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Von Dwingelo J, Chung IYW, Price CT, Li L, Jones S, Cygler M, Abu Kwaik Y. Interaction of the Ankyrin H Core Effector of Legionella with the Host LARP7 Component of the 7SK snRNP Complex. mBio 2019; 10:e01942-19. [PMID: 31455655 PMCID: PMC6712400 DOI: 10.1128/mbio.01942-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022] Open
Abstract
Species of the Legionella genus encode at least 18,000 effector proteins that are translocated through the Dot/Icm type IVB translocation system into macrophages and protist hosts to enable intracellular growth. Eight effectors, including ankyrin H (AnkH), are common to all Legionella species. The AnkH effector is also present in Coxiella and Rickettsiella To date, no pathogenic effectors have ever been described that directly interfere with host cell transcription. We determined that the host nuclear protein La-related protein 7 (LARP7), which is a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, interacts with AnkH in the host cell nucleus. The AnkH-LARP7 interaction partially impedes interactions of the 7SK snRNP components with LARP7, interfering with transcriptional elongation by polymerase (Pol) II. Consistent with that, our data show AnkH-dependent global reprogramming of transcription of macrophages infected by Legionella pneumophila The crystal structure of AnkH shows that it contains four N-terminal ankyrin repeats, followed by a cysteine protease-like domain and an α-helical C-terminal domain. A substitution within the β-hairpin loop of the third ankyrin repeat results in diminishment of LARP7-AnkH interactions and phenocopies the ankH null mutant defect in intracellular growth. LARP7 knockdown partially suppresses intracellular proliferation of wild-type (WT) bacteria and increases the severity of the defect of the ΔankH mutant, indicating a role for LARP7 in permissiveness of host cells to intracellular bacterial infection. We conclude that the AnkH-LARP7 interaction impedes interaction of LARP7 with 7SK snRNP, which would block transcriptional elongation by Pol II, leading to host global transcriptional reprogramming and permissiveness to L. pneumophilaIMPORTANCE For intracellular pathogens to thrive in host cells, an environment that supports survival and replication needs to be established. L. pneumophila accomplishes this through the activity of the ∼330 effector proteins that are injected into host cells during infection. Effector functions range from hijacking host trafficking pathways to altering host cell machinery, resulting in altered cell biology and innate immunity. One such pathway is the host protein synthesis pathway. Five L. pneumophila effectors have been identified that alter host cell translation, and 2 effectors have been identified that indirectly affect host cell transcription. No pathogenic effectors have been described that directly interfere with host cell transcription. Here we show a direct interaction of the AnkH effector with a host cell transcription complex involved in transcriptional elongation. We identify a novel process by which AnkH interferes with host transcriptional elongation through interference with formation of a functional complex and show that this interference is required for pathogen proliferation.
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Affiliation(s)
- Juanita Von Dwingelo
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christopher T Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Lei Li
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Snake Jones
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding. Structure 2011; 19:349-60. [PMID: 21397186 DOI: 10.1016/j.str.2010.12.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 11/23/2010] [Accepted: 12/10/2010] [Indexed: 11/22/2022]
Abstract
Cooperativity is a defining feature of protein folding, but its thermodynamic and structural origins are not completely understood. By constructing consensus ankyrin repeat protein arrays that have nearly identical sequences, we quantify cooperativity by resolving stability into intrinsic and interfacial components. Heteronuclear NMR and CD spectroscopy show that these constructs adopt ankyrin repeat structures. Applying a one-dimensional Ising model to a series of constructs chosen to maximize information content in unfolding transitions, we quantify stabilities of the terminal capping repeats, and resolve the effects of denaturant into intrinsic and interfacial components. Reversible thermal denaturation resolves interfacial and intrinsic free energies into enthalpic, entropic, and heat capacity terms. Intrinsic folding is entropically disfavored, whereas interfacial interaction is entropically favored and attends a decrease in heat capacity. These results suggest that helix formation and backbone ordering occurs upon intrinsic folding, whereas hydrophobic desolvation occurs upon interfacial interaction, contributing to cooperativity.
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Kramer MA, Wetzel SK, Plückthun A, Mittl PR, Grütter MG. Structural Determinants for Improved Stability of Designed Ankyrin Repeat Proteins with a Redesigned C-Capping Module. J Mol Biol 2010; 404:381-91. [DOI: 10.1016/j.jmb.2010.09.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 09/06/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
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Sklenovský P, Otyepka M. In SilicoStructural and Functional Analysis of Fragments of the Ankyrin Repeat Protein p18INK4c. J Biomol Struct Dyn 2010; 27:521-40. [DOI: 10.1080/07391102.2010.10507336] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Winger M, van Gunsteren W. Use of Molecular-Dynamics Simulation for Optimizing Protein Stability: Consensus-Designed Ankyrin Repeat Proteins. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Barrick D, Ferreiro DU, Komives EA. Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr Opin Struct Biol 2008; 18:27-34. [PMID: 18243686 DOI: 10.1016/j.sbi.2007.12.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 12/04/2007] [Accepted: 12/05/2007] [Indexed: 10/22/2022]
Abstract
Nearly 6% of eukaryotic protein sequences contain ankyrin repeat (AR) domains, which consist of several repeats and often function in binding. AR proteins show highly cooperative folding despite a lack of long-range contacts. Both theory and experiment converge to explain that formation of the interface between elements is more favorable than formation of any individual repeat unit. IkappaBalpha and Notch both undergo partial folding upon binding perhaps influencing the binding free energy. The simple architecture, combined with identification of consensus residues that are important for stability, has enabled systematic perturbation of the energy landscape by single point mutations that affect stability or by addition of consensus repeats. The folding energy landscapes appear highly plastic, with small perturbations re-routing folding pathways.
