAP1-SETDB1 repressor complex tames the expression of KZFP/rGUs within clusters, yet that the primary targets of this regulation are not the KZFP/rGUs themselves but enhancers contained in neighboring endogenous retroelements and that, underneath, KZFPs conserve highly individualized patterns of expression.
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Affiliation(s)
- Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marco Cassano
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Imbeault
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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18
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Haas SA, Dettmer V, Cathomen T. Therapeutic genome editing with engineered nucleases. Hamostaseologie 2017; 37:45-52. [PMID: 28070592 DOI: 10.5482/hamo-16-09-0035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/20/2016] [Indexed: 01/17/2023] Open
Abstract
Targeted genome editing with designer nucleases, such as zinc finger nucleases, TALE nucleases, and CRISPR-Cas nucleases, has heralded a new era in gene therapy. Genetic disorders, which have not been amenable to conventional gene-addition-type gene therapy approaches, such as disorders with dominant inheritance or diseases caused by mutations in tightly regulated genes, can now be treated by precise genome surgery. Moreover, engineered nucleases enable novel genetic interventions to fight infectious diseases or to improve cancer immunotherapies. Here, we review the development of the different classes of programmable nucleases, discuss the challenges and improvements in translating gene editing into clinical use, and give an outlook on what applications can expect to enter the clinic in the near future.
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Affiliation(s)
| | | | - Toni Cathomen
- Toni Cathomen, Ph.D., Institute for Cell and Gene Therapy, Medical Center - University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, Phone: +49 761 270 34800, Fax: + 49 761 270 37900, E-Mail:
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19
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Pereira CV, Moraes CT. Current strategies towards therapeutic manipulation of mtDNA heteroplasmy. Front Biosci (Landmark Ed) 2017; 22:991-1010. [PMID: 27814659 DOI: 10.2741/4529] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mitochondrial disease is a multifactorial disorder involving both nuclear and mitochondrial genomes. Over the past 20 years, great progress was achieved in the field of gene editing which raised the possibility of partial or complete elimination of mutant mtDNA that causes disease phenotypes. Each cell contains thousands of copies of mtDNA which can be either wild-type (WT) or mutant, a condition called heteroplasmy. As there are multiple copies of mtDNA inside a cell, the percentage of mutant mtDNA can vary and a directional shift in the heteroplasmy ratio towards an increase of WT mtDNA copies would have therapeutic value. Gene editing tools have been adapted to translocate to mitochondria and were able to change heteroplasmy in a predictable manner. These include mitochondrial targeted restriction endonucleases, Zinc-finger nucleases, and TAL-effector nucleases. These procedures could also be adapted to reduce the levels of mutant mtDNA in embryos, offering an option to the controversial mitochondrial replacement techniques during in vitro fertilization. The current strategies to induce heteroplasmy shift of mtDNA and its implications will be comprehensively discussed.
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Affiliation(s)
- Claudia V Pereira
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA,
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20
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Loviglio MN, Beck CR, White JJ, Leleu M, Harel T, Guex N, Niknejad A, Bi W, Chen ES, Crespo I, Yan J, Charng WL, Gu S, Fang P, Coban-Akdemir Z, Shaw CA, Jhangiani SN, Muzny DM, Gibbs RA, Rougemont J, Xenarios I, Lupski JR, Reymond A. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Med 2016; 8:105. [PMID: 27799067 PMCID: PMC5088687 DOI: 10.1186/s13073-016-0359-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/16/2016] [Indexed: 02/13/2023] Open
Abstract
Background Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. Methods We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes. Results Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1–/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1–/– mouse model. Conclusions These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Nicla Loviglio
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marion Leleu
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicolas Guex
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Anne Niknejad
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Crespo
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Jiong Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Laboratory Medicine Program, UHN, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 2C4, Canada
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Fang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: WuXiNextCODE, 101Main Street, Cambridge, MA, 02142, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacques Rougemont
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
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21
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Golas MM, Sander B. Use of human stem cells in Huntington disease modeling and translational research. Exp Neurol 2016; 278:76-90. [PMID: 26826449 DOI: 10.1016/j.expneurol.2016.01.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/08/2023]
Abstract
Huntington disease (HD) is a devastating neurological disorder caused by an extended CAG repeat in exon 1 of the gene that encodes the huntingtin (HTT) protein. HD pathology involves a loss of striatal medium spiny neurons (MSNs) and progressive neurodegeneration affects the striatum and other brain regions. Because HTT is involved in multiple cellular processes, the molecular mechanisms of HD pathogenesis should be investigated on multiple levels. On the cellular level, in vitro stem cell models, such as induced pluripotent stem cells (iPSCs) derived from HD patients and HD embryonic stem cells (ESCs), have yielded progress. Approaches to differentiate functional MSNs from ESCs, iPSCs, and neural stem/progenitor cells (NSCs/NPCs) have been established, enabling MSN differentiation to be studied and disease phenotypes to be recapitulated. Isolation of target stem cells and precursor cells may also provide a resource for grafting. In animal models, transplantation of striatal precursors differentiated in vitro to the striatum has been reported to improve disease phenotype. Initial clinical trials examining intrastriatal transplantation of fetal neural tissue suggest a more favorable clinical course in a subset of HD patients, though shortcomings persist. Here, we review recent advances in the development of cellular HD models and approaches aimed at cell regeneration with human stem cells. We also describe how genome editing tools could be used to correct the HTT mutation in patient-specific stem cells. Finally, we discuss the potential and the remaining challenges of stem cell-based approaches in HD research and therapy development.
