1
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Bonchuk AN, Georgiev PG. C2H2 proteins: Evolutionary aspects of domain architecture and diversification. Bioessays 2024; 46:e2400052. [PMID: 38873893 DOI: 10.1002/bies.202400052] [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: 03/11/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.
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Affiliation(s)
- Artem N Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel G Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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2
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Feng XA, Yamadi M, Fu Y, Ness KM, Liu C, Ahmed I, Bowman GD, Johnson ME, Ha T, Wu C. GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.14.549009. [PMID: 37502885 PMCID: PMC10369947 DOI: 10.1101/2023.07.14.549009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site by 1D or 3D diffusion on bare DNA and rapidly slides back-and-forth between naturally clustered motifs for seconds before escape. Multimeric, full-length GAF also finds clustered motifs on DNA by 1D-3D diffusion, but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D-sliding into the histone core but favors retention of GAF-DBD when targeting solvent-exposed sites by 3D-diffusion. Despite the occlusive power of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosome and nucleosome-free sites by a member of the largest TF family.
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Affiliation(s)
- Xinyu A Feng
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yiben Fu
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kaitlin M Ness
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Celina Liu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ishtiyaq Ahmed
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gregory D Bowman
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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3
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Bellino C, Herrera FE, Rodrigues D, Garay AS, Huck SV, Reinheimer R. Molecular Evolution of RAMOSA1 (RA1) in Land Plants. Biomolecules 2024; 14:550. [PMID: 38785957 PMCID: PMC11117814 DOI: 10.3390/biom14050550] [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: 03/16/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein-protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication.
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Affiliation(s)
- Carolina Bellino
- Fellow of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina;
| | - Fernando E. Herrera
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina; (F.E.H.); (D.R.)
| | - Daniel Rodrigues
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina; (F.E.H.); (D.R.)
| | - A. Sergio Garay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina;
| | - Sofía V. Huck
- Fellow of Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina;
| | - Renata Reinheimer
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, FCA, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina
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4
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Rua AJ, Whitehead RD, Alexandrescu AT. NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol X 2023; 8:100093. [PMID: 37655311 PMCID: PMC10465944 DOI: 10.1016/j.yjsbx.2023.100093] [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: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+ and a thermal stability >80 °C. Of three alternative Zn2+ ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein-protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.
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Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | - Richard D. Whitehead
- Department of Molecular and Cellular Biology, University of Connecticut, United States
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Rua AJ, Whitehead Iii RD, Alexandrescu AT. WITHDRAWN: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol 2023:108003. [PMID: 37487847 DOI: 10.1016/j.jsb.2023.108003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This article was initially published in the Journal of Structural Biology, instead of the Journal of Structural Biology: X, due to a publisher error. We regret the inconvenience. The link to the article published in Journal of Structural Biology: X is presented below: https://www.sciencedirect.com/science/article/pii/S2590152423000090. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
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Kinetic principles underlying pioneer function of GAGA transcription factor in live cells. Nat Struct Mol Biol 2022; 29:665-676. [PMID: 35835866 PMCID: PMC10177624 DOI: 10.1038/s41594-022-00800-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/27/2022] [Indexed: 11/09/2022]
Abstract
How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement of GAF's DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF's neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for transcriptional responses to homeostatic, environmental and developmental signals.
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Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
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Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Dorogova NV, Zubkova AE, Fedorova ЕV, Bolobolova ЕU, Baricheva ЕМ. [Lack of GAGA protein in Trl mutants causes massive cell death in Drosophila spermatogenesis and oogenesis]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:292-300. [PMID: 34901726 PMCID: PMC8627872 DOI: 10.18699/vj21.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 11/26/2022] Open
Abstract
Белок дрозофилы GAGA (GAF) является фактором эпигенетической регуляции транскрипции
большой группы генов с широким разнообразием клеточных функций. GAF кодируется геном Trithorax-like
(Trl), который экспрессируется в различных органах и тканях на всех стадиях онтогенеза дрозофилы. Мутации этого гена вызывают множественные нарушения развития. В предыдущих работах мы показали, что этот
белок необходим для развития половой системы как самцов, так и самок дрозофилы. Снижение экспрессии
гена Trl приводило ко множественным нарушениям спермато- и оогенеза. Одно из значительных нарушений было связано с массовой деградацией и потерей клеток зародышевого пути, что позволило предположить, что этот белок вовлечен в регуляцию клеточной гибели. В представленной работе мы провели более
детальное цитологическое исследование, чтобы определить, какой тип гибели клеток зародышевого пути
характерен для Trl-мутантов, и происходят ли нарушения или изменения этого процесса по сравнению с
нормой. Полученные результаты показали, что недостаток белка GAF вызывает массовую гибель клеток зародышевого пути как у самок, так и самцов дрозофилы, но проявляется эта гибель в зависимости от пола
по-разному. У самок, мутантных по гену Trl, фенотипически этот процесс не отличается от нормы и в гибнущих яйцевых камерах выявлены признаки апоптоза и аутофагии клеток зародышевого пути. У самцов, мутантных по гену Trl, в отличие от самок, не обнаружены признаки апоптоза. У самцов мутации Trl индуцируют
массовую гибель клеток через аутофагию, что не характерно для сперматогенеза дрозофилы и не описано
ранее ни в норме, ни у мутаций по другим генам. Таким образом, недостаток GAF у мутантов Trl приводит
к усилению апоптотической и аутофагической гибели клеток зародышевого пути. Эктопическая клеточная
гибель и атрофия зародышевой линии, вероятно, связаны с нарушением экспрессии генов-мишеней GAGAфактора, среди которых есть гены, регулирующие как апоптоз, так и аутофагию.
