1
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Kim HJ, Szurgot MR, van Eeuwen T, Ricketts MD, Basnet P, Zhang AL, Vogt A, Sharmin S, Kaplan CD, Garcia BA, Marmorstein R, Murakami K. Structure of the Hir histone chaperone complex. Mol Cell 2024; 84:2601-2617.e12. [PMID: 38925115 DOI: 10.1016/j.molcel.2024.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4)2 tetramers on DNA for replication-independent chromatin assembly. The molecular architecture of the HIRA/Hir complex and its mode of histone deposition have remained unknown. Here, we report the cryo-EM structure of the S. cerevisiae Hir complex with Asf1/H3/H4 at 2.9-6.8 Å resolution. We find that the Hir complex forms an arc-shaped dimer with a Hir1/Hir2/Hir3/Hpc2 stoichiometry of 2/4/2/4. The core of the complex containing two Hir1/Hir2/Hir2 trimers and N-terminal segments of Hir3 forms a central cavity containing two copies of Hpc2, with one engaged by Asf1/H3/H4, in a suitable position to accommodate a histone (H3/H4)2 tetramer, while the C-terminal segments of Hir3 harbor nucleic acid binding activity to wrap DNA around the Hpc2-assisted histone tetramer. The structure suggests a model for how the Hir/Asf1 complex promotes the formation of histone tetramers for their subsequent deposition onto DNA.
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Affiliation(s)
- Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mary R Szurgot
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Trevor van Eeuwen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Daniel Ricketts
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pratik Basnet
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Athena L Zhang
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Austin Vogt
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samah Sharmin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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2
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Stuwe H, Reardon PN, Yu Z, Shah S, Hughes K, Barbar EJ. Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix. J Biol Chem 2024; 300:107354. [PMID: 38718862 PMCID: PMC11180338 DOI: 10.1016/j.jbc.2024.107354] [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: 04/01/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, evading host immunity, and virus maturation. N is a multidomain protein composed of an independently folded monomeric N-terminal domain that is the primary site for RNA binding and a dimeric C-terminal domain that is essential for efficient phase separation and condensate formation with RNA. The domains are separated by a disordered Ser/Arg-rich region preceding a self-associating Leu-rich helix. Phosphorylation in the Ser/Arg region in infected cells decreases the viscosity of N:RNA condensates promoting viral replication and host immune evasion. The molecular level effect of phosphorylation, however, is missing from our current understanding. Using NMR spectroscopy and analytical ultracentrifugation, we show that phosphorylation destabilizes the self-associating Leu-rich helix 30 amino-acids distant from the phosphorylation site. NMR and gel shift assays demonstrate that RNA binding by the linker is dampened by phosphorylation, whereas RNA binding to the full-length protein is not significantly affected presumably due to retained strong interactions with the primary RNA-binding domain. Introducing a switchable self-associating domain to replace the Leu-rich helix confirms the importance of linker self-association to droplet formation and suggests that phosphorylation not only increases solubility of the positively charged elongated Ser/Arg region as observed in other RNA-binding proteins but can also inhibit self-association of the Leu-rich helix. These data highlight the effect of phosphorylation both at local sites and at a distant self-associating hydrophobic helix in regulating liquid-liquid phase separation of the entire protein.
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Affiliation(s)
- Hannah Stuwe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | | | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Sahana Shah
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
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3
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Surya W, Honey SS, Torres J. Flavivirus Zika NS4A protein forms large oligomers in liposomes and in mild detergent. Sci Rep 2024; 14:12533. [PMID: 38822066 PMCID: PMC11143224 DOI: 10.1038/s41598-024-63407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/28/2024] [Indexed: 06/02/2024] Open
Abstract
In flaviviruses such as Dengue or Zika, non-structural (NS) NS4A protein forms homo-oligomers, participates in membrane remodelling and is critical for virulence. In both viruses, mature NS4A has the same length and three predicted hydrophobic domains. The oligomers formed by Dengue NS4A are reported to be small (n = 2, 3), based on denaturing SDS gels, but no high-resolution structure of a flavivirus NS4A protein is available, and the size of the oligomer in lipid membranes is not known. Herein we show that crosslinking Zika NS4A protein in lipid membranes results in oligomers at least up to hexamers. Further, sedimentation velocity shows that NS4A in mild detergent C14-betaine appears to be in fast equilibrium between at least two species, where one is smaller, and the other larger, than a trimer or a tetramer. Consistently, sedimentation equilibrium data was best fitted to a model involving an equilibrium between dimers (n = 2) and hexamers (n = 6). Overall, the large, at least hexameric, oligomers obtained herein in liposomes and in mild detergent are more likely to represent the forms of NS4A present in cell membranes.
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Affiliation(s)
- Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Shwe Sin Honey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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4
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Alcorlo M, Luque-Ortega JR, Gago F, Ortega A, Castellanos M, Chacón P, de Vega M, Blanco L, Hermoso J, Serrano M, Rivas G, Hermoso J. Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29. Nucleic Acids Res 2024; 52:2045-2065. [PMID: 38281216 PMCID: PMC10899789 DOI: 10.1093/nar/gkae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024] Open
Abstract
The genome-organizing protein p6 of Bacillus subtilis bacteriophage φ29 plays an essential role in viral development by activating the initiation of DNA replication and participating in the early-to-late transcriptional switch. These activities require the formation of a nucleoprotein complex in which the DNA adopts a right-handed superhelix wrapping around a multimeric p6 scaffold, restraining positive supercoiling and compacting the viral genome. Due to the absence of homologous structures, prior attempts to unveil p6's structural architecture failed. Here, we employed AlphaFold2 to engineer rational p6 constructs yielding crystals for three-dimensional structure determination. Our findings reveal a novel fold adopted by p6 that sheds light on its self-association mechanism and its interaction with DNA. By means of protein-DNA docking and molecular dynamic simulations, we have generated a comprehensive structural model for the nucleoprotein complex that consistently aligns with its established biochemical and thermodynamic parameters. Besides, through analytical ultracentrifugation, we have confirmed the hydrodynamic properties of the nucleocomplex, further validating in solution our proposed model. Importantly, the disclosed structure not only provides a highly accurate explanation for previously experimental data accumulated over decades, but also enhances our holistic understanding of the structural and functional attributes of protein p6 during φ29 infection.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, CSIC, 28006 Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas “Margarita Salas”, CSIC, 28040Madrid, Spain
| | - Federico Gago
- Departamento de Farmacología and CSIC-IQM Associate Unit, Universidad de Alcalá, Alcalá de Henares, 28871Madrid, Spain
| | - Alvaro Ortega
- Department of Biochemistry and Molecular Biology ‘B’ and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence ‘Campus Mare Nostrum, Murcia, Spain
| | - Milagros Castellanos
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Nanotechnology for Health-Care, 28049 Madrid, Spain
| | - Pablo Chacón
- Department of Biological Physical-Chemistry, Institute of Physical-Chemistry “Blas Cabrera”, CSIC, 28006Madrid, Spain
| | - Miguel de Vega
- Genome maintenance and instability, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049Cantoblanco, Madrid, Spain
| | - Luis Blanco
- Genome maintenance and instability, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049Cantoblanco, Madrid, Spain
| | - José M Hermoso
- Genome maintenance and instability, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049Cantoblanco, Madrid, Spain
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
- Cambridge Institute of Science, Altos Labs, Cambridge, UK
| | - Germán Rivas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas “Margarita Salas”, CSIC, 28040Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, CSIC, 28006 Madrid, Spain
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5
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Goodell DJ, Whitby FG, Mellem JE, Lei N, Brockie PJ, Maricq AJ, Eckert DM, Hill CP, Madsen DM, Maricq AV. Mechanistic and structural studies reveal NRAP-1-dependent coincident activation of NMDARs. Cell Rep 2024; 43:113694. [PMID: 38265937 DOI: 10.1016/j.celrep.2024.113694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/27/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
N-methyl-D-aspartate (NMDA)-type ionotropic glutamate receptors have essential roles in neurotransmission and synaptic plasticity. Previously, we identified an evolutionarily conserved protein, NRAP-1, that is required for NMDA receptor (NMDAR) function in C. elegans. Here, we demonstrate that NRAP-1 was sufficient to gate NMDARs and greatly enhanced glutamate-mediated NMDAR gating, thus conferring coincident activation properties to the NMDAR. Intriguingly, vertebrate NMDARs-and chimeric NMDARs where the amino-terminal domain (ATD) of C. elegans NMDARs was replaced by the ATD from vertebrate receptors-were spontaneously active when ectopically expressed in C. elegans neurons. Thus, the ATD is a primary determinant of NRAP-1- and glutamate-mediated gating of NMDARs. We determined the crystal structure of NRAP-1 at 1.9-Å resolution, which revealed two distinct domains positioned around a central low-density lipoprotein receptor class A domain. The NRAP-1 structure, combined with chimeric and mutational analyses, suggests a model where the three NRAP-1 domains work cooperatively to modify the gating of NMDARs.