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Affiliation(s)
- Monika M Golas
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.
| | - Bjoern Sander
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Aarhus University, Aarhus C, Denmark
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22
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Rewriting DNA Methylation Signatures at Will: The Curable Genome Within Reach? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:475-490. [DOI: 10.1007/978-3-319-43624-1_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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23
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Kapopoulou A, Mathew L, Wong A, Trono D, Jensen JD. The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution 2015; 70:167-80. [PMID: 26593440 DOI: 10.1111/evo.12819] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 01/08/2023]
Abstract
The KRAB-containing zinc finger (KRAB-ZF) proteins represent the largest family of transcription factors (TFs) in humans, yet for the great majority, their function and specific genomic target remain unknown. However, it has been shown that a large fraction of these genes arose from segmental duplications, and that they have expanded in gene and zinc finger number throughout vertebrate evolution. To determine whether this expansion is linked to selective pressures acting on different domains, we have manually curated all KRAB-ZF genes present in the human genome together with their orthologous genes in three closely related species and assessed the evolutionary forces acting at the sequence level as well as on their expression profiles. We provide evidence that KRAB-ZFs can be separated into two categories according to the polymorphism present in their DNA-contacting residues. Those carrying a nonsynonymous single nucleotide polymorphism (SNP) in their DNA-contacting amino acids exhibit significantly reduced expression in all tissues, have emerged in a recent lineage, and seem to be less strongly constrained evolutionarily than those without such a polymorphism. This work provides evidence for a link between age of the TF, as well as polymorphism in their DNA-contacting residues and expression levels-both of which may be jointly affected by selection.
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Affiliation(s)
- Adamandia Kapopoulou
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 1015
| | - Lisha Mathew
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 1015
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Canada, K15 5B6
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 1015.
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24
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Azia A, Levy R, Unger R, Edelman M, Sobolev V. Genome-wide computational determination of the human metalloproteome. Proteins 2015; 83:931-9. [PMID: 25739467 DOI: 10.1002/prot.24790] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/06/2015] [Accepted: 02/25/2015] [Indexed: 11/08/2022]
Abstract
Accurate prediction of protein function in humans is important for understanding biological processes at the molecular level in biomedicine and drug design. Over a third of proteins are commonly held to bind metal, and ∼10% of human proteins, to bind zinc. Therefore, an initial step in protein function prediction frequently involves predicting metal ion binding. In recent years, methods have been developed to predict a set of residues in 3D space forming the metal-ion binding site, often with a high degree of accuracy. Here, using extensions of these methods, we provide an extensive list of human proteins and their putative metal ion binding site residues, using translated gene sequences derived from the complete, resolved human genome. Under conditions of ∼90% selectivity, over 900 new human putative metal ion binding proteins are identified. A statistical analysis of resolved metal ion binding sites in the human metalloproteome is furnished and the importance of remote homology analysis is demonstrated. As an example, a novel metal-ion binding site involving a complex of a botulinum substrate with its inhibitor is presented. On the basis of the location of the predicted site and the interactions of the contacting residues at the complex interface, we postulate that metal ion binding in this region could influence complex formation and, consequently, the functioning of the protein. Thus, this work provides testable hypotheses about novel functions of known proteins.