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Affiliation(s)
- N V Dorogova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A E Zubkova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - Е V Fedorova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Е U Bolobolova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Е М Baricheva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization. Nat Commun 2021; 12:5579. [PMID: 34552088 PMCID: PMC8458463 DOI: 10.1038/s41467-021-25761-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2021] [Indexed: 12/29/2022] Open
Abstract
Expression of a few master transcription factors can reprogram the epigenetic landscape and three-dimensional chromatin topology of differentiated cells and achieve pluripotency. During reprogramming, thousands of long-range chromatin contacts are altered, and changes in promoter association with enhancers dramatically influence transcription. Molecular participants at these sites have been identified, but how this re-organization might be orchestrated is not known. Biomolecular condensation is implicated in subcellular organization, including the recruitment of RNA polymerase in transcriptional activation. Here, we show that reprogramming factor KLF4 undergoes biomolecular condensation even in the absence of its intrinsically disordered region. Liquid–liquid condensation of the isolated KLF4 DNA binding domain with a DNA fragment from the NANOG proximal promoter is enhanced by CpG methylation of a KLF4 cognate binding site. We propose KLF4-mediated condensation as one mechanism for selectively organizing and re-organizing the genome based on the local sequence and epigenetic state. KLF4, OCT4, SOX2 and MYC cooperate to reorganize chromatin during somatic cell reprogramming. Here the authors show that KLF4 forms a liquid-like biomolecular condensate that recruits OCT4 and SOX2, and that condensation of the isolated KLF4 DNA binding domain with DNA is enhanced by CpG methylation
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Eggers N, Becker PB. Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions. Nucleic Acids Res 2021; 49:7602-7617. [PMID: 34181732 PMCID: PMC8287947 DOI: 10.1093/nar/gkab558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/08/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Metazoan transcription factors distinguish their response elements from a large excess of similar sequences. We explored underlying principles of DNA shape read-out and factor cooperativity in chromatin using a unique experimental system. We reconstituted chromatin on Drosophila genomes in extracts of preblastoderm embryos, mimicking the naïve state of the zygotic genome prior to developmental transcription activation. We then compared the intrinsic binding specificities of three recombinant transcription factors, alone and in combination, with GA-rich recognition sequences genome-wide. For MSL2, all functional elements reside on the X chromosome, allowing to distinguish physiological elements from non-functional 'decoy' sites. The physiological binding profile of MSL2 is approximated through interaction with other factors: cooperativity with CLAMP and competition with GAF, which sculpts the profile by occluding non-functional sites. An extended DNA shape signature is differentially read out in chromatin. Our results reveal novel aspects of target selection in a complex chromatin environment.
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Affiliation(s)
- Nikolas Eggers
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, 82152 Planegg, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, 82152 Planegg, Germany
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11
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Marcianò G, Ishii M, Nerusheva OO, Akiyoshi B. Kinetoplastid kinetochore proteins KKT2 and KKT3 have unique centromere localization domains. J Cell Biol 2021; 220:212224. [PMID: 34081090 PMCID: PMC8178753 DOI: 10.1083/jcb.202101022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/29/2021] [Accepted: 05/12/2021] [Indexed: 12/31/2022] Open
Abstract
The kinetochore is the macromolecular protein complex that assembles onto centromeric DNA and binds spindle microtubules. Evolutionarily divergent kinetoplastids have an unconventional set of kinetochore proteins. It remains unknown how kinetochores assemble at centromeres in these organisms. Here, we characterize KKT2 and KKT3 in the kinetoplastid parasite Trypanosoma brucei. In addition to the N-terminal kinase domain and C-terminal divergent polo boxes, these proteins have a central domain of unknown function. We show that KKT2 and KKT3 are important for the localization of several kinetochore proteins and that their central domains are sufficient for centromere localization. Crystal structures of the KKT2 central domain from two divergent kinetoplastids reveal a unique zinc-binding domain (termed the CL domain for centromere localization), which promotes its kinetochore localization in T. brucei. Mutations in the equivalent domain in KKT3 abolish its kinetochore localization and function. Our work shows that the unique central domains play a critical role in mediating the centromere localization of KKT2 and KKT3.
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Affiliation(s)
| | - Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
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Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci 2021; 78:4125-4141. [PMID: 33528710 DOI: 10.1007/s00018-021-03776-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/08/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
The Drosophila GAGA factor (GAF) is a multifunctional protein implicated in nucleosome organization and remodeling, activation and repression of gene expression, long distance enhancer-promoter communication, higher order chromosome structure, and mitosis. This broad range of activities poses questions about how a single protein can perform so many seemingly different and unrelated functions. Current studies argue that GAF acts as a "pioneer" factor, generating nucleosome-free regions of chromatin for different classes of regulatory elements. The removal of nucleosomes from regulatory elements in turn enables other factors to bind to these elements and carry out their specialized functions. Consistent with this view, GAF associates with a collection of chromatin remodelers and also interacts with proteins implicated in different regulatory functions. In this review, we summarize the known activities of GAF and the functions of its protein partners.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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13
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Brödel AK, Rodrigues R, Jaramillo A, Isalan M. Accelerated evolution of a minimal 63-amino acid dual transcription factor. SCIENCE ADVANCES 2020; 6:eaba2728. [PMID: 32577520 PMCID: PMC7286687 DOI: 10.1126/sciadv.aba2728] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/14/2020] [Indexed: 05/13/2023]
Abstract
Transcription factors control gene expression in all life. This raises the question of what is the smallest protein that can support such activity. In nature, Cro from bacteriophage λ is one of the smallest known repressors (66 amino acids), and activators are typically much larger (e.g., λ cI, 237 amino acids). Previous efforts to engineer a minimal activator from λ Cro resulted in no activity in vivo in cells. In this study, we show that directed evolution results in a new Cro activator-repressor that functions as efficiently as λ cI in vivo. To achieve this, we develop phagemid-assisted continuous evolution (PACEmid). We find that a peptide as small as 63 amino acids functions efficiently as an activator and/or repressor. To our knowledge, this is the smallest protein activator that enables polymerase recruitment, highlighting the capacity of transcription factors to evolve from very short peptide sequences.
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Affiliation(s)
- Andreas K. Brödel
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Rui Rodrigues
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- CNRS-UMR8030, Laboratoire iSSB and Université Paris-Saclay and Université d’Évry and CEA, DRF, IG, Genoscope, Évry 91000, France
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Corresponding author.
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Puig Giribets M, Santos M, García Guerreiro MP. Basal hsp70 expression levels do not explain adaptive variation of the warm- and cold-climate O 3 + 4 + 7 and O ST gene arrangements of Drosophila subobscura. BMC Evol Biol 2020; 20:17. [PMID: 32005133 PMCID: PMC6995229 DOI: 10.1186/s12862-020-1584-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background Drosophila subobscura exhibits a rich inversion polymorphism, with some adaptive inversions showing repeatable spatiotemporal patterns in frequencies related to temperature. Previous studies reported increased basal HSP70 protein levels in homokaryotypic strains for a warm-climate arrangement compared to a cold-climate one. These findings do not match the similar hsp70 genomic organization between arrangements, where gene expression levels are expected to be similar. In order to test this hypothesis and understand the molecular basis for hsp70 expression, we compared basal hsp70 mRNA levels in males and females, and analysed the 5′ and 3′ regulatory regions of hsp70 genes in warm- and cold-climate isochromosomal O3 + 4 + 7 and OST lines of D. subobscura. Results We observed comparable mRNA levels between the two arrangements and a sex-biased hsp70 gene expression. The number of heat-shock elements (HSEs) and GAGA sites on the promoters were identical amongst the OST and O3 + 4 + 7 lines analysed. This is also true for 3′ AU-rich elements where most A and B copies of hsp70 have, respectively, two and one element in both arrangements. Beyond the regulatory elements, the only notable difference between both arrangements is the presence in 3′ UTR of a 14 bp additional fragment after the stop codon in the hsp70A copy in five O3 + 4 + 7 lines, which was not found in any of the six OST lines. Conclusions The equivalent hsp70 mRNA amounts in OST and O3 + 4 + 7 arrangements provide the first evidence of a parallelism between gene expression and genetic organization in D. subobscura lines having these arrangements. This is reinforced by the lack of important differential features in the number and structure of regulatory elements between both arrangements, despite the genetic differentiation observed when the complete 5′ and 3′ regulatory regions were considered. Therefore, the basal levels of hsp70 mRNA cannot account, in principle, for the adaptive variation of the two arrangements studied. Consequently, further studies are necessary to understand the intricate molecular mechanisms of hsp70 gene regulation in D. subobscura.