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Affiliation(s)
- Dayton J Goodell
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Jerry E Mellem
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Ning Lei
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Penelope J Brockie
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | | | - Debra M Eckert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - David M Madsen
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Andres V Maricq
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA.
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6
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Surya W, Liu Y, Torres J. The cytoplasmic N-terminal tail of Zika virus NS4A protein forms oligomers in the absence of detergent or lipids. Sci Rep 2023; 13:7360. [PMID: 37147499 PMCID: PMC10163220 DOI: 10.1038/s41598-023-34621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/04/2023] [Indexed: 05/07/2023] Open
Abstract
The non-structural (NS) NS4A protein in flaviviruses has three predicted transmembrane domains, is critical for virulence and participates in membrane morphogenesis. In Dengue virus (DENV), both hydrophylic N-terminal tail and its first transmembrane domain participate in the formation of oligomers which are important for pathogenicity. However, the relative importance of the N-terminal domain in oligomerization has been under debate. In particular, since in the absence of detergent or lipids, this domain (residues 1-48) in both DENV and Zika virus (ZIKV) NS4A, was found to be disordered. Recently, however, we reported preliminary data that showed that peptide ZIKV NS4A 4-58 adopts a defined secondary structure in aqueous solution and forms oligomers, signaling its importance for full length NS4A oligomerization. Herein we have performed detailed analytical ultracentrifugation experiments to further characterize the oligomerization of this peptide and also a shorter variant (residues 4-44). In both cases, sedimentation velocity produced a single species with concentration-dependent sedimentation coefficient, consistent with a fast equilibrium between at least two species. Combining sedimentation velocity and equilibrium experiments, data is best fitted to a monomer-dimer-trimer equilibrium. Possible models of NS4A oligomers obtained with AlphaFold-2 predict the stabilizing role for residues in this N-terminal domain, such as Arg20, Asn27, Ala44 and Glu50, all at highly conserved positions in flavivirus NS4A proteins. Our results are thus consistent with N-terminal domain interactions acting as one of the driving forces for NS4A homo-oligomerization.
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Affiliation(s)
- Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Yiting Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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7
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Pinar M, Alonso A, de los Ríos V, Bravo-Plaza I, de la Gandara Á, Galindo A, Arias-Palomo E, Peñalva MÁ. The type V myosin-containing complex HUM is a RAB11 effector powering movement of secretory vesicles. iScience 2022; 25:104514. [PMID: 35754728 PMCID: PMC9213775 DOI: 10.1016/j.isci.2022.104514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 01/01/2023] Open
Abstract
In the apex-directed RAB11 exocytic pathway of Aspergillus nidulans, kinesin-1/KinA conveys secretory vesicles (SVs) to the hyphal tip, where they are transferred to the type V myosin MyoE. MyoE concentrates SVs at an apical store located underneath the PM resembling the presynaptic active zone. A rod-shaped RAB11 effector, UDS1, and the intrinsically disordered and coiled-coil HMSV associate with MyoE in a stable HUM (HMSV-UDS1-MyoE) complex recruited by RAB11 to SVs through an interaction network involving RAB11 and HUM components, with the MyoE globular tail domain (GTD) binding both HMSV and RAB11-GTP and RAB11-GTP binding both the MyoE-GTD and UDS1. UDS1 bridges RAB11-GTP to HMSV, an avid interactor of the MyoE-GTD. The interaction between the UDS1-HMSV sub-complex and RAB11-GTP can be reconstituted in vitro. Ablating UDS1 or HMSV impairs actomyosin-mediated transport of SVs to the apex, resulting in spreading of RAB11 SVs across the apical dome as KinA/microtubule-dependent transport gains prominence.
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Affiliation(s)
- Mario Pinar
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana Alonso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Vivian de los Ríos
- Proteomics Facility, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ignacio Bravo-Plaza
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Álvaro de la Gandara
- Department of Chemical and Structural Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Galindo
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK
| | - Ernesto Arias-Palomo
- Department of Chemical and Structural Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Á. Peñalva
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Corresponding author
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8
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Erlandsen H, Jecrois AM, Nichols JC, Cole JL, Royer WE. NADH/NAD + binding and linked tetrameric assembly of the oncogenic transcription factors CtBP1 and CtBP2. FEBS Lett 2022; 596:479-490. [PMID: 34997967 DOI: 10.1002/1873-3468.14276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022]
Abstract
The activation of oncogenic C-terminal binding Protein (CtBP) transcriptional activity is coupled with NAD(H) binding and homo-oligomeric assembly, although the level of CtBP assembly and nucleotide binding affinity continues to be debated. Here, we apply biophysical techniques to address these fundamental issues for CtBP1 and CtBP2. Our ultracentrifugation results unambiguously demonstrate that CtBP assembles into tetramers in the presence of saturating NAD+ or NADH with tetramer to dimer dissociation constants about 100 nm. Isothermal titration calorimetry measurements of NAD(H) binding to CtBP show dissociation constants between 30 and 500 nm, depending on the nucleotide and paralog. Given cellular levels of NAD+ , CtBP is likely to be fully saturated with NAD under physiological concentrations suggesting that CtBP is unable to act as a sensor for NADH levels.