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Affiliation(s)
- Ariel Azia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
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25
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Khedkar SA, Sun X, Rigby AC, Feinberg MW. Discovery of small molecule inhibitors to Krüppel-like factor 10 (KLF10): implications for modulation of T regulatory cell differentiation. J Med Chem 2015; 58:1466-78. [PMID: 25581017 DOI: 10.1021/jm5018187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Krüppel-like family of transcription factors (KLFs) constitute a subfamily of C2H2-type zinc finger proteins with distinct cell-type expression patterns and regulate functional aspects of cell growth and differentiation, activation, or development. KLF10 has been previously shown to critically regulate the acquisition of CD4+CD25+ T regulatory cell differentiation and function, an effect important to the maintenance of self-tolerance, immune suppression, and tumor immunosurveillance. To date, there are no selective pharmacological inhibitors to KLF10. Herein, we report on the discovery of first-in-class small molecule compounds that inhibit the KLF10-DNA interaction interface using computer-aided drug design (CADD) screens of chemical libraries. Interrogation of a "druggable" pocket in the second zinc finger of KLF10 revealed three small molecules, #48, #48-15, and #15-09, with similar scaffolds and binding patterns. Each of these small molecules inhibited KLF10-DNA binding and transcriptional activity, conversion of CD4+CD25- T cells to CD4+CD25+ T regulatory cells, and KLF10 target gene expression. Taken together, these findings support the feasibility of using CADD with functional assays to identify small molecules that target members of the KLF subfamily of transcription factors to regulate biological functions in health and disease. We hope these novel compounds will serve as useful mechanistic probes for KLF10-mediated effects and T regulatory cell biology.
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Affiliation(s)
- Santosh A Khedkar
- Department of Medicine, Division of Molecular and Vascular Medicine, Center for Vascular Biology Research, Beth Israel Deaconess Medical Center , 99 Brookline Avenue, RN-227, Boston, Massachusetts 02215, United States
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Liu H, Chang LH, Sun Y, Lu X, Stubbs L. Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies. Genome Biol Evol 2014; 6:510-25. [PMID: 24534434 PMCID: PMC3971581 DOI: 10.1093/gbe/evu030] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While many vertebrate transcription factor (TF) families are conserved, the C2H2 zinc finger (ZNF) family stands out as a notable exception. In particular, novel ZNF gene types have arisen, duplicated, and diverged independently throughout evolution to yield many lineage-specific TF genes. This evolutionary dynamic not only raises many intriguing questions but also severely complicates identification of those ZNF genes that remain functionally conserved. To address this problem, we searched for vertebrate “DNA binding orthologs” by mining ZNF loci from eight sequenced genomes and then aligning the patterns of DNA-binding amino acids, or “fingerprints,” extracted from the encoded ZNF motifs. Using this approach, we found hundreds of lineage-specific genes in each species and also hundreds of orthologous groups. Most groups of orthologs displayed some degree of fingerprint divergence between species, but 174 groups showed fingerprint patterns that have been very rigidly conserved. Focusing on the dynamic KRAB-ZNF subfamily—including nearly 400 human genes thought to possess potent KRAB-mediated epigenetic silencing activities—we found only three genes conserved between mammals and nonmammalian groups. These three genes, members of an ancient familial cluster, encode an unusual KRAB domain that functions as a transcriptional activator. Evolutionary analysis confirms the ancient provenance of this activating KRAB and reveals the independent expansion of KRAB-ZNFs in every vertebrate lineage. Most human ZNF genes, from the most deeply conserved to the primate-specific genes, are highly expressed in immune and reproductive tissues, indicating that they have been enlisted to regulate evolutionarily divergent biological traits.
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Affiliation(s)
- Hui Liu
- Center for Biophysics and Computational Biology, University of Illinois, Urbana
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Németh E, Schilli GK, Nagy G, Hasenhindl C, Gyurcsik B, Oostenbrink C. Design of a colicin E7 based chimeric zinc-finger nuclease. J Comput Aided Mol Des 2014; 28:841-50. [PMID: 24952471 PMCID: PMC4104000 DOI: 10.1007/s10822-014-9765-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/13/2014] [Indexed: 12/02/2022]
Abstract
Colicin E7 is a natural bacterial toxin. Its nuclease domain (NColE7) enters the target cell and kills it by digesting the nucleic acids. The HNH-motif as the catalytic centre of NColE7 at the C-terminus requires the positively charged N-terminal loop for the nuclease activity-offering opportunities for allosteric control in a NColE7-based artificial nuclease. Accordingly, four novel zinc finger nucleases were designed by computational methods exploiting the special structural features of NColE7. The constructed models were subjected to MD simulations. The comparison of structural stability and functional aspects showed that these models may function as safely controlled artificial nucleases. This study was complemented by random mutagenesis experiments identifying potentially important residues for NColE7 function outside the catalytic region.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720 Hungary
| | - Gabriella K. Schilli
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720 Hungary
| | - Gábor Nagy
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Christoph Hasenhindl
- Christian Doppler Laboratory for Antibody Engineering, Department of Chemistry, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720 Hungary
- MTA-SzTE Bioinorganic Chemistry Research Group of Hungarian Academy of Sciences, Dóm tér 7, Szeged, 6720 Hungary
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
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Pröpper K, Meindl K, Sammito M, Dittrich B, Sheldrick GM, Pohl E, Usón I. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1743-57. [PMID: 24914984 PMCID: PMC4051508 DOI: 10.1107/s1399004714007603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/04/2014] [Indexed: 11/11/2022]
Abstract
Protein-DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein-DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein-DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein-DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.