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Affiliation(s)
- Marta Puig Giribets
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Mauro Santos
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - María Pilar García Guerreiro
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
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15
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Novel alternatively spliced isoforms of pig ZNF280D and their diverse mRNA expression patterns. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00304-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Nepravishta R, Ferrentino F, Mandaliti W, Mattioni A, Weber J, Polo S, Castagnoli L, Cesareni G, Paci M, Santonico E. CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1. Biomolecules 2019; 9:biom9070284. [PMID: 31319543 PMCID: PMC6681339 DOI: 10.3390/biom9070284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin binding domains (UBDs) are modular elements that bind non-covalently to ubiquitin and act as downstream effectors and amplifiers of the ubiquitination signal. With few exceptions, UBDs recognize the hydrophobic path centered on Ile44, including residues Leu8, Ile44, His68, and Val70. A variety of different orientations, which can be attributed to specific contacts between each UBD and surface residues surrounding the hydrophobic patch, specify how each class of UBD specifically contacts ubiquitin. Here, we describe the structural model of a novel ubiquitin-binding domain that we identified in NEDD4 binding protein 1 (N4BP1). By performing protein sequence analysis, mutagenesis, and nuclear magnetic resonance (NMR) spectroscopy of the 15N isotopically labeled protein, we demonstrate that a Phe-Pro motif in N4BP1 recognizes the canonical hydrophobic patch of ubiquitin. This recognition mode resembles the molecular mechanism evolved in the coupling of ubiquitin conjugation to endoplasmic-reticulum (ER) degradation (CUE) domain family, where an invariant proline, usually following a phenylalanine, is required for ubiquitin binding. Interestingly, this novel UBD, which is not evolutionary related to CUE domains, shares a 40% identity and 47% similarity with cullin binding domain associating with NEDD8 (CUBAN), a protein module that also recognizes the ubiquitin-like NEDD8. Based on these features, we dubbed the region spanning the C-terminal 50 residues of N4BP1 the CoCUN domain, for Cousin of CUBAN. By performing circular dichroism and 15N NMR chemical shift perturbation of N4BP1 in complex with ubiquitin, we demonstrate that the CoCUN domain lacks the NEDD8 binding properties observed in CUBAN. We also show that, in addition to mediating the interaction with ubiquitin and ubiquitinated substrates, both CUBAN and CoCUN are poly-ubiquitinated in cells. The structural and the functional characterization of this novel UBD can contribute to a deeper understanding of the molecular mechanisms governing N4BP1 function, providing at the same time a valuable tool for clarifying how the discrimination between ubiquitin and the highly related NEDD8 is achieved.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy East Anglia, University of Norwich, Norwich NR4 7TJ, UK
| | | | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, Tor Vergata University, 00133 Rome, Italy
| | - Anna Mattioni
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
| | - Janine Weber
- IFOM, The FIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Simona Polo
- IFOM, The FIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
| | - Gianni Cesareni
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
- DIPO, Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, 20122 Milan, Italy
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, Tor Vergata University, 00133 Rome, Italy
| | - Elena Santonico
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
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17
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Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM. Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com. PLoS One 2019; 14:e0214481. [PMID: 31022205 PMCID: PMC6483171 DOI: 10.1371/journal.pone.0214481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/13/2019] [Indexed: 11/18/2022] Open
Abstract
The bacteriophage Mu Com is a small zinc finger protein that binds to its cognate mom mRNA and activates its translation. The Mom protein, in turn, elicits a chemical modification (momification) of the bacteriophage genome, rendering the DNA resistant to cleavage by bacterial restriction endonucleases, and thereby protecting it from defense mechanisms of the host. We examined the basis of specificity in Com-RNA interactions by in vitro selection and probing of RNA structure. We demonstrated that Com recognizes a sequence motif within a hairpin-loop structure of its target RNA. Our data support the model of Com interaction with mom mRNA, in which Com binds to the short hairpin structure proximal to the so-called translation inhibition structure. We also observed that Com binds its target motif weakly if it is within an RNA duplex. These results suggest that the RNA structure, in addition to its sequence, is crucial for Com to recognize its target and that RNA conformational changes may constitute another level of Mom regulation. We determined a crystal structure of a Com binding site variant designed to form an RNA duplex preferentially. Our crystal model forms a 19-mer self-complementary double helix composed of the canonical and non-canonical base pairs. The helical parameters of crystalized RNA indicate why Com may bind it more weakly than a monomeric hairpin form.
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Affiliation(s)
- Martyna Nowacka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- * E-mail: ; (JMB)
| | - Humberto Fernandes
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agata Bernat
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Grzegorz Lach
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M. Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
- * E-mail: ; (JMB)
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18
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Mackeh R, Marr AK, Fadda A, Kino T. C2H2-Type Zinc Finger Proteins: Evolutionarily Old and New Partners of the Nuclear Hormone Receptors. NUCLEAR RECEPTOR SIGNALING 2018; 15:1550762918801071. [PMID: 30718982 PMCID: PMC6348741 DOI: 10.1177/1550762918801071] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/02/2017] [Indexed: 12/21/2022]
Abstract
Nuclear hormone receptors (NRs) are evolutionarily conserved ligand-dependent
transcription factors. They are essential for human life, mediating the actions
of lipophilic molecules, such as steroid hormones and metabolites of fatty acid,
cholesterol, and external toxic compounds. The C2H2-type zinc finger proteins
(ZNFs) form the largest family of the transcription factors in humans and are
characterized by multiple, tandemly arranged zinc fingers. Many of the C2H2-type
ZNFs are conserved throughout evolution, suggesting their involvement in
preserved biological activities, such as general transcriptional regulation and
development/differentiation of organs/tissues observed in the early embryonic
phase. However, some C2H2-type ZNFs, such as those with the Krüppel-associated
box (KRAB) domain, appeared relatively late in evolution and have significantly
increased family members in mammals including humans, possibly modulating their
complicated transcriptional network and/or supporting the morphological
development/functions specific to them. Such evolutional characteristics of the
C2H2-type ZNFs indicate that these molecules influence the NR functions
conserved through evolution, whereas some also adjust them to meet with specific
needs of higher organisms. We review the interaction between NRs and C2H2-type
ZNFs by focusing on some of the latter molecules.