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Affiliation(s)
- Heidi Erlandsen
- Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, USA
| | - Anne M Jecrois
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA
| | - Jeffry C Nichols
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA.,Chemistry Department, Worcester State University, MA, USA
| | - James L Cole
- Department of Molecular and Cell Biology, Department of Chemistry, University of Connecticut, CT, USA
| | - William E Royer
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA
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9
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Meier AA, Moon HJ, Toth R, Folta-Stogniew E, Kuczera K, Middaugh CR, Mure M. Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2. Biomolecules 2021; 11:biom11121846. [PMID: 34944490 PMCID: PMC8699698 DOI: 10.3390/biom11121846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 11/16/2022] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) has emerged as a promising therapeutic target against metastatic/invasive tumors and organ and tissue fibrosis. LOXL2 catalyzes the oxidative deamination of lysine and hydroxylysine residues in extracellular matrix (ECM) proteins to promote crosslinking of these proteins, and thereby plays a major role in ECM remodeling. LOXL2 secretes as 100-kDa full-length protein (fl-LOXL2) and then undergoes proteolytic cleavage of the first two scavenger receptor cysteine-rich (SRCR) domains to yield 60-kDa protein (Δ1-2SRCR-LOXL2). This processing does not affect the amine oxidase activity of LOXL2 in vitro. However, the physiological importance of this cleavage still remains elusive. In this study, we focused on characterization of biophysical properties of fl- and Δ1-2SRCR-LOXL2s (e.g., oligomeric states, molecular weights, and hydrodynamic radii in solution) to gain insight into the structural role of the first two SRCR domains. Our study reveals that fl-LOXL2 exists predominantly as monomer but also dimer to the lesser extent when its concentration is <~1 mM. The hydrodynamic radius (Rh) determined by multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) indicates that fl-LOXL2 is a moderately asymmetric protein. In contrast, Δ1-2SRCR-LOXL2 exists solely as monomer and its Rh is in good agreement with the predicted value. The Rh values calculated from a 3D modeled structure of fl-LOXL2 and the crystal structure of the precursor Δ1-2SRCR-LOXL2 are within a reasonable margin of error of the values determined by SEC-MALS for fl- and Δ1-2SRCR-LOXL2s in mature forms in this study. Based on superimposition of the 3D model and the crystal structure of Δ1-2SRCR-LOXL2 (PDB:5ZE3), we propose a configuration of fl-LOXL2 that explains the difference observed in Rh between fl- and Δ1-2SRCR-LOXL2s in solution.
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Affiliation(s)
- Alex A. Meier
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
| | - Hee-Jung Moon
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
| | - Ronald Toth
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA; (R.T.IV); (C.R.M.)
| | - Ewa Folta-Stogniew
- W.M. Keck Biotechnology Resource Laboratory, Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06511, USA;
| | - Krzysztof Kuczera
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - C. Russell Middaugh
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA; (R.T.IV); (C.R.M.)
| | - Minae Mure
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
- Correspondence:
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10
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Boyko KV, Rosenkranz EA, Smith DM, Miears HL, Oueld es cheikh M, Lund MZ, Young JC, Reardon PN, Okon M, Smirnov SL, Antos JM. Sortase-mediated segmental labeling: A method for segmental assignment of intrinsically disordered regions in proteins. PLoS One 2021; 16:e0258531. [PMID: 34710113 PMCID: PMC8553144 DOI: 10.1371/journal.pone.0258531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
A significant number of proteins possess sizable intrinsically disordered regions (IDRs). Due to the dynamic nature of IDRs, NMR spectroscopy is often the tool of choice for characterizing these segments. However, the application of NMR to IDRs is often hindered by their instability, spectral overlap and resonance assignment difficulties. Notably, these challenges increase considerably with the size of the IDR. In response to these issues, here we report the use of sortase-mediated ligation (SML) for segmental isotopic labeling of IDR-containing samples. Specifically, we have developed a ligation strategy involving a key segment of the large IDR and adjacent folded headpiece domain comprising the C-terminus of A. thaliana villin 4 (AtVLN4). This procedure significantly reduces the complexity of NMR spectra and enables group identification of signals arising from the labeled IDR fragment, a process we refer to as segmental assignment. The validity of our segmental assignment approach is corroborated by backbone residue-specific assignment of the IDR using a minimal set of standard heteronuclear NMR methods. Using segmental assignment, we further demonstrate that the IDR region adjacent to the headpiece exhibits nonuniform spectral alterations in response to temperature. Subsequent residue-specific characterization revealed two segments within the IDR that responded to temperature in markedly different ways. Overall, this study represents an important step toward the selective labeling and probing of target segments within much larger IDR contexts. Additionally, the approach described offers significant savings in NMR recording time, a valuable advantage for the study of unstable IDRs, their binding interfaces, and functional mechanisms.
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Affiliation(s)
- Kristina V. Boyko
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Erin A. Rosenkranz
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Derrick M. Smith
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Heather L. Miears
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Melissa Oueld es cheikh
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Micah Z. Lund
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Jeffery C. Young
- Department of Biology, Western Washington University, Bellingham, Washington, United States of America
| | - Patrick N. Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - John M. Antos
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
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11
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Nguyen B, Shinn MK, Weiland E, Lohman TM. Regulation of E. coli Rep helicase activity by PriC. J Mol Biol 2021; 433:167072. [PMID: 34081984 DOI: 10.1016/j.jmb.2021.167072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 11/28/2022]
Abstract
Stalled DNA replication forks can result in incompletely replicated genomes and cell death. DNA replication restart pathways have evolved to deal with repair of stalled forks and E. coli Rep helicase functions in this capacity. Rep and an accessory protein, PriC, assemble at a stalled replication fork to facilitate loading of other replication proteins. A Rep monomer is a rapid and processive single stranded (ss) DNA translocase but needs to be activated to function as a helicase. Activation of Rep in vitro requires self-assembly to form a dimer, removal of its auto-inhibitory 2B sub-domain, or interactions with an accessory protein. Rep helicase activity has been shown to be stimulated by PriC, although the mechanism of activation is not clear. Using stopped flow kinetics, analytical sedimentation and single molecule fluorescence methods, we show that a PriC dimer activates the Rep monomer helicase and can also stimulate the Rep dimer helicase. We show that PriC can self-assemble to form dimers and tetramers and that Rep and PriC interact in the absence of DNA. We further show that PriC serves as a Rep processivity factor, presumably co-translocating with Rep during DNA unwinding. Activation is specific for Rep since PriC does not activate the UvrD helicase. Interaction of PriC with the C-terminal acidic tip of the ssDNA binding protein, SSB, eliminates Rep activation by stabilizing the PriC monomer. This suggests a likely mechanism for Rep activation by PriC at a stalled replication fork.
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Affiliation(s)
- Binh Nguyen
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Min Kyung Shinn
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States.
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12
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Clark S, Jowitt TA, Harris LK, Knight CG, Dobson CB. The lexicon of antimicrobial peptides: a complete set of arginine and tryptophan sequences. Commun Biol 2021; 4:605. [PMID: 34021253 PMCID: PMC8140080 DOI: 10.1038/s42003-021-02137-7] [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: 08/09/2020] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Our understanding of the activity of cationic antimicrobial peptides (AMPs) has focused on well-characterized natural sequences, or limited sets of synthetic peptides designed de novo. We have undertaken a comprehensive investigation of the underlying primary structural features that give rise to the development of activity in AMPs. We consider a complete set of all possible peptides, up to 7 residues long, composed of positively charged arginine (R) and / or hydrophobic tryptophan (W), two features most commonly associated with activity. We found the shortest active peptides were 4 or 5 residues in length, and the overall landscapes of activity against gram-positive and gram-negative bacteria and a yeast were positively correlated. For all three organisms we found a single activity peak corresponding to sequences with around 40% R; the presence of adjacent W duplets and triplets also conferred greater activity. The mechanistic basis of these activities comprises a combination of lipid binding, particularly to negatively charged membranes, and additionally peptide aggregation, a mode of action previously uninvestigated for such peptides. The maximum specific antimicrobial activity appeared to occur in peptides of around 10 residues, suggesting ‘diminishing returns’ for developing larger peptides, when activity is considered per residue of peptide. Clark et al. comprehensively explore the primary structural features underlying the activity of a complete set of antimicrobial peptides (AMPs). They find that the shortest active peptides were 4 or 5 residues in length, with activity being associated with 40% arginine, and multiple adjacent tryptophan residues. This study provides insights into the design of effective AMPs.
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Affiliation(s)
- Sam Clark
- Division of Pharmacy & Optometry, School of Health Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester, UK
| | - Thomas A Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, The University of Manchester, Oxford Road, Manchester, UK
| | - Lynda K Harris
- Division of Pharmacy & Optometry, School of Health Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester, UK.,Maternal and Fetal Health Research Centre, The University of Manchester, St Mary's Hospital, Oxford Road, Manchester, UK.,St Mary's Hospital, Manchester Foundation Trust, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Christopher G Knight
- Department of Earth and Environmental Sciences, School of Natural Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, UK
| | - Curtis B Dobson
- Division of Pharmacy & Optometry, School of Health Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester, UK.