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Affiliation(s)
- Kevin Pröpper
- University of Göttingen, Germany
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Kathrin Meindl
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Massimo Sammito
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | | | | | | | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Spain
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29
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Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD. An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res 2014; 42:4800-12. [PMID: 24523353 PMCID: PMC4005693 DOI: 10.1093/nar/gku132] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/17/2022] Open
Abstract
Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan G. Christensen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Heather A. Bell
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Mathew Goodwin
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ronak Y. Patel
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Manishi Pandey
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Metewo Selase Enuameh
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Stacey Thibodeau-Beganny
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H. Brodsky
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - J. Keith Joung
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Gary D. Stormo
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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30
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Zhang Y, Lei CQ, Hu YH, Xia T, Li M, Zhong B, Shu HB. Krüppel-like factor 6 is a co-activator of NF-κB that mediates p65-dependent transcription of selected downstream genes. J Biol Chem 2014; 289:12876-85. [PMID: 24634218 DOI: 10.1074/jbc.m113.535831] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor NF-κB plays a pivotal role in a broad range of physiological and pathological processes, including development, inflammation, and immunity. How NF-κB integrates activating signals to expression of specific sets of target genes is of great interest. Here, we identified Krüppel-like factor 6 (KLF6) as a co-activator of NF-κB after TNFα and IL-1β stimulation. Overexpression of KLF6 enhanced TNFα- and IL-1β-induced activation of NF-κB and transcription of a subset of downstream genes, whereas knockdown of KLF6 had opposite effects. KLF6 interacted with p65 in the nucleus and bound to the promoters of target genes. Upon IL-1β stimulation, KLF6 was recruited to promoters of a subset of NF-κB target genes in a p65-dependent manner, which was in turn required for the optimal binding of p65 to the target gene promoters. Our findings thus identified KLF6 as a previously unknown but essential co-activator of NF-κB and provided new insight into the molecular regulation of p65-dependent gene expression.
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Affiliation(s)
- Yu Zhang
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
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31
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Pillay LM, Selland LG, Fleisch VC, Leighton PLA, Cheng CS, Famulski JK, Ritzel RG, March LD, Wang H, Allison WT, Waskiewicz AJ. Evaluating the mutagenic activity of targeted endonucleases containing a Sharkey FokI cleavage domain variant in zebrafish. Zebrafish 2013; 10:353-64. [PMID: 23781947 DOI: 10.1089/zeb.2012.0832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic targeted endonucleases such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) have recently emerged as powerful tools for targeted mutagenesis, especially in organisms that are not amenable to embryonic stem cell manipulation. Both ZFNs and TALENs consist of DNA-binding arrays that are fused to the nonspecific FokI nuclease domain. In an effort to improve targeted endonuclease mutagenesis efficiency, we enhanced their catalytic activity using the Sharkey FokI nuclease domain variant. All constructs tested display increased DNA cleavage activity in vitro. We demonstrate that one out of four ZFN arrays containing the Sharkey FokI variant exhibits a dramatic increase in mutagenesis frequency in vivo in zebrafish. The other three ZFNs exhibit no significant alteration of activity in vivo. Conversely, we demonstrate that TALENs containing the Sharkey FokI variant exhibit absent or severely reduced in vivo mutagenic activity in zebrafish. Notably, Sharkey ZFNs and TALENs do not generate increased toxicity-related defects or mortality. Our results present Sharkey ZFNs as an effective alternative to conventional ZFNs, but advise against the use of Sharkey TALENs.
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Affiliation(s)
- Laura M Pillay
- Department of Biological Sciences, University of Alberta , Edmonton, Canada
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32
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Vandevenne M, Jacques DA, Artuz C, Nguyen CD, Kwan AHY, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay JP. New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217. J Biol Chem 2013; 288:10616-27. [PMID: 23436653 DOI: 10.1074/jbc.m112.441451] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Classical zinc fingers (ZFs) are one of the most abundant and best characterized DNA-binding domains. Typically, tandem arrays of three or more ZFs bind DNA target sequences with high affinity and specificity, and the mode of DNA recognition is sufficiently well understood that tailor-made ZF-based DNA-binding proteins can be engineered. We have shown previously that a two-zinc finger unit found in the transcriptional coregulator ZNF217 recognizes DNA but with an affinity and specificity that is lower than other ZF arrays. To investigate the basis for these differences, we determined the structure of a ZNF217-DNA complex. We show that although the overall position of the ZFs on the DNA closely resembles that observed for other ZFs, the side-chain interaction pattern differs substantially from the canonical model. The structure also reveals the presence of two methyl-π interactions, each featuring a tyrosine contacting a thymine methyl group. To our knowledge, interactions of this type have not previously been described in classical ZF-DNA complexes. Finally, we investigated the sequence specificity of this two-ZF unit and discuss how ZNF217 might discriminate its target DNA sites in the cell.