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19
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Rodríguez J, Learte-Aymamí S, Mosquera J, Celaya G, Rodríguez-Larrea D, Vázquez ME, Mascareñas JL. DNA-binding miniproteins based on zinc fingers. Assessment of the interaction using nanopores. Chem Sci 2018; 9:4118-4123. [PMID: 29780541 PMCID: PMC5941273 DOI: 10.1039/c7sc05441f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022] Open
Abstract
We report a synthetic miniprotein that combines zinc finger modules of the transcription factor GAGA with the AT-hook peptide. This designed chimera binds to extended DNA sites with high affinity and selectivity, as shown by nanopore force spectroscopy.
Obtaining artificial proteins that mimic the DNA binding properties of natural transcription factors could open new ways of manipulating gene expression at will. In this context it is particularly interesting to develop simple synthetic systems. Inspired by the modularity of natural transcription factors, we have designed synthetic miniproteins that combine the zinc finger module of the transcription factor GAGA and AT-hook peptide domains. These constructs are capable of binding to composite DNA sequences of up to 14 base pairs with high affinity and good selectivity. In particular, we have synthesized three different chimeras and characterized their DNA binding properties by electrophoresis and fluorescence anisotropy. We have also used, for the first time in the study of peptide-based DNA binders, nanopore force spectroscopy to obtain further data on the DNA interaction.
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Garbiñe Celaya
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU) , Leioa 48940 , Spain
| | - David Rodríguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU) , Leioa 48940 , Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
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20
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Kaye EG, Booker M, Kurland JV, Conicella AE, Fawzi NL, Bulyk ML, Tolstorukov MY, Larschan E. Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome. Cell Rep 2018; 22:3227-3239. [PMID: 29562179 PMCID: PMC6402580 DOI: 10.1016/j.celrep.2018.02.098] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/09/2018] [Accepted: 02/25/2018] [Indexed: 01/28/2023] Open
Abstract
Little is known about how variation in sequence composition alters transcription factor occupancy to precisely recruit large transcription complexes. A key model for understanding how transcription complexes are targeted is the Drosophila dosage compensation system in which the male-specific lethal (MSL) transcription complex specifically identifies and regulates the male X chromosome. The chromatin-linked adaptor for MSL proteins (CLAMP) zinc-finger protein targets MSL to the X chromosome but also binds to GA-rich sequence elements throughout the genome. Furthermore, the GAGA-associated factor (GAF) transcription factor also recognizes GA-rich sequences but does not associate with the MSL complex. Here, we demonstrate that MSL complex recruitment sites are optimal CLAMP targets. Specificity for CLAMP binding versus GAF binding is driven by variability in sequence composition within similar GA-rich motifs. Therefore, variation within seemingly similar cis elements drives the context-specific targeting of a large transcription complex.
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Affiliation(s)
- Emily G Kaye
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Matthew Booker
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA; Department of Molecular Biology, Massachusetts General Hospital, Cambridge, MA 02114, USA
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexander E Conicella
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Cambridge, MA 02114, USA.
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA.
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21
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Srivastava A, Kumar AS, Mishra RK. Vertebrate GAF/ThPOK: emerging functions in chromatin architecture and transcriptional regulation. Cell Mol Life Sci 2018; 75:623-633. [PMID: 28856379 PMCID: PMC11105447 DOI: 10.1007/s00018-017-2633-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/09/2017] [Accepted: 08/25/2017] [Indexed: 12/31/2022]
Abstract
GAGA factor of Drosophila melanogaster (DmGAF) is a multifaceted transcription factor with diverse roles in chromatin regulation. Recently, ThPOK/c-Krox was identified as its vertebrate homologue (vGAF), which has a basic domain structure similar to DmGAF and is decorated with a number of post-translationally modified residues. In vertebrate genomes, vGAF associates with purine-rich GAGA sequences and performs diverse chromatin-mediated functions, viz., gene activation, repression and enhancer blocking. Expansion of regulatory chromatin proteins with the acquisition of PTMs appears to be the general trend that facilitated the evolution of complexity in vertebrates. Here, we compare the structural and functional features of vGAF with those of DmGAF and also assess the possible functional redundancy among paralogues of vGAF. We also discuss the underlying mechanisms which aid in the diverse and context-dependent functions of this protein.
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Affiliation(s)
- Avinash Srivastava
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Amitha Sampath Kumar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India.
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22
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Lin CY, Lin LY. The conserved basic residues and the charged amino acid residues at the α-helix of the zinc finger motif regulate the nuclear transport activity of triple C2H2 zinc finger proteins. PLoS One 2018; 13:e0191971. [PMID: 29381770 PMCID: PMC5790263 DOI: 10.1371/journal.pone.0191971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/15/2018] [Indexed: 11/19/2022] Open
Abstract
Zinc finger (ZF) motifs on proteins are frequently recognized as a structure for DNA binding. Accumulated reports indicate that ZF motifs contain nuclear localization signal (NLS) to facilitate the transport of ZF proteins into nucleus. We investigated the critical factors that facilitate the nuclear transport of triple C2H2 ZF proteins. Three conserved basic residues (hot spots) were identified among the ZF sequences of triple C2H2 ZF proteins that reportedly have NLS function. Additional basic residues can be found on the α-helix of the ZFs. Using the ZF domain (ZFD) of Egr-1 as a template, various mutants were constructed and expressed in cells. The nuclear transport activity of various mutants was estimated by analyzing the proportion of protein localized in the nucleus. Mutation at any hot spot of the Egr-1 ZFs reduced the nuclear transport activity. Changes of the basic residues at the α-helical region of the second ZF (ZF2) of the Egr-1 ZFD abolished the NLS activity. However, this activity can be restored by substituting the acidic residues at the homologous positions of ZF1 or ZF3 with basic residues. The restored activity dropped again when the hot spots at ZF1 or the basic residues in the α-helix of ZF3 were mutated. The variations in nuclear transport activity are linked directly to the binding activity of the ZF proteins with importins. This study was extended to other triple C2H2 ZF proteins. SP1 and KLF families, similar to Egr-1, have charged amino acid residues at the second (α2) and the third (α3) positions of the α-helix. Replacing the amino acids at α2 and α3 with acidic residues reduced the NLS activity of the SP1 and KLF6 ZFD. The reduced activity can be restored by substituting the α3 with histidine at any SP1 and KLF6 ZFD. The results show again the interchangeable role of ZFs and charge residues in the α-helix in regulating the NLS activity of triple C2H2 ZF proteins.