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13
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Durante-Rodríguez G, Páez-Espino D, de Lorenzo V. A Bifan Motif Shaped by ArsR1, ArsR2, and Their Cognate Promoters Frames Arsenic Tolerance of Pseudomonas putida. Front Microbiol 2021; 12:641440. [PMID: 33776973 PMCID: PMC7994332 DOI: 10.3389/fmicb.2021.641440] [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: 12/14/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic tolerance to inorganic arsenic is a widespread trait habitually determined by operons encoding an As (III)-responsive repressor (ArsR), an As (V)-reductase (ArsC), and an As (III)-export pump (ArsB), often accompanied by other complementary genes. Enigmatically, the genomes of many environmental bacteria typically contain two or more copies of this basic genetic device arsRBC. To shed some light on the logic of such apparently unnecessary duplication(s) we have inspected the regulation—together and by separate—of the two ars clusters borne by the soil bacterium Pseudomonas putida strain KT2440, in particular the cross talk between the two repressors ArsR1/ArsR2 and the respective promoters. DNase I footprinting and gel retardation analyses of Pars1 and Pars2 with their matching regulators revealed non-identical binding sequences and interaction patterns for each of the systems. However, in vitro transcription experiments exposed that the repressors could downregulate each other’s promoters, albeit within a different set of parameters. The regulatory frame that emerges from these data corresponds to a particular type of bifan motif where all key interactions have a negative sign. The distinct regulatory architecture that stems from coexistence of various ArsR variants in the same cells could enter an adaptive advantage that favors the maintenance of the two proteins as separate repressors.
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Affiliation(s)
| | - David Páez-Espino
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
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14
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Eastep GN, Ghanam RH, Green TJ, Saad JS. Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation. J Biol Chem 2021; 296:100321. [PMID: 33485964 PMCID: PMC7952133 DOI: 10.1016/j.jbc.2021.100321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/05/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022] Open
Abstract
During the late phase of HIV-1 infection, viral Gag polyproteins are targeted to the plasma membrane (PM) for assembly. Gag localization at the PM is a prerequisite for the incorporation of the envelope protein (Env) into budding particles. Gag assembly and Env incorporation are mediated by the N-terminal myristoylated matrix (MA) domain of Gag. Nonconservative mutations in the trimer interface of MA (A45E, T70R, and L75G) were found to impair Env incorporation and infectivity, leading to the hypothesis that MA trimerization is an obligatory step for Env incorporation. Conversely, Env incorporation can be rescued by a compensatory mutation in the MA trimer interface (Q63R). The impact of these MA mutations on the structure and trimerization properties of MA is not known. In this study, we employed NMR spectroscopy, X-ray crystallography, and sedimentation techniques to characterize the structure and trimerization properties of HIV-1 MA A45E, Q63R, T70R, and L75G mutant proteins. NMR data revealed that these point mutations did not alter the overall structure and folding of MA but caused minor structural perturbations in the trimer interface. Analytical ultracentrifugation data indicated that mutations had a minimal effect on the MA monomer–trimer equilibrium. The high-resolution X-ray structure of the unmyristoylated MA Q63R protein revealed hydrogen bonding between the side chains of adjacent Arg-63 and Ser-67 on neighboring MA molecules, providing the first structural evidence for an additional intermolecular interaction in the trimer interface. These findings advance our knowledge of the interplay of MA trimerization and Env incorporation into HIV-1 particles.
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Affiliation(s)
- Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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15
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Gamiz-Arco G, Gutierrez-Rus LI, Risso VA, Ibarra-Molero B, Hoshino Y, Petrović D, Justicia J, Cuerva JM, Romero-Rivera A, Seelig B, Gavira JA, Kamerlin SCL, Gaucher EA, Sanchez-Ruiz JM. Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase. Nat Commun 2021; 12:380. [PMID: 33452262 PMCID: PMC7810902 DOI: 10.1038/s41467-020-20630-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed. Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.
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Affiliation(s)
- Gloria Gamiz-Arco
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Luis I Gutierrez-Rus
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Yosuke Hoshino
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Dušan Petrović
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.,Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, 431 50, Gothenburg, Sweden
| | - Jose Justicia
- Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Juan Manuel Cuerva
- Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Adrian Romero-Rivera
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America, & BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Jose A Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Avenida de las Palmeras 4, Granada, 18100, Armilla, Spain
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain.
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16
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Crespo I, Bernardo N, Miguel-Arribas A, Singh PK, Luque-Ortega JR, Alfonso C, Malfois M, Meijer WJJ, Boer DR. Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization. Nucleic Acids Res 2020; 48:8113-8127. [PMID: 32658272 PMCID: PMC7430634 DOI: 10.1093/nar/gkaa540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022] Open
Abstract
Quorum sensing allows bacterial cells to communicate through the release of soluble signaling molecules into the surrounding medium. It plays a pivotal role in controlling bacterial conjugation in Gram-positive cells, a process that has tremendous impact on health. Intracellular regulatory proteins of the RRNPP family are common targets of these signaling molecules. The RRNPP family of gene regulators bind signaling molecules at their C-terminal domain (CTD), but have highly divergent functionalities at their N-terminal effector domains (NTD). This divergence is also reflected in the functional states of the proteins, and is highly interesting from an evolutionary perspective. RappLS20 is an RRNPP encoded on the Bacillus subtilis plasmid pLS20. It relieves the gene repression effectuated by RcopLS20 in the absence of the mature pLS20 signaling peptide Phr*pLS20. We report here an in-depth structural study of apo and Phr*pLS20-bound states of RappLS20 at various levels of atomic detail. We show that apo-RappLS20 is dimeric and that Phr*pLS20-bound Rap forms NTD-mediated tetramers. In addition, we show that RappLS20 binds RcopLS20 directly in the absence of Phr*pLS20 and that addition of Phr*pLS20 releases RcopLS20 from RappLS20. This allows RcopLS20 to bind the promotor region of crucial conjugation genes blocking their expression.
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Affiliation(s)
- Isidro Crespo
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Nerea Bernardo
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Praveen K Singh
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Juan R Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carlos Alfonso
- Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Marc Malfois
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Dirk Roeland Boer
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
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17
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Singh PK, Serrano E, Ramachandran G, Miguel-Arribas A, Gago-Cordoba C, Val-Calvo J, López-Pérez A, Alfonso C, Wu LJ, Luque-Ortega JR, Meijer WJJ. Reversible regulation of conjugation of Bacillus subtilis plasmid pLS20 by the quorum sensing peptide responsive anti-repressor RappLS20. Nucleic Acids Res 2020; 48:10785-10801. [PMID: 33045732 PMCID: PMC7641744 DOI: 10.1093/nar/gkaa797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/02/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Quorum sensing plays crucial roles in bacterial communication including in the process of conjugation, which has large economical and health-related impacts by spreading antibiotic resistance. The conjugative Bacillus subtilis plasmid pLS20 uses quorum sensing to determine when to activate the conjugation genes. The main conjugation promoter, Pc, is by default repressed by a regulator RcopLS20 involving DNA looping. A plasmid-encoded signalling peptide, Phr*pLS20, inactivates the anti-repressor of RcopLS20, named RappLS20, which belongs to the large group of RRNPP family of regulatory proteins. Here we show that DNA looping occurs through interactions between two RcopLS20 tetramers, each bound to an operator site. We determined the relative promoter strengths for all the promoters involved in synthesizing the regulatory proteins of the conjugation genes, and constructed an in vivo system uncoupling these regulatory genes to show that RappLS20 is sufficient for activating conjugation in vivo. We also show that RappLS20 actively detaches RcopLS20 from DNA by preferentially acting on the RcopLS20 molecules involved in DNA looping, resulting in sequestration but not inactivation of RcopLS20. Finally, results presented here in combination with our previous results show that activation of conjugation inhibits competence and competence development inhibits conjugation, indicating that both processes are mutually exclusive.