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Affiliation(s)
- Marylène Vandevenne
- School of Molecular Bioscience, University of Sydney, New South Wales, 2006 Australia
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33
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Structure and dynamics of a primordial catalytic fold generated by in vitro evolution. Nat Chem Biol 2012; 9:81-3. [PMID: 23222886 PMCID: PMC3552148 DOI: 10.1038/nchembio.1138] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 11/01/2012] [Indexed: 11/15/2022]
Abstract
Engineering functional protein scaffolds capable of carrying out chemical catalysis is a major challenge in enzyme design. Starting from a non-catalytic protein scaffold, we recently generated a novel RNA ligase by in vitro directed evolution. This artificial enzyme lost its original fold and adopted an entirely novel structure with dramatically enhanced conformational dynamics, demonstrating that a primordial fold with suitable flexibility is sufficient to carry out enzymatic function.
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Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM. Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger. Nucleic Acids Res 2012; 40:11563-70. [PMID: 23042681 PMCID: PMC3526281 DOI: 10.1093/nar/gks885] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribonucleases (RNases) are valuable tools applied in the analysis of RNA sequence, structure and function. Their substrate specificity is limited to recognition of single bases or distinct secondary structures in the substrate. Currently, there are no RNases available for purely sequence-dependent fragmentation of RNA. Here, we report the development of a new enzyme that cleaves the RNA strand in DNA-RNA hybrids 5 nt from a nonanucleotide recognition sequence. The enzyme was constructed by fusing two functionally independent domains, a RNase HI, that hydrolyzes RNA in DNA-RNA hybrids in processive and sequence-independent manner, and a zinc finger that recognizes a sequence in DNA-RNA hybrids. The optimization of the fusion enzyme's specificity was guided by a structural model of the protein-substrate complex and involved a number of steps, including site-directed mutagenesis of the RNase moiety and optimization of the interdomain linker length. Methods for engineering zinc finger domains with new sequence specificities are readily available, making it feasible to acquire a library of RNases that recognize and cleave a variety of sequences, much like the commercially available assortment of restriction enzymes. Potentially, zinc finger-RNase HI fusions may, in addition to in vitro applications, be used in vivo for targeted RNA degradation.
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Affiliation(s)
- Agata A Sulej
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena Street 4, 02-109 Warsaw, Poland
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35
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Boyle AL, Bromley EHC, Bartlett GJ, Sessions RB, Sharp TH, Williams CL, Curmi PMG, Forde NR, Linke H, Woolfson DN. Squaring the circle in peptide assembly: from fibers to discrete nanostructures by de novo design. J Am Chem Soc 2012; 134:15457-67. [PMID: 22917063 DOI: 10.1021/ja3053943] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The design of bioinspired nanostructures and materials of defined size and shape is challenging as it pushes our understanding of biomolecular assembly to its limits. In such endeavors, DNA is the current building block of choice because of its predictable and programmable self-assembly. The use of peptide- and protein-based systems, however, has potential advantages due to their more-varied chemistries, structures and functions, and the prospects for recombinant production through gene synthesis and expression. Here, we present the design and characterization of two complementary peptides programmed to form a parallel heterodimeric coiled coil, which we use as the building blocks for larger, supramolecular assemblies. To achieve the latter, the two peptides are joined via peptidic linkers of variable lengths to produce a range of assemblies, from flexible fibers of indefinite length, through large colloidal-scale assemblies, down to closed and discrete nanoscale objects of defined stoichiometry. We posit that the different modes of assembly reflect the interplay between steric constraints imposed by short linkers and the bulk of the helices, and entropic factors that favor the formation of many smaller objects as the linker length is increased. This approach, and the resulting linear and proteinogenic polypeptides, represents a new route for constructing complex peptide-based assemblies and biomaterials.
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Affiliation(s)
- Aimee L Boyle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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36
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Sun N, Abil Z, Zhao H. Recent advances in targeted genome engineering in mammalian systems. Biotechnol J 2012; 7:1074-87. [PMID: 22777886 DOI: 10.1002/biot.201200038] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/22/2012] [Accepted: 06/15/2012] [Indexed: 12/21/2022]
Abstract
Targeted genome engineering enables researchers to disrupt, insert, or replace a genomic sequence precisely at a predetermined locus. One well-established technology to edit a mammalian genome is known as gene targeting, which is based on the homologous recombination (HR) mechanism. However, the low HR frequency in mammalian cells (except for mice) prevents its wide application. To address this limitation, a custom-designed nuclease is used to introduce a site-specific DNA double-strand break (DSB) on the chromosome and the subsequent repair of the DSB by the HR mechanism or the non-homologous end joining mechanism results in efficient targeted genome modifications. Engineered homing endonucleases (also called meganucleases), zinc finger nucleases, and transcription activator-like effector nucleases represent the three major classes of custom-designed nucleases that have been successfully applied in many different organisms for targeted genome engineering. This article reviews the recent developments of these genome engineering tools and highlights a few representative applications in mammalian systems. Recent advances in gene delivery strategies of these custom-designed nucleases are also briefly discussed.