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Affiliation(s)
- Chih-Ying Lin
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC
| | - Lih-Yuan Lin
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC
- * E-mail:
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23
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The Drosophila CLAMP protein associates with diverse proteins on chromatin. PLoS One 2017; 12:e0189772. [PMID: 29281702 PMCID: PMC5744976 DOI: 10.1371/journal.pone.0189772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/13/2017] [Indexed: 11/29/2022] Open
Abstract
Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that regulates chromatin accessibility at promoters genome-wide. To identify associations between CLAMP and other factors in both male and female cells, we used two complementary mass spectrometry approaches. We demonstrate that CLAMP associates with the transcriptional regulator complex Negative Elongation Factor (NELF) in both sexes and determine that CLAMP reduces NELF recruitment to several target genes. In sum, we have identified many new CLAMP-associated factors and provide a resource for further study of this little understood essential protein.
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24
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Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, Adelman K, Tolstorukov M, Larschan E. Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS One 2017; 12:e0186855. [PMID: 29077765 PMCID: PMC5659772 DOI: 10.1371/journal.pone.0186855] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023] Open
Abstract
The essential process of dosage compensation is required to equalize gene expression of X-chromosome genes between males (XY) and females (XX). In Drosophila, the conserved Male-specific lethal (MSL) histone acetyltransferase complex mediates dosage compensation by increasing transcript levels from genes on the single male X-chromosome approximately two-fold. Consistent with its increased levels of transcription, the male X-chromosome has enhanced chromatin accessibility, distinguishing it from the autosomes. Here, we demonstrate that the non-sex-specific CLAMP (Chromatin-linked adaptor for MSL proteins) zinc finger protein that recognizes GA-rich sequences genome-wide promotes the specialized chromatin environment on the male X-chromosome and can act over long genomic distances (~14 kb). Although MSL complex is required for increasing transcript levels of X-linked genes, it is not required for enhancing global male X-chromosome chromatin accessibility, and instead works cooperatively with CLAMP to facilitate an accessible chromatin configuration at its sites of highest occupancy. Furthermore, CLAMP regulates chromatin structure at strong MSL complex binding sites through promoting recruitment of the Nucleosome Remodeling Factor (NURF) complex. In contrast to the X-chromosome, CLAMP regulates chromatin and gene expression on autosomes through a distinct mechanism that does not involve NURF recruitment. Overall, our results support a model where synergy between a non-sex-specific transcription factor (CLAMP) and a sex-specific cofactor (MSL) creates a specialized chromatin domain on the male X-chromosome.
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Affiliation(s)
- Jennifer Urban
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Guray Kuzu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sarah Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Benjamin Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Robert Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Michael Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MT); (EL)
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (MT); (EL)
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25
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Pauli T, Vedder L, Dowling D, Petersen M, Meusemann K, Donath A, Peters RS, Podsiadlowski L, Mayer C, Liu S, Zhou X, Heger P, Wiehe T, Hering L, Mayer G, Misof B, Niehuis O. Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins. BMC Genomics 2016; 17:861. [PMID: 27809783 PMCID: PMC5094011 DOI: 10.1186/s12864-016-3205-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/25/2016] [Indexed: 01/19/2023] Open
Abstract
Background Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. Results Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection. Conclusions Our results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Pauli
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.
| | - Lucia Vedder
- University of Tübingen, Geschwister-Scholl-Platz, 72074, Tübingen, Germany
| | - Daniel Dowling
- Johannes Gutenberg University Mainz, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Malte Petersen
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Karen Meusemann
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.,Department for Evolutionary Biology and Ecology (Institut for Biology I, Zoology), University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany.,Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Acton, ACT, 2601, Australia
| | - Alexander Donath
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Ralph S Peters
- Zoological Research Museum Alexander Koenig, Arthropod Department, Adenauerallee 160, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- University of Bonn, Institute of Evolutionary Biology and Ecology, An der Immenburg 1, 53121, Bonn, Germany
| | - Christoph Mayer
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Peter Heger
- University of Cologne, Cologne Biocenter, Institute for Genetics, Zülpicher Straße 47a, 50674, Köln, Germany
| | - Thomas Wiehe
- University of Cologne, Cologne Biocenter, Institute for Genetics, Zülpicher Straße 47a, 50674, Köln, Germany
| | - Lars Hering
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Bernhard Misof
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Oliver Niehuis
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.
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26
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Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT. Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. Genes Dev 2016; 30:1731-46. [PMID: 27492368 PMCID: PMC5002978 DOI: 10.1101/gad.284430.116] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/11/2016] [Indexed: 12/24/2022]
Abstract
The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-associated factor (GAF) and HS factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA polymerase II (Pol II) formation (likely at the step of chromatin opening) and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing but is critical for the release of paused Pol II into the gene body at a subset of highly activated genes. Additionally, HSF has no detectable role in the rapid HS repression of thousands of genes.
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Affiliation(s)
- Fabiana M Duarte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Nicholas J Fuda
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Dig B Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
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27
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Rodríguez J, Mosquera J, García-Fandiño R, Vázquez ME, Mascareñas JL. A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves. Chem Sci 2016; 7:3298-3303. [PMID: 27252825 PMCID: PMC4885664 DOI: 10.1039/c6sc00045b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/01/2016] [Indexed: 12/28/2022] Open
Abstract
We report the rational design of a DNA-binding peptide construct composed of the DNA-contacting regions of two transcription factors (GCN4 and GAGA) linked through an AT-hook DNA anchor. The resulting chimera, which represents a new, non-natural DNA binding motif, binds with high affinity and selectivity to a long composite sequence of 13 base pairs (TCAT-AATT-GAGAG).
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Rebeca García-Fandiño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
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28
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Tremblay C, Bédard M, Bonin MA, Lavigne P. Solution structure of the 13th C2H2 Zinc Finger of Miz-1. Biochem Biophys Res Commun 2016; 473:471-5. [PMID: 26972249 DOI: 10.1016/j.bbrc.2016.03.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
Miz-1 is a BTB/POZ transcription factor that contains 13C2H2 Zinc Finger domains (ZF). Miz-1 transactivates and represses the transcription of a myriad of genes involved in many aspects of the biology of the cell. The detailed molecular interactions through which Miz-1 controls transcription, including its specific DNA binding via its ZF domains, remain to be understood and documented. In our effort to shed light into the structural biology of Miz-1, we have undertaken the determination of the structure of all its ZF and the characterization of their interactions with cognate DNA. The structure of ZF 1 to 10 have already been solved and characterized. Here, we present the structure of the synthetic Miz-1 ZF13 determined by 2D (1)H-(1)H NMR.