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Affiliation(s)
- Praveen K Singh
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ester Serrano
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Gayetri Ramachandran
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Cordoba
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Arancha López-Pérez
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Juan R Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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18
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Val-Calvo J, Luque-Ortega JR, Crespo I, Miguel-Arribas A, Abia D, Sánchez-Hevia DL, Serrano E, Gago-Córdoba C, Ares S, Alfonso C, Rojo F, Wu LJ, Boer DR, Meijer WJJ. Novel regulatory mechanism of establishment genes of conjugative plasmids. Nucleic Acids Res 2019; 46:11910-11926. [PMID: 30380104 PMCID: PMC6294495 DOI: 10.1093/nar/gky996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/10/2018] [Indexed: 11/12/2022] Open
Abstract
The principal route for dissemination of antibiotic resistance genes is conjugation by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugative elements contain genes that are important for their establishment in the new host, for instance by counteracting the host defense mechanisms acting against incoming foreign DNA. Little is known about these establishment genes and how they are regulated. Here, we deciphered the regulation mechanism of possible establishment genes of plasmid p576 from the Gram-positive bacterium Bacillus pumilus. Unlike the ssDNA promoters described for some conjugative plasmids, the four promoters of these p576 genes are repressed by a repressor protein, which we named Reg576. Reg576 also regulates its own expression. After transfer of the DNA, these genes are de-repressed for a period of time until sufficient Reg576 is synthesized to repress the promoters again. Complementary in vivo and in vitro analyses showed that different operator configurations in the promoter regions of these genes lead to different responses to Reg576. Each operator is bound with extreme cooperativity by two Reg576-dimers. The X-ray structure revealed that Reg576 has a Ribbon-Helix-Helix core and provided important insights into the high cooperativity of DNA recognition.
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Affiliation(s)
- Jorge Val-Calvo
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Juan R Luque-Ortega
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Isidro Crespo
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Andrés Miguel-Arribas
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa"
| | | | - Ester Serrano
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Saúl Ares
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganes, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Fernando Rojo
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE4AX, UK
| | - D Roeland Boer
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Wilfried J J Meijer
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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19
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Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. J Biol Chem 2019; 294:9239-9259. [PMID: 31040182 DOI: 10.1074/jbc.ra119.007480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/01/2019] [Indexed: 02/04/2023] Open
Abstract
The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to specifically bind and deposit H3.3/H4 into chromatin. We recently reported that the UBN1 Hpc2-related domain (HRD) specifically binds to H3.3/H4 over H3.1/H4. However, the mechanism for HIRA complex deposition of H3.3/H4 into nucleosomes remains unclear. Here, we characterize a central region of UBN1 (UBN1 middle domain) that is evolutionarily conserved and predicted to have helical secondary structure. We report that the UBN1 middle domain has dimer formation activity and binds to H3/H4 in a manner that does not discriminate between H3.1 and H3.3. We additionally identify a nearby DNA-binding domain in UBN1, located between the UBN1 HRD and middle domain, which binds DNA through electrostatic contacts involving several conserved lysine residues. Together, these observations suggest a mechanism for HIRA-mediated H3.3/H4 deposition whereby UBN1 associates with DNA and dimerizes to mediate formation of an (H3.3/H4)2 heterotetramer prior to chromatin deposition.
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Affiliation(s)
- M Daniel Ricketts
- From the Department of Biochemistry and Biophysics and.,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Nirmalya Dasgupta
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Jiayi Fan
- From the Department of Biochemistry and Biophysics and
| | - Joseph Han
- From the Department of Biochemistry and Biophysics and.,the Department of Chemistry Graduate Group and
| | - Morgan Gerace
- From the Department of Biochemistry and Biophysics and
| | - Yong Tang
- the Wistar Institute, Philadelphia, Pennsylvania 19104, and
| | - Ben E Black
- From the Department of Biochemistry and Biophysics and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Peter D Adams
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Ronen Marmorstein
- From the Department of Biochemistry and Biophysics and .,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,the Department of Chemistry Graduate Group and.,the Wistar Institute, Philadelphia, Pennsylvania 19104, and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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20
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Martín-García B, Martín-González A, Carrasco C, Hernández-Arriaga AM, Ruíz-Quero R, Díaz-Orejas R, Aicart-Ramos C, Moreno-Herrero F, Oliva MA. The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems. Nucleic Acids Res 2018; 46:5704-5716. [PMID: 29762781 PMCID: PMC6009700 DOI: 10.1093/nar/gky370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/27/2018] [Indexed: 11/26/2022] Open
Abstract
In prokaryotes, the centromere is a specialized segment of DNA that promotes the assembly of the segrosome upon binding of the Centromere Binding Protein (CBP). The segrosome structure exposes a specific surface for the interaction of the CBP with the motor protein that mediates DNA movement during cell division. Additionally, the CBP usually controls the transcriptional regulation of the segregation system as a cell cycle checkpoint. Correct segrosome functioning is therefore indispensable for accurate DNA segregation. Here, we combine biochemical reconstruction and structural and biophysical analysis to bring light to the architecture of the segrosome complex in Type III partition systems. We present the particular features of the centromere site, tubC, of the model system encoded in Clostridium botulinum prophage c-st. We find that the split centromere site contains two different iterons involved in the binding and spreading of the CBP, TubR. The resulting nucleoprotein complex consists of a novel double-ring structure that covers part of the predicted promoter. Single molecule data provides a mechanism for the formation of the segrosome structure based on DNA bending and unwinding upon TubR binding.
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Affiliation(s)
- Bárbara Martín-García
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | | | - Carolina Carrasco
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - Ana M Hernández-Arriaga
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Rubén Ruíz-Quero
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Ramón Díaz-Orejas
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - María A Oliva
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
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21
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Ruiz-Cruz S, Moreno-Blanco A, Espinosa M, Bravo A. DNA-binding properties of MafR, a global regulator of Enterococcus faecalis. FEBS Lett 2018. [PMID: 29537484 PMCID: PMC5947639 DOI: 10.1002/1873-3468.13032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Global transcriptional regulators play key roles during bacterial adaptation to environmental fluctuations. Protein MafR from Enterococcus faecalis was shown to activate the transcription of many genes on a genome-wide scale. We proposed that MafR is a global regulator of the Mga/AtxA family. Here, we purified an untagged form of the MafR protein and found that it binds to linear double-stranded DNAs in a nonsequence-specific manner. Moreover, multiple MafR units (likely dimers) bind sequentially to the DNA molecule generating multimeric complexes. On DNAs that contain the promoter of the mafR gene, MafR recognizes a potentially curved DNA region. We discuss that a characteristic of the Mga/AtxA regulators might be their ability to recognize particular DNA shapes across the bacterial genomes.