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Affiliation(s)
- Ning Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 61801, USA
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37
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Inhibition of Binding of Tomato Yellow Leaf Curl Virus Rep to its Replication Origin by Artificial Zinc-Finger Protein. Mol Biotechnol 2012; 54:198-203. [DOI: 10.1007/s12033-012-9552-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Nomura W, Masuda A, Ohba K, Urabe A, Ito N, Ryo A, Yamamoto N, Tamamura H. Effects of DNA binding of the zinc finger and linkers for domain fusion on the catalytic activity of sequence-specific chimeric recombinases determined by a facile fluorescent system. Biochemistry 2012; 51:1510-7. [PMID: 22304662 DOI: 10.1021/bi201878x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial zinc finger proteins (ZFPs) consist of Cys(2)-His(2)-type modules composed of ∼30 amino acids with a ββα structure that coordinates a zinc ion. ZFPs that recognize specific DNA target sequences can substitute for the binding domains of enzymes that act on DNA to create designer enzymes with programmable sequence specificity. The most studied of these engineered enzymes are zinc finger nucleases (ZFNs). ZFNs have been widely used to model organisms and are currently in human clinical trials with an aim of therapeutic gene editing. Difficulties with ZFNs arise from unpredictable mutations caused by nonhomologous end joining and off-target DNA cleavage and mutagenesis. A more recent strategy that aims to address the shortcomings of ZFNs involves zinc finger recombinases (ZFRs). A thorough understanding of ZFRs and methods for their modification promises powerful new tools for gene manipulation in model organisms as well as in gene therapy. In an effort to design efficient and specific ZFRs, the effects of the DNA binding affinity of the zinc finger domains and the linker sequence between ZFPs and recombinase catalytic domains have been assessed. A plasmid system containing ZFR target sites was constructed for evaluation of catalytic activities of ZFRs with variable linker lengths and numbers of zinc finger modules. Recombination efficiencies were evaluated by restriction enzyme analysis of isolated plasmids after reaction in Escherichia coli and changes in EGFP fluorescence in mammalian cells. The results provide information relevant to the design of ZFRs that will be useful for sequence-specific genome modification.
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Affiliation(s)
- Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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39
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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Abstract
Vertebrate genomes encode large and highly variable numbers of tandem C2H2 zinc finger (tandem ZF) transcription factor proteins. In mammals, most tandem ZF genes also encode a KRAB domain (KZNF proteins). Very little is known about what forces have driven the number and diversity of tandem ZF genes. Recent studies suggest that one role of KZNF proteins is to bind and repress transcription of exogenous retroviruses and their endogenous counterpart LTR retroelements. We report a striking correlation across vertebrate genomes between the number of LTR retroelements and the number of host tandem ZF genes. This correlation is specific to LTR retroelements and ZF genes and was not explained by covariation in other genomic features. We further show that recently active LTR retroelements are correlated with recent tandem ZF gene duplicates across vertebrates. On branches of the primate phylogeny, we find that the appearance of new families of endogenous retroviruses is strongly predictive of the appearance of new duplicate KZNF genes. We hypothesize that retroviral and LTR retroelement burden drives evolution of host tandem ZF genes. This hypothesis is consistent with previously described molecular evolutionary patterns in duplicate ZF genes throughout vertebrates. To further explore these patterns, we investigated 34 duplicate human KZNF gene pairs, all of which underwent an early burst of divergence in the major nucleotide contact residues of their ZF domains, followed by purifying selection in both duplicates. Our results support a host-pathogen model for tandem ZF gene evolution, in which new LTR retroelement challenges drive duplication and divergence of host tandem ZF genes.
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Affiliation(s)
- James H Thomas
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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41
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Payne MA. Zinc finger structure-function in Ikaros Marvin A Payne. World J Biol Chem 2011; 2:161-6. [PMID: 21765982 PMCID: PMC3135863 DOI: 10.4331/wjbc.v2.i6.161] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/06/2011] [Accepted: 05/13/2011] [Indexed: 02/05/2023] Open
Abstract
The zinc finger motif was used as a vehicle for the initial discovery of Ikaros in the context of T-cell differentiation and has been central to all subsequent analyses of Ikaros function. The Ikaros gene is alternately spliced to produce several isoforms that confer diversity of function and consequently have complicated analysis of the function of Ikaros in vivo. Key features of Ikaros in vivo function are associated with six C2H2 zinc fingers; four of which are alternately incorporated in the production of the various Ikaros isoforms. Although no complete structures are available for the Ikaros protein or any of its family members, considerable evidence has accumulated about the structure of zinc fingers and the role that this structure plays in the functions of the Ikaros family of proteins. This review summarizes the structural aspects of Ikaros zinc fingers, individually, and in tandem to provide a structural context for Ikaros function and to provide a structural basis to inform the design of future experiments with Ikaros and its family members.