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Affiliation(s)
- Cynthia Tremblay
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada; PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada; GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec, Canada
| | - Mikaël Bédard
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada; PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada; GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec, Canada
| | - Marc-André Bonin
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Pierre Lavigne
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada; PROTEO; Regroupement Stratégique sur la Fonction, la Structure et l'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada; GRASP; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec, Canada.
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29
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New studies about the insertion mechanism of Thymosin α1 in negative regions of model membranes as starting point of the bioactivity. Amino Acids 2016; 48:1231-9. [DOI: 10.1007/s00726-016-2169-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 01/05/2016] [Indexed: 10/25/2022]
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30
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Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
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31
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Rodríguez J, Mosquera J, Couceiro JR, Vázquez ME, Mascareñas JL. The AT-Hook motif as a versatile minor groove anchor for promoting DNA binding of transcription factor fragments. Chem Sci 2015; 6:4767-4771. [PMID: 26290687 PMCID: PMC4538796 DOI: 10.1039/c5sc01415h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - Jose R. Couceiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
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32
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Stratigi K, Kapsetaki M, Aivaliotis M, Town T, Flavell RA, Spilianakis CG. Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression. Proc Natl Acad Sci U S A 2015; 112:E1577-86. [PMID: 25770217 PMCID: PMC4386343 DOI: 10.1073/pnas.1502182112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Physiological processes rely on the regulation of total mRNA levels in a cell. In diploid organisms, the transcriptional activation of one or both alleles of a gene may involve trans-allelic interactions that provide a tight spatial and temporal level of gene expression regulation. The mechanisms underlying such interactions still remain poorly understood. Here, we demonstrate that lipopolysaccharide stimulation of murine macrophages rapidly resulted in the actin-mediated and transient homologous spatial proximity of Tnfα alleles, which was necessary for the mono- to biallelic switch in gene expression. We identified two new complementary long noncoding RNAs transcribed from the TNFα locus and showed that their knockdown had opposite effects in Tnfα spatial proximity and allelic expression. Moreover, the observed spatial proximity of Tnfα alleles depended on pyruvate kinase muscle isoform 2 (PKM2) and T-helper-inducing POZ-Krüppel-like factor (ThPOK). This study suggests a role for lncRNAs in the regulation of somatic homologous spatial proximity and allelic expression control necessary for fine-tuning mammalian immune responses.
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Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece; Department of Biology, University of Crete, GR70013 Heraklion, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece
| | - Terrence Town
- Department of Physiology and Biophysics, Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089; and
| | - Richard A Flavell
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520
| | - Charalampos G Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece; Department of Biology, University of Crete, GR70013 Heraklion, Greece;
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33
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Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet 2015; 11:e1005108. [PMID: 25815464 PMCID: PMC4376892 DOI: 10.1371/journal.pgen.1005108] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/26/2015] [Indexed: 11/28/2022] Open
Abstract
Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters. Transcriptional regulation is critical for proper gene expression in response to environmental changes and developmental programs. Eukaryotes have evolved multiple mechanisms by which transcription factors regulate transcription. One mechanism is the reorganization of chromatin to allow Pol II recruitment. Another is the release of promoter-proximal paused Pol II, where Pol II transcription that is halted 20–60 bases downstream of the transcription start site (TSS) is allowed to enter into productive elongation through the gene body. The Drosophila transcription factor GAF binds to genes that undergo pausing and interacts with nucleosome remodelers and the pausing factor NELF. Thus, GAF can regulate multiple points necessary for transcription, but its mechanistic role is not fully understood genome-wide. We depleted GAF from cells and examined the genome-wide changes in Pol II and nucleosome distributions across genes. We found that GAF depletion reduces polymerase density at genes where GAF binds just upstream of the TSS, and results in nucleosomes moving into the promoter region. Our results show that GAF is important for maintaining the promoter accessibility, allowing Pol II to be recruited to promoters and enter the pause sites downstream of the TSS. Thus, GAF is critical for providing the chromatin environment necessary for the proper control of gene expression.
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Affiliation(s)
- Nicholas J. Fuda
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael J. Guertin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sumeet Sharma
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Charles G. Danko
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - André L. Martins
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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34
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Nepravishta R, Mandaliti W, Eliseo T, Vallebona PS, Pica F, Garaci E, Paci M. Thymosin α1 inserts N terminus into model membranes assuming a helical conformation. Expert Opin Biol Ther 2015; 15 Suppl 1:S71-81. [DOI: 10.1517/14712598.2015.1009034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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35
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Structure of the cyclic peptide [W8S]contryphan Vn: effect of the tryptophan/serine substitution on trans-cis proline isomerization. Amino Acids 2014; 46:2841-53. [PMID: 25261131 DOI: 10.1007/s00726-014-1841-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
The structural characterization of [W8S]contryphan Vn, an analogue of Contryphan Vn with tryptophan 8 substituted with a serine residue (W8S), was performed by NMR spectroscopy, molecular dynamics simulations and fluorescence spectroscopy. Contryphan Vn, a bioactive cyclic peptide from the venom of the cone snail Conus ventricosus, contains an S-S bridge between two cysteines and a D-tryptophan. Like other Contryphans, [W8S]contryphan Vn has proline 7 isomerized trans, while the proline 4 has nearly equivalent populations of cis and trans configurations. The thermodynamic and kinetic parameters of the trans-cis isomerization of proline 4 were measured. The isomers of [W8S]contryphan Vn with proline 4 in cis and trans show structural differences. The absence of the salt bridge between the same Asp2 and Lys6, present in Contryphan Vn, may be attributed to the lack of the hydrophobic side chain of Trp8 where it likely protects the electrostatic interactions. These results may contribute to identifying, in these cyclic peptides, the structural determinants of the mechanism of proline trans-cis isomerization, this being also an important step in protein folding.
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36
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Russo L, Palmieri M, Caso JV, D'Abrosca G, Diana D, Malgieri G, Baglivo I, Isernia C, Pedone PV, Fattorusso R. Towards understanding the molecular recognition process in prokaryotic zinc-finger domain. Eur J Med Chem 2014; 91:100-8. [PMID: 25240418 DOI: 10.1016/j.ejmech.2014.09.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first α-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design applications.