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Affiliation(s)
- Sofía Ruiz-Cruz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Moreno-Blanco
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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22
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Quirk S, Hopkins MM, Bureau H, Lusk RJ, Allen C, Hernandez R, Bain DL. Mutational Analysis of Neuropeptide Y Reveals Unusual Thermal Stability Linked to Higher-Order Self-Association. ACS OMEGA 2018; 3:2141-2154. [PMID: 29619413 PMCID: PMC5876621 DOI: 10.1021/acsomega.7b01949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
Neuropeptide Y (NPY) is a 36-residue peptide, abundant in the central and peripheral nervous system. The peptide interacts with membrane-bound receptors to control processes such as food intake, vasoconstriction, and memory retention. The N-terminal polyproline sequence of NPY folds back onto a C-terminal α-helix to form a hairpin structure. The hairpin undergoes transient unfolding to allow the monomer to interact with its target membranes and receptors and to form reversible dimers in solution. Using computational, functional, and biophysical approaches, we characterized the role of two conserved tyrosines (Y20 and Y27) located within the hydrophobic core of the hairpin fold. Successive mutation of the tyrosines to more hydrophobic phenylalanines increased the thermal stability of NPY and reduced functional activity, consistent with computational studies predicting a more stable hairpin structure. However, mutant stability was high relative to wild-type: melting temperatures increased by approximately 20 °C for the single mutants (Y20F and Y27F) and by 30 °C for the double mutant (Y20F + Y27F). These findings suggested that the mutations were not just simply enhancing hairpin structure stability, but might also be driving self-association to dimer. Using analytical ultracentrifugation, we determined that the mutations indeed increased self-association, but shifted the equilibrium toward hexamer-like species. Notably, these latter species were not unique to the NPY mutants, but were found to preexist at low levels in the wild-type population. Collectively, the findings indicate that NPY self-association is more complex than previously recognized and that the ensemble of NPY quaternary states is tunable by modulating hairpin hydrophobicity.
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Affiliation(s)
- Stephen Quirk
- Archeus
Bioscience, 7094 Peachtree
Industrial Blvd., Norcross, Georgia 30071, United
States
| | - Mandi M. Hopkins
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, 12850 E Montview Blvd., Aurora, Colorado 80045, United
States
| | - Hailey Bureau
- Center
for Computational and Molecular Science and Technology, School of
Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic
Dr, Atlanta, Georgia 30332, United States
| | - Ryan J. Lusk
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, 12850 E Montview Blvd., Aurora, Colorado 80045, United
States
| | - Caley Allen
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Rigoberto Hernandez
- Center
for Computational and Molecular Science and Technology, School of
Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic
Dr, Atlanta, Georgia 30332, United States
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - David L. Bain
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, 12850 E Montview Blvd., Aurora, Colorado 80045, United
States
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23
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2′-Deoxyribosyltransferase from Bacillus psychrosaccharolyticus: A Mesophilic-Like Biocatalyst for the Synthesis of Modified Nucleosides from a Psychrotolerant Bacterium. Catalysts 2018. [DOI: 10.3390/catal8010008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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24
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Bolós M, Pallas-Bazarra N, Terreros-Roncal J, Perea JR, Jurado-Arjona J, Ávila J, Llorens-Martín M. Soluble Tau has devastating effects on the structural plasticity of hippocampal granule neurons. Transl Psychiatry 2017; 7:1267. [PMID: 29217824 PMCID: PMC5802513 DOI: 10.1038/s41398-017-0013-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/03/2017] [Accepted: 07/30/2017] [Indexed: 12/26/2022] Open
Abstract
Tau is a neuronal microtubule-associated protein with countless physiological functions. Although the detrimental effects of insoluble aggregated Tau have been widely studied, recent evidence supports the notion that soluble Tau (composed mostly of monomers and dimers) is also toxic for neurons. Here we evaluated the long-term impact of a single stereotaxic injection of human soluble Tau on hippocampal granule neurons in mice. At the ultrastructural level, soluble Tau reduced the number of afferent synapses and caused a dramatic depletion of synaptic vesicles both in afferent and efferent synapses. Furthermore, the use of an RFP-expressing retrovirus revealed that soluble Tau altered the morphology of newborn granule neurons and reduced their afferent (dendritic spines) and efferent (mossy fiber terminals) connectivity. Finally, soluble Tau caused specific impairment of behavioral pattern separation capacity. Our results thus demonstrate for the first time that soluble Tau causes long-term detrimental effects on the morphology and connectivity of newborn granule neurons and that these effects correlate with impaired behavioral pattern separation skills. These data might be relevant for the field of neurodegenerative disorders, since they contribute to reinforcing the pathological roles played by distinct Tau species in vivo.
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Affiliation(s)
- M Bolós
- grid.465524.4Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, CBMSO, CSICUAM, Madrid, Spain ,0000 0004 1762 4012grid.418264.dNetwork Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - N Pallas-Bazarra
- grid.465524.4Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, CBMSO, CSICUAM, Madrid, Spain ,0000 0004 1762 4012grid.418264.dNetwork Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - J Terreros-Roncal
- grid.465524.4Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, CBMSO, CSICUAM, Madrid, Spain ,0000 0004 1762 4012grid.418264.dNetwork Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - JR Perea
- grid.465524.4Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, CBMSO, CSICUAM, Madrid, Spain ,0000 0004 1762 4012grid.418264.dNetwork Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - J Jurado-Arjona
- grid.465524.4Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, CBMSO, CSICUAM, Madrid, Spain ,0000 0004 1762 4012grid.418264.dNetwork Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - J Ávila
- grid.465524.4Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, CBMSO, CSICUAM, Madrid, Spain ,0000 0004 1762 4012grid.418264.dNetwork Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - M Llorens-Martín
- Department of Molecular Neuropathology, Centro de Biología Molecular "Severo Ochoa", CBMSO, CSICUAM, Madrid, Spain. .,Network Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain. .,Department of Molecular Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain.
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25
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Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc Natl Acad Sci U S A 2017; 114:E7939-E7948. [PMID: 28874570 DOI: 10.1073/pnas.1707063114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Loquacious-PD (Loqs-PD) is required for biogenesis of many endogenous siRNAs in Drosophila In vitro, Loqs-PD enhances the rate of dsRNA cleavage by Dicer-2 and also enables processing of substrates normally refractory to cleavage. Using purified components, and Loqs-PD truncations, we provide a mechanistic basis for Loqs-PD functions. Our studies indicate that the 22 amino acids at the C terminus of Loqs-PD, including an FDF-like motif, directly interact with the Hel2 subdomain of Dicer-2's helicase domain. This interaction is RNA-independent, but we find that modulation of Dicer-2 cleavage also requires dsRNA binding by Loqs-PD. Furthermore, while the first dsRNA-binding motif of Loqs-PD is dispensable for enhancing cleavage of optimal substrates, it is essential for enhancing cleavage of suboptimal substrates. Finally, our studies define a previously unrecognized Dicer interaction interface and suggest that Loqs-PD is well positioned to recruit substrates into the helicase domain of Dicer-2.