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Affiliation(s)
- Marvin A Payne
- Department of Chemistry and Biochemistry, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA, USA
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42
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Abstract
Due to specific recognization of DNA sequences and designability, zinc finger nucleases (ZFN) has been used in knock in and knock out genes. Because of high ratio of homologous recombination of DSB-GT induces by ZFN, ZFN technology has been considered as the most powerful tool for gene modification. It has been successfully used at cell or embryo levels in plants and animals. Under the rapid development of high affinity zinc finger protein (ZFP), this technique will be applied to genetic engineering and breeding extensively in the future. This review discussed the DNA recognization mechanism and double strand break gene targeting (DSB-GT) of zinc finger nucleases (ZFN). Some application examples of ZFN were summarized.
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43
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Lee SJ, Michalek JL, Besold AN, Rokita SE, Michel SLJ. Classical Cys2His2 Zinc Finger Peptides Are Rapidly Oxidized by Either H2O2 or O2 Irrespective of Metal Coordination. Inorg Chem 2011; 50:5442-50. [DOI: 10.1021/ic102252a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Seung Jae Lee
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Jamie L. Michalek
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Angelique N. Besold
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Steven E. Rokita
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-4454, United States
| | - Sarah L. J. Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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44
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Persikov AV, Singh M. An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. Phys Biol 2011; 8:035010. [PMID: 21572177 DOI: 10.1088/1478-3975/8/3/035010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cys(2)His(2) zinc finger (C2H2-ZF) proteins comprise the largest class of eukaryotic transcription factors. The 'canonical model' for C2H2-ZF protein-DNA interaction consists of only four amino acid-nucleotide contacts per zinc finger domain, and this model has been the basis for several efforts for computationally predicting and experimentally designing protein-DNA interfaces. Here, we perform a systematic analysis of structural and experimental binding data and find that, in addition to the canonical contacts, several other amino acid and base pair combinations frequently play a role in C2H2-ZF protein-DNA binding. We suggest an expansion of the canonical C2H2-ZF model to include one to three additional contacts, and show that computational approaches including these additional contacts improve predictions of DNA targets of zinc finger proteins.
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Affiliation(s)
- Anton V Persikov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ, USA
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45
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Nagy G, Gyurcsik B, Hoffmann EA, Körtvélyesi T. Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods. J Mol Graph Model 2011; 29:928-34. [PMID: 21470886 DOI: 10.1016/j.jmgm.2011.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 02/24/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
The interactions of a zinc-finger (ZF) protein with DNA containing the specific recognition site of the ZF and with a non-specific DNA were studied with the semi-empirical quantum chemical method of PM6/Mozyme. The ZF protein (1MEY)-DNA complex structures were generated by docking calculations. The complex structures were reoptimized with the PM6/Mozyme method with implicit solvation in water. The structures were also calculated in the gas phase. The interaction enthalpies between the protein and DNA within the complexes obtained in the PM6/Mozyme with solvation optimized structures were calculated with the single-point PM6-DH2/Mozyme method (PM6 with dispersion, H-bond correction and Mozyme) with solvation. The results supported the specific and non-specific interactions in the complexes obtained from the docking experiments. The binding enthalpies of the specific and non-specific DNA binding to the protein differed significantly. The interactions between the nucleic acid strands in duplexes were also evaluated; these interactions between the base pairs were different because of the different "G…C:A…T" ratios in the DNA molecules studied. The stacking interactions between the nucleic bases were also characterized in the DNA duplexes.
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Affiliation(s)
- Gábor Nagy
- Department of Physical Chemistry and Material Sciences, University of Szeged, Aradi Vértanuk tere 1, H-6720 Szeged, Hungary
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46
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Berezovskaya Y, Armstrong CT, Boyle AL, Porrini M, Woolfson DN, Barran PE. Metal binding to a zinc-finger peptide: a comparison between solution and the gas phase. Chem Commun (Camb) 2011; 47:412-4. [DOI: 10.1039/c0cc02445g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Guerrerio AL, Berg JM. Design of single-stranded nucleic acid binding peptides based on nucleocapsid CCHC-box zinc-binding domains. J Am Chem Soc 2010; 132:9638-43. [PMID: 20586464 DOI: 10.1021/ja910942v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structures of nucleocapsid (NC)-like CCHC zinc-binding domains bound to nucleic acid targets have revealed that these domains bind guanosine residues within single-stranded nucleic acids. Here, we have performed initial studies examining the potential use of NC-like CCHC zinc-binding domains as modules to construct single-stranded nucleic acid binding peptides. The affinity for guanosine-containing single-stranded deoxyribooligonucleotides increases with the number of CCHC domains in the peptide. The length of the linker between domains affects the spacing of guanosine residues in oligonucleotides that are preferentially bound. These studies provide a proof of principle that NC-like CCHC zinc-binding domains can be utilized as a basis for designing peptides that bind specific single-stranded nucleic acid sequences.