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Jolanda Valentina Caso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Donatella Diana
- Institute of Biostructures and Bioimaging -CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
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Siggers T, Reddy J, Barron B, Bulyk ML. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell 2014; 55:640-8. [PMID: 25042805 DOI: 10.1016/j.molcel.2014.06.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/27/2014] [Accepted: 06/09/2014] [Indexed: 12/25/2022]
Abstract
A major challenge in obtaining a full molecular description of evolutionary adaptation is to characterize how transcription factor (TF) DNA-binding specificity can change. To identify mechanisms of TF diversification, we performed detailed comparisons of yeast C2H2 ZF proteins with identical canonical recognition residues that are expected to bind the same DNA sequences. Unexpectedly, we found that ZF proteins can adapt to recognize new binding sites in a modular fashion whereby binding to common core sites remains unaffected. We identified two distinct mechanisms, conserved across multiple Ascomycota species, by which this molecular adaptation occurred. Our results suggest a route for TF evolution that alleviates negative pleiotropic effects by modularly gaining new binding sites. These findings expand our current understanding of ZF DNA binding and provide evidence for paralogous ZFs utilizing alternate modes of DNA binding to recognize unique sets of noncanonical binding sites.
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Affiliation(s)
- Trevor Siggers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Boston University, Boston, MA 02215, USA.
| | - Jessica Reddy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Brian Barron
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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38
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Cheng X, Blumenthal RM. Response to mackay et Al. Trends Biochem Sci 2014; 38:423. [PMID: 23992946 DOI: 10.1016/j.tibs.2013.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 11/30/2022]
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39
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Rodríguez J, Mosquera J, Vázquez O, Vázquez ME, Mascareñas JL. The ββα fold of zinc finger proteins as a “natural” protecting group. Chemoselective synthesis of a DNA-binding zinc finger derivative. Chem Commun (Camb) 2014; 50:2258-60. [DOI: 10.1039/c3cc47599a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Eveland AL, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis MW, Kumari S, Hiraga S, Yang F, Unger-Wallace E, Olson A, Hake S, Vollbrecht E, Grotewold E, Ware D, Jackson D. Regulatory modules controlling maize inflorescence architecture. Genome Res 2013; 24:431-43. [PMID: 24307553 PMCID: PMC3941108 DOI: 10.1101/gr.166397.113] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.
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Affiliation(s)
- Andrea L Eveland
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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41
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Abstract
Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified. Among the factors we describe are the pausing factors--NELF (negative elongation factor) and DSIF (DRB sensitivity-inducing factor)--and P-TEFb (positive elongation factor b), which is the key player in pause release. We also describe the high-resolution view of Pol II pausing and propose nonexclusive models for how pausing is achieved. We then discuss Pol II elongation through the bodies of genes and the roles of FACT and SPT6, factors that allow Pol II to move through nucleosomes.
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Affiliation(s)
- Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703; ,
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42
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Piñeyro D, Blanch M, Badal M, Kosoy A, Bernués J. GAGA factor repression of transcription is a rare event but the negative regulation of Trl is conserved in Drosophila species. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1056-65. [PMID: 23860261 DOI: 10.1016/j.bbagrm.2013.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
Abstract
GAGA is a highly conserved Drosophila transcription factor encoded by the Trithorax-like (Trl) gene. While GAGA usually activates transcription, it represses its own promoter. Here we show that GAGA-mediated repression of Trl is conserved between two distant Drosophila species. A detailed promoter study showed that GAGA repressive activity can't be attributed to any discrete element in the Trl promoter. Genome-wide analysis of the transcriptome in S2 cells indicated that repression of Trl is very likely unique, being GAGA factor a transactivator for all the other promoters. Taken together, our results suggest a new mechanism to explain GAGA-mediated repression that involves a dose-dependent change in the architecture of the Trl promoter.
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Affiliation(s)
- David Piñeyro
- Departament. de Genòmica Molecular, Institut de Biologia Molecular de Barcelona-CSIC, Parc Científic de Barcelona, 08028 Barcelona, Spain; Cell and Developmental Biology Programme, Institute for Research in Biomedicine, Barcelona, Spain
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43
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Sánchez MI, Vázquez O, Vázquez ME, Mascareñas JL. Sequence-selective DNA recognition with peptide-bisbenzamidine conjugates. Chemistry 2013; 19:9923-9. [PMID: 23780839 DOI: 10.1002/chem.201300519] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 12/15/2022]
Abstract
Transcription factors (TFs) are specialized proteins that play a key role in the regulation of genetic expression. Their mechanism of action involves the interaction with specific DNA sequences, which usually takes place through specialized domains of the protein. However, achieving an efficient binding usually requires the presence of the full protein. This is the case for bZIP and zinc finger TF families, which cannot interact with their target sites when the DNA binding fragments are presented as isolated monomers. Herein it is demonstrated that the DNA binding of these monomeric peptides can be restored when conjugated to aza-bisbenzamidines, which are readily accessible molecules that interact with A/T-rich sites by insertion into their minor groove. Importantly, the fluorogenic properties of the aza-benzamidine unit provide details of the DNA interaction that are eluded in electrophoresis mobility shift assays (EMSA). The hybrids based on the GCN4 bZIP protein preferentially bind to composite sequences containing tandem bisbenzamidine-GCN4 binding sites (TCAT⋅AAATT). Fluorescence reverse titrations show an interesting multiphasic profile consistent with the formation of competitive nonspecific complexes at low DNA/peptide ratios. On the other hand, the conjugate with the DNA binding domain of the zinc finger protein GAGA binds with high affinity (KD≈12 nM) and specificity to a composite AATTT⋅GAGA sequence containing both the bisbenzamidine and the TF consensus binding sites.
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Affiliation(s)
- Mateo I Sánchez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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44
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Netti F, Malgieri G, Esposito S, Palmieri M, Baglivo I, Isernia C, Omichinski JG, Pedone PV, Lartillot N, Fattorusso R. An Experimentally Tested Scenario for the Structural Evolution of Eukaryotic Cys2His2 Zinc Fingers from Eubacterial Ros Homologs. Mol Biol Evol 2013; 30:1504-13. [DOI: 10.1093/molbev/mst068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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45
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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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46
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Guillière F, Danioux C, Jaubert C, Desnoues N, Delepierre M, Prangishvili D, Sezonov G, Guijarro JI. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold. PLoS One 2013; 8:e52908. [PMID: 23326363 PMCID: PMC3541406 DOI: 10.1371/journal.pone.0052908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/23/2012] [Indexed: 11/18/2022] Open
Abstract
While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.