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26
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Monroe N, Han H, Shen PS, Sundquist WI, Hill CP. Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase. eLife 2017; 6. [PMID: 28379137 PMCID: PMC5413351 DOI: 10.7554/elife.24487] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/04/2017] [Indexed: 12/18/2022] Open
Abstract
Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP·BeFx, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating. The final Vps4 subunit completes a notched-washer configuration as if transitioning between the ends of the helix. We propose that ATP binding propagates growth at one end of the helix while hydrolysis promotes disassembly at the other end, so that Vps4 ‘walks’ along ESCRT-III until it encounters the ordered N-terminal domain to destabilize the ESCRT-III lattice. This model may be generally applicable to other protein-translocating AAA ATPases. DOI:http://dx.doi.org/10.7554/eLife.24487.001 Membranes surround multiple compartments within cells as well as the cell itself. In living cells, these membranes are remodeled continuously. This allows cells to divide, move molecules between different compartments and perform other essential activities. One important remodeling event is known as fission, which splits a membrane into separate parts. Large repeating structures (or polymers) of ESCRT-III proteins play a crucial role in membrane fission. Breaking apart ESCRT-III polymers triggers membrane fission and also recycles the ESCRT-III proteins so that they can be used again. An enzyme called Vps4 converts chemical energy (stored in the form of a molecule called ATP) into the mechanical force that breaks apart the ESCRT-III polymers. The active form of Vps4 consists of six Vps4 subunits working together to form a complex that includes a cofactor protein called Vta1. Monroe et al. have now used a technique called cryo-electron microscopy to determine the structure of an active yeast Vps4-Vta1 complex while it is bound to a segment of an ESCRT-III protein. This revealed that four of the six Vps4 subunits form a helix (which resembles a spiral staircase) that binds ESCRT-III in its central pore. The structure implies that binding of ATP causes the Vps4 helix to grow at one end and that converting ATP into a molecule called ADP (to release energy) causes disassembly at the other end. The two additional Vps4 subunits move from the disassembling end to the growing end of the helix. In this manner, Vps4 ‘walks’ along ESCRT-III, thereby pulling it through the pore at the center of the Vps4 complex and triggering breakdown of the ESCRT-III polymer. Further work is now needed to understand exactly how this activity leads to membrane fission. DOI:http://dx.doi.org/10.7554/eLife.24487.002
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Affiliation(s)
- Nicole Monroe
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Han Han
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Peter S Shen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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27
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Ramachandran G, Miguel-Arribas A, Abia D, Singh PK, Crespo I, Gago-Córdoba C, Hao JA, Luque-Ortega JR, Alfonso C, Wu LJ, Boer DR, Meijer WJJ. Discovery of a new family of relaxases in Firmicutes bacteria. PLoS Genet 2017; 13:e1006586. [PMID: 28207825 PMCID: PMC5313138 DOI: 10.1371/journal.pgen.1006586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research.
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Affiliation(s)
- Gayetri Ramachandran
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Praveen K. Singh
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Isidro Crespo
- XALOC beamline, ALBA synchrotron Light Source, Cerdanyola del Vallès, Barcelona, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Jian An Hao
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ling J. Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - D. Roeland Boer
- XALOC beamline, ALBA synchrotron Light Source, Cerdanyola del Vallès, Barcelona, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
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28
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Samanta D, Guo H, Rubinstein R, Ramagopal UA, Almo SC. Structural, mutational and biophysical studies reveal a canonical mode of molecular recognition between immune receptor TIGIT and nectin-2. Mol Immunol 2016; 81:151-159. [PMID: 27978489 DOI: 10.1016/j.molimm.2016.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 02/07/2023]
Abstract
In addition to antigen-specific stimulation of T cell receptor (TCR) by a peptide-MHC complex, the functional outcome of TCR engagement is regulated by antigen-independent costimulatory signals. Costimulatory signals are provided by an array of interactions involving activating and inhibitory receptors expressed on T cells and their cognate ligands on antigen presenting cells. T cell immunoglobulin and ITIM domain (TIGIT), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or poliovirus receptor (PVR), inhibits activation of T and NK cells. Here we report the crystal structure of the human TIGIT ectodomain, which exhibits the classic two-layer β-sandwich topology observed in other immunoglobulin super family (IgSF) members. Biophysical studies indicate that TIGIT is monomeric in solution but can form a dimer at high concentrations, consistent with the observation of a canonical immunoglobulin-like dimer interface in the crystalline state. Based on existing structural data, we present a model of the TIGIT:nectin-2 complex and utilized complementary biochemical studies to map the nectin-binding interface on TIGIT. Our data provide important structural and biochemical determinants responsible for the recognition of nectin-2 by TIGIT. Defining the TIGIT:nectin-2 binding interface provides the basis for rational manipulation of this molecular interaction for the development of immunotherapeutic reagents in autoimmunity and cancer.
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Affiliation(s)
- Dibyendu Samanta
- Department of Biochemistry, Albert Einstein College of Medicine, New York, USA
| | - Haisu Guo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, USA
| | - Rotem Rubinstein
- Department of Biochemistry, Albert Einstein College of Medicine, New York, USA
| | - Udupi A Ramagopal
- Department of Biochemistry, Albert Einstein College of Medicine, New York, USA; Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, India.
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, New York, USA.
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29
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Oroz J, Barrera-Vilarmau S, Alfonso C, Rivas G, de Alba E. ASC Pyrin Domain Self-associates and Binds NLRP3 Protein Using Equivalent Binding Interfaces. J Biol Chem 2016; 291:19487-501. [PMID: 27432880 PMCID: PMC5016686 DOI: 10.1074/jbc.m116.741082] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/08/2016] [Indexed: 11/06/2022] Open
Abstract
Death domain superfamily members typically act as adaptors mediating in the assembly of supramolecular complexes with critical apoptosis and inflammation functions. These modular proteins consist of death domains, death effector domains, caspase recruitment domains, and pyrin domains (PYD). Despite the high structural similarity among them, only homotypic interactions participate in complex formation, suggesting that subtle factors differentiate each interaction type. It is thus critical to identify these factors as an essential step toward the understanding of the molecular basis of apoptosis and inflammation. The proteins apoptosis-associated speck-like protein containing a CARD (ASC) and NLRP3 play key roles in the regulation of apoptosis and inflammation through self-association and protein-protein interactions mediated by their PYDs. To better understand the molecular basis of their function, we have characterized ASC and NLRP3 PYD self-association and their intermolecular interaction by solution NMR spectroscopy and analytical ultracentrifugation. We found that ASC self-associates and binds NLRP3 PYD through equivalent protein regions, with higher binding affinity for the latter. These regions are located at opposite sides of the protein allowing multimeric complex formation previously shown in ASC PYD fibril assemblies. We show that NLRP3 PYD coexists in solution as a monomer and highly populated large-order oligomerized species. Despite this, we determined its monomeric three-dimensional solution structure by NMR and characterized its binding to ASC PYD. Using our novel structural data, we propose molecular models of ASC·ASC and ASC·NLRP3 PYD early supramolecular complexes, providing new insights into the molecular mechanisms of inflammasome and apoptosis signaling.
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Affiliation(s)
- Javier Oroz
- From the Centro de Investigaciones Biológicas, Departments of Chemical and Physical Biology and the German Center for Neurodegenerative Diseases (DZNE), ℅Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen-37077, Germany, and
| | - Susana Barrera-Vilarmau
- From the Centro de Investigaciones Biológicas, Departments of Chemical and Physical Biology and
| | | | | | - Eva de Alba
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9 Madrid-28040, Spain, the Health Sciences Research Institute, University of California at Merced, Merced, California 95343
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30
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Mohedano ML, Amblar M, de la Fuente A, Wells JM, López P. The Response Regulator YycF Inhibits Expression of the Fatty Acid Biosynthesis Repressor FabT in Streptococcus pneumoniae. Front Microbiol 2016; 7:1326. [PMID: 27610104 PMCID: PMC4996995 DOI: 10.3389/fmicb.2016.01326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/11/2016] [Indexed: 11/25/2022] Open
Abstract
The YycFG (also known as WalRK, VicRK, MicAB, or TCS02) two-component system (TCS) is highly conserved among Gram-positive bacteria with a low G+C content. In Streptococcus pneumoniae the YycF response regulator has been reported to be essential due to its control of pcsB gene expression. Previously we showed that overexpression of yycF in S. pneumoniae TIGR4 altered the transcription of genes involved in cell wall metabolism and fatty acid biosynthesis, giving rise to anomalous cell division and increased chain length of membrane fatty acids. Here, we have overexpressed the yycFG system in TIGR4 wild-type strain and yycF in a TIGR4 mutant depleted of YycG, and analyzed their effects on expression of proteins involved in fatty acid biosynthesis during activation of the TCS. We demonstrate that transcription of the fab genes and levels of their products were only altered in the YycF overexpressing strain, indicating that the unphosphorylated form of YycF is involved in the regulation of fatty acid biosynthesis. In addition, DNA-binding assays and in vitro transcription experiments with purified YycF and the promoter region of the FabTH-acp operon support a direct inhibition of transcription of the FabT repressor by YycF, thus confirming the role of the unphosphorylated form in transcriptional regulation.