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Affiliation(s)
- Doug Barrick
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400N, Charles St. Baltimore, MD 21218, USA
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Merz T, Wetzel SK, Firbank S, Plückthun A, Grütter MG, Mittl PR. Stabilizing Ionic Interactions in a Full-consensus Ankyrin Repeat Protein. J Mol Biol 2008; 376:232-40. [DOI: 10.1016/j.jmb.2007.11.047] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 09/28/2007] [Accepted: 11/16/2007] [Indexed: 11/26/2022]
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Wetzel SK, Settanni G, Kenig M, Binz HK, Plückthun A. Folding and Unfolding Mechanism of Highly Stable Full-Consensus Ankyrin Repeat Proteins. J Mol Biol 2008; 376:241-57. [DOI: 10.1016/j.jmb.2007.11.046] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 10/03/2007] [Accepted: 11/16/2007] [Indexed: 11/29/2022]
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Steinmetz MO, Gattin Z, Verel R, Ciani B, Stromer T, Green JM, Tittmann P, Schulze-Briese C, Gross H, van Gunsteren WF, Meier BH, Serpell LC, Müller SA, Kammerer RA. Atomic Models of De Novo Designed ccβ-Met Amyloid-Like Fibrils. J Mol Biol 2008; 376:898-912. [DOI: 10.1016/j.jmb.2007.11.100] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 11/27/2007] [Accepted: 11/28/2007] [Indexed: 10/22/2022]
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Abstract
Over the last 30 years, computation based on molecular models is playing an increasingly important role in biology, biological chemistry and biophysics. Since only a very limited number of properties of biomolecular systems are actually accessible to measurement by experimental means, computer simulation complements experiments by providing not only averages, but also distributions and time series of any definable, observable or non-observable, quantity. Biomolecular simulation may be used (i) to interpret experimental data, (ii) to provoke new experiments, (iii) to replace experiments and (iv) to protect intellectual property. Progress over the last 30 years is sketched and perspectives are outlined for the future.
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Tsai CJ, Zheng J, Zanuy D, Haspel N, Wolfson H, Alemán C, Nussinov R. Principles of nanostructure design with protein building blocks. Proteins 2007; 68:1-12. [PMID: 17407160 DOI: 10.1002/prot.21413] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Currently there is increasing interest in nanostructures and their design. Nanostructure design involves the ability to predictably manipulate the properties of the self-assembly of autonomous units. Autonomous units have preferred conformational states. The units can be synthetic material science-based or derived from functional biological macromolecules. Autonomous biological building blocks with available structures provide an extremely rich and useful resource for design. For proteins, the structural databases contain large libraries of protein molecules and their building blocks with a range of shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these can expand the available chemical space and enhance the desired properties. Here we focus on the principles of nanostructure design with protein building blocks.
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Affiliation(s)
- Chung-Jung Tsai
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA
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Missimer JH, Steinmetz MO, Baron R, Winkler FK, Kammerer RA, Daura X, van Gunsteren WF. Configurational entropy elucidates the role of salt-bridge networks in protein thermostability. Protein Sci 2007; 16:1349-59. [PMID: 17586770 PMCID: PMC2206687 DOI: 10.1110/ps.062542907] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Detailed knowledge of how networks of surface salt bridges contribute to protein thermal stability is essential not only to understand protein structure and function but also to design thermostable proteins for industrial applications. Experimental studies investigating thermodynamic stability through measurements of free energy associated with mutational alterations in proteins provide only macroscopic evidence regarding the structure of salt-bridge networks and assessment of their contribution to protein stability. Using explicit-solvent molecular dynamics simulations to provide insight on the atomic scale, we investigate here the structural stability, defined in terms of root-mean-square fluctuations, of a short polypeptide designed to fold into a stable trimeric coiled coil with a well-packed hydrophobic core and an optimal number of intra- and interhelical surface salt bridges. We find that the increase of configurational entropy of the backbone and side-chain atoms and decreased pair correlations of these with increased temperature are consistent with nearly constant atom-positional root-mean-square fluctuations, increased salt-bridge occupancies, and stronger electrostatic interactions in the coiled coil. Thus, our study of the coiled coil suggests a mechanism in which well-designed salt-bridge networks could accommodate stochastically the disorder of increased thermal motion to produce thermostability.
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Affiliation(s)
- John H Missimer
- Biomolecular Research, Structural Biology Paul Scherrer Institut, Villigen, Switzerland.
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