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Affiliation(s)
- Florence Guillière
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS UMR 3528, Paris, France
- Université Paris 7 Denis Diderot, Paris, France
| | - Chloé Danioux
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Carole Jaubert
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Nicole Desnoues
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
| | - Muriel Delepierre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
| | - Guennadi Sezonov
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
- Université Pierre et Marie Curie, Paris, France
- * E-mail: (JIG); (GS)
| | - J. Iñaki Guijarro
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS UMR 3528, Paris, France
- * E-mail: (JIG); (GS)
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47
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Yang YJ, Baltus AE, Mathew RS, Murphy EA, Evrony GD, Gonzalez DM, Wang EP, Marshall-Walker CA, Barry BJ, Murn J, Tatarakis A, Mahajan MA, Samuels HH, Shi Y, Golden JA, Mahajnah M, Shenhav R, Walsh CA. Microcephaly gene links trithorax and REST/NRSF to control neural stem cell proliferation and differentiation. Cell 2012; 151:1097-112. [PMID: 23178126 PMCID: PMC3567437 DOI: 10.1016/j.cell.2012.10.043] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/27/2012] [Accepted: 10/17/2012] [Indexed: 11/23/2022]
Abstract
Microcephaly is a neurodevelopmental disorder causing significantly reduced cerebral cortex size. Many known microcephaly gene products localize to centrosomes, regulating cell fate and proliferation. Here, we identify and characterize a nuclear zinc finger protein, ZNF335/NIF-1, as a causative gene for severe microcephaly, small somatic size, and neonatal death. Znf335 null mice are embryonically lethal, and conditional knockout leads to severely reduced cortical size. RNA-interference and postmortem human studies show that ZNF335 is essential for neural progenitor self-renewal, neurogenesis, and neuronal differentiation. ZNF335 is a component of a vertebrate-specific, trithorax H3K4-methylation complex, directly regulating REST/NRSF, a master regulator of neural gene expression and cell fate, as well as other essential neural-specific genes. Our results reveal ZNF335 as an essential link between H3K4 complexes and REST/NRSF and provide the first direct genetic evidence that this pathway regulates human neurogenesis and neuronal differentiation.
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Affiliation(s)
- Yawei J. Yang
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA and MIT, Cambridge, MA 02142, USA
- Harvard MD-PhD MSTP Program, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew E. Baltus
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute
| | - Rebecca S. Mathew
- Howard Hughes Medical Institute
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Elisabeth A. Murphy
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Department of Neuroscience, Northeastern University, Boston, MA 02115, USA
| | - Gilad D. Evrony
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute
- Harvard MD-PhD MSTP Program, Harvard Medical School, Boston, MA 02115, USA
| | - Dilenny M. Gonzalez
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute
| | - Estee P. Wang
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute
- Harvard School of Dental Medicine, Boston, MA 02115, USA; Current Address: Department of Orthodontics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christine A. Marshall-Walker
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Howard Hughes Medical Institute
| | - Brenda J. Barry
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute
| | - Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, MA 02115, USA
| | - Antonis Tatarakis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Muktar A. Mahajan
- Department of Pharmacology and Medicine, New York University, New York, NY 10016, USA
| | - Herbert H. Samuels
- Department of Pharmacology and Medicine, New York University, New York, NY 10016, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, MA 02115, USA
| | - Jeffrey A. Golden
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Muhammad Mahajnah
- Child Development and Pediatric Neurology, Hillel Yaffe Medical Center, Hadera 38100, Israel, The Technion, Israel Institue of Technology, Haifa 32000, Israel
| | - Ruthie Shenhav
- Raphael Recanati Genetics Institue, Rabin Medical Center, Beilinson Campus, Petah Tikva 49100, Israel
| | - Christopher A. Walsh
- Division of Genetics, and Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute
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Sousounis K, Haney CE, Cao J, Sunchu B, Tsonis PA. Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Hum Genomics 2012; 6:10. [PMID: 23244440 PMCID: PMC3500211 DOI: 10.1186/1479-7364-6-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 12/12/2022] Open
Abstract
In this review, we examine examples of conservation of protein structural motifs in unrelated or non-homologous proteins. For this, we have selected three DNA-binding motifs: the histone fold, the helix-turn-helix motif, and the zinc finger, as well as the globin-like fold. We show that indeed similar structures exist in unrelated proteins, strengthening the concept that three-dimensional conservation might be more important than the primary amino acid sequence.
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49
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Clore GM. Exploring translocation of proteins on DNA by NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:209-19. [PMID: 21847629 PMCID: PMC3207612 DOI: 10.1007/s10858-011-9555-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
While an extensive body of knowledge has accumulated on the structures of transcription factors, DNA and their complexes from both NMR and crystallography, much less is known at a molecular level regarding the mechanisms whereby transcription factors locate their specific DNA target site within an overwhelming sea of non-specific DNA sites. Indirect kinetic data suggested that three processes are involved in the search procedure: jumping by dissociation of the protein from the DNA followed by re-association at another site, direct transfer from one DNA molecule or segment to another, and one-dimensional sliding. In this brief perspective I summarize recent NMR developments from our laboratory that have permitted direct characterization of the species and molecular mechanisms involved in the target search process, including the detection of highly transient sparsely-populated states. The main tool in these studies involves the application of paramagnetic relaxation enhancement, supplemented by z-exchange spectroscopy, lineshape analysis and residual dipolar couplings. These studies led to the first direct demonstration of rotation-coupled sliding of a protein along the DNA and the direct transfer of a protein from one DNA molecule to another without dissociating into free solution.
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Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 02892-0520, USA.
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50
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Omelina ES, Baricheva EM, Oshchepkov DY, Merkulova TI. Analysis and recognition of the GAGA transcription factor binding sites in Drosophila genes. Comput Biol Chem 2011; 35:363-70. [PMID: 22099633 DOI: 10.1016/j.compbiolchem.2011.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 01/03/2023]
Abstract
The transcription factor GAGA, encoded by the gene Trl, controls expression of many Drosophila melanogaster genes. We have compiled the presently largest sample (120 sites) of published nucleotide sequences with experimentally confirmed binding to GAGA protein. Analysis of the sample has demonstrated that despite an apparent structural diversity of the GAGA sites, they fall into four distinct groups, namely, (1) the sites containing two GAG trinucleotides with no more than one nucleotide substitution in each and separated by spacers with a length of 1 or 3 nucleotides (GAGnGAG and GAGnnnGAG); (2) the sites containing a single GAGAG motif; (3) (GA)(3-9) microsatellite repeats; and (4) the sites corresponding to three and more direct repeats of GAG trinucleotide homolog and its inverted repeats separated by spacers of various lengths. Using the software package SITECON, the methods were elaborated for recognizing the sites of GAGnGAG (method 1) and GAGnnnGAG (method 2) types in DNA sequences. Experimental verification confirmed the ability to interact with the GAGA factor for 72% of the sites predicted using method 1 and 94.5% of the sites predicted by method 2. Application of the experimentally verified methods to analyzing the localization of potential GAGA binding sites in the target genes of this transcription factor has demonstrated that the 5'-untranslated regions (5'UTRs) and first introns are enriched for these sites (two-threefold relative to the average occurrence frequency in the D. melanogaster genome) as compared with a moderate enrichment (not exceeding 1.5-fold) of promoter regions (-4000/+200 bp or -1000/+100 bp).
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Affiliation(s)
- E S Omelina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk 630090, Russian Federation.
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