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Affiliation(s)
- Anthony L Guerrerio
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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48
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Takayama Y, Sahu D, Iwahara J. NMR studies of translocation of the Zif268 protein between its target DNA Sites. Biochemistry 2010; 49:7998-8005. [PMID: 20718505 DOI: 10.1021/bi100962h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zif268 is a zinc-finger protein containing three Cys(2)-His(2)-type zinc-finger domains that bind the target DNA sequence GCGTGGGCG in a cooperative manner. In this work, we characterized translocation of the Zif268 protein between its target DNA sites using NMR spectroscopy. The residual dipolar coupling data and NMR chemical shift data suggested that the structure of the sequence-specific complex between Zif268 and its target DNA in solution is the same as the crystal structure. Using two-dimensional heteronuclear (1)H-(15)N correlation spectra recorded with the fast acquisition method, we analyzed the kinetics of the process in which the Zif268 protein transfers from a target site to another on a different DNA molecule on a minute to hour time scale. By globally fitting the time-course data collected at some different DNA concentrations, we determined the dissociation rate constant for the specific complex and the second-order rate constant for direct transfer of Zif268 from one target site to another. Interestingly, direct transfer of the Zif268 protein between its target sites is >30000-fold slower than corresponding direct transfers of the HoxD9 and the Oct-1 proteins, although the affinities of the three proteins to their target DNA sites are comparable. We also analyzed translocation of the Zif268 protein between two target sites on the same DNA molecules. The populations of the proteins bound to the target sites were found to depend on locations and orientations of the target sites.
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Affiliation(s)
- Yuki Takayama
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
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49
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Nowick K, Hamilton AT, Zhang H, Stubbs L. Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol 2010; 27:2606-17. [PMID: 20573777 DOI: 10.1093/molbev/msq157] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent segmental duplications (SDs), arising from duplication events that occurred within the past 35-40 My, have provided a major resource for the evolution of proteins with primate-specific functions. KRAB zinc finger (KRAB-ZNF) transcription factor genes are overrepresented among genes contained within these recent human SDs. Here, we examine the structural and functional diversity of the 70 human KRAB-ZNF genes involved in the most recent primate SD events including genes that arose in the hominid lineage. Despite their recent advent, many parent-daughter KRAB-ZNF gene pairs display significant differences in zinc finger structure and sequence, expression, and splicing patterns, each of which could significantly alter the regulatory functions of the paralogous genes. Paralogs that emerged on the lineage to humans and chimpanzees have undergone more evolutionary changes per unit of time than genes already present in the common ancestor of rhesus macaques and great apes. Taken together, these data indicate that a substantial fraction of the recently evolved primate-specific KRAB-ZNF gene duplicates have acquired novel functions that may possibly define novel regulatory pathways and suggest an active ongoing selection for regulatory diversity in primates.
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Affiliation(s)
- Katja Nowick
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, USA
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50
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Jantz D, Berg JM. Probing the DNA-binding affinity and specificity of designed zinc finger proteins. Biophys J 2010; 98:852-60. [PMID: 20197039 DOI: 10.1016/j.bpj.2009.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/17/2022] Open
Abstract
Engineered transcription factors and endonucleases based on designed Cys(2)His(2) zinc finger domains have proven to be effective tools for the directed regulation and modification of genes. The introduction of this technology into both research and clinical settings necessitates the development of rapid and accurate means of evaluating both the binding affinity and binding specificity of designed zinc finger domains. Using a fluorescence anisotropy-based DNA-binding assay, we examined the DNA-binding properties of two engineered zinc finger proteins that differ by a single amino acid. We demonstrate that the protein with the highest affinity for a particular DNA site need not be the protein that binds that site with the highest degree of specificity. Moreover, by comparing the binding characteristics of the two proteins at varying salt concentrations, we show that the ionic strength makes significant and variable contributions to both affinity and specificity. These results have significant implications for zinc finger design as they highlight the importance of considering affinity, specificity, and environmental requirements in designing a DNA-binding domain for a particular application.
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Affiliation(s)
- Derek Jantz
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
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