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Affiliation(s)
- Maria L Mohedano
- Laboratorio de Biología Molecular de Bacterias Gram positivas, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Mónica Amblar
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Majadahonda, Spain
| | - Alicia de la Fuente
- Laboratorio de Biología Molecular de Bacterias Gram positivas, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Jerry M Wells
- Host-Microbe Interactomics, Animal Sciences Department, University of Wageningen Wageningen, Netherlands
| | - Paloma López
- Laboratorio de Biología Molecular de Bacterias Gram positivas, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
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31
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Neti SS, Eckert DM, Poulter CD. Construction of Functional Monomeric Type 2 Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase. Biochemistry 2016; 55:4229-38. [PMID: 27379573 DOI: 10.1021/acs.biochem.6b00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the isoprenoid biosynthetic pathway. The enzyme from Streptomyces pneumoniae (spIDI-2) is a homotetramer in solution with behavior, including a substantial increase in the rate of FMN reduction by NADPH in the presence of IPP, suggesting that substrate binding at one subunit alters the kinetic and binding properties of another. We now report the construction of catalytically active monomeric spIDI-2. The monomeric enzyme contains a single-point mutation (N37A) and a six-residue C-terminal deletion that preserves the secondary structure of the subunits in the wild-type (wt) homotetramer. UV-vis spectra of the enzyme-bound flavin mononucleotide (FMN) cofactor in FMNox, FMNred, and FMNred·IPP/DMAPP states are the same for monomeric and wt homotetrameric spIDI-2. The mutations in monomeric IDI-2 lower the melting temperature of the protein by 20 °C and reduce the binding affinities of FMN and IDI by 40-fold but have a minimal effect on kcat. Stopped-flow kinetic studies of monomeric spIDI-2 showed that the rate of reduction of FMN by NADH (k = 1.64 × 10(-3) s(-1)) is substantially faster when IPP is added to the monomeric enzyme (k = 0.57 s(-1)), similar to behavior seen for wt-spIDI-2. Our results indicate that cooperative interactions among subunits in the wt homotetramer are not responsible for the increased rate of reduction of spIDI-2·FMN by NADH, and two possible scenarios for the enhancement are suggested.
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Affiliation(s)
- Syam Sundar Neti
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Debra M Eckert
- Department of Biochemistry, University of Utah School of Medicine , Salt Lake City, Utah 84112, United States
| | - C Dale Poulter
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
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32
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Wagner JM, Roganowicz MD, Skorupka K, Alam SL, Christensen D, Doss G, Wan Y, Frank GA, Ganser-Pornillos BK, Sundquist WI, Pornillos O. Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α. eLife 2016; 5. [PMID: 27253059 PMCID: PMC4936894 DOI: 10.7554/elife.16309] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/20/2016] [Indexed: 11/13/2022] Open
Abstract
Restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. Mammalian TRIM5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. Here, we report crystallographic and functional studies of the TRIM5α B-box 2 domain, which mediates higher-order assembly of TRIM5 proteins. The B-box can form both dimers and trimers, and the trimers can link multiple TRIM5α proteins into a hexagonal net that matches the lattice arrangement of capsid subunits and enables avid capsid binding. Two modes of conformational flexibility allow TRIM5α to accommodate the variable curvature of retroviral capsids. B-box mediated interactions also modulate TRIM5α's E3 ubiquitin ligase activity, by stereochemically restricting how the N-terminal RING domain can dimerize. Overall, these studies define important molecular details of cellular recognition of retroviruses, and how recognition links to downstream processes to disable the virus.
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Affiliation(s)
- Jonathan M Wagner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Marcin D Roganowicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Katarzyna Skorupka
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Steven L Alam
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Devin Christensen
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Ginna Doss
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Yueping Wan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Gabriel A Frank
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheeva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheeva, Israel
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
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33
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Spínola-Amilibia M, Davó-Siguero I, Ruiz FM, Santillana E, Medrano FJ, Romero A. The structure of VgrG1 fromPseudomonas aeruginosa, the needle tip of the bacterial type VI secretion system. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:22-33. [DOI: 10.1107/s2059798315021142] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/06/2015] [Indexed: 11/10/2022]
Abstract
The type VI secretion system (T6SS) is a mechanism that is commonly used by pathogenic bacteria to infect host cells and for survival in competitive environments. This system assembles on a core baseplate and elongates like a phage puncturing device; it is thought to penetrate the target membrane and deliver effectors into the host or competing bacteria. Valine–glycine repeat protein G1 (VgrG1) forms the spike at the tip of the elongating tube formed by haemolysin co-regulated protein 1 (Hcp1); it is structurally similar to the T4 phage (gp27)3–(gp5)3puncturing complex. Here, the crystal structure of full-length VgrG1 fromPseudomonas aeruginosais reported at a resolution of 2.0 Å, which through a trimeric arrangement generates a needle-like shape composed of two main parts, the head and the spike, connectedviaa small neck region. The structure reveals several remarkable structural features pointing to the possible roles of the two main segments of VgrG1: the head as a scaffold cargo domain and the β-roll spike with implications in the cell-membrane puncturing process and as a carrier of cognate toxins.
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34
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Gonzalez-Perez D, Mateljak I, Garcia-Ruiz E, Ruiz-Dueñas FJ, Martinez AT, Alcalde M. Alkaline versatile peroxidase by directed evolution. Catal Sci Technol 2016. [DOI: 10.1039/c6cy01044j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A ligninolytic versatile peroxidase was engineered by directed evolution to be active and stable at alkaline pH.
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Affiliation(s)
| | - Ivan Mateljak
- Department of Biocatalysis
- Institute of Catalysis
- 28049 Madrid
- Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | | | | | - Miguel Alcalde
- Department of Biocatalysis
- Institute of Catalysis
- 28049 Madrid
- Spain
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35
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Husain B, Mayo C, Cole JL. Role of the Interdomain Linker in RNA-Activated Protein Kinase Activation. Biochemistry 2015; 55:253-61. [PMID: 26678943 DOI: 10.1021/acs.biochem.5b01171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA-activated protein kinase (PKR) is a key component of the interferon-induced antiviral pathway in higher eukaryotes. Upon recognition of viral dsRNA, PKR is activated via dimerization and autophosphorylation. PKR contains two N-terminal dsRNA binding domains (dsRBD) and a C-terminal kinase domain. The dsRBDs and the kinase are separated by a long, unstructured ∼80-amino acid linker in the human enzyme. The length of the N-terminal portion of the linker varies among PKR sequences, and it is completely absent in one ortholog. Here, we characterize the effects of deleting the variable region from the human enzyme to produce PKRΔV. The linker deletion results in quantitative but not qualitative changes in catalytic activity, RNA binding, and conformation. PKRΔV is somewhat more active and exhibits more cooperative RNA binding. As we previously observed for the full-length enzyme, PKRΔV is flexible in solution and adopts a range of compact and extended conformations. The conformational ensemble is biased toward compact states that might be related to weak interactions between the dsRBD and kinase domains. PKR retains RNA-induced autophosphorylation upon complete removal of the linker, indicating that the C-terminal, basic region is also not required for activity.
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Affiliation(s)
- Bushra Husain
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Christopher Mayo
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - James L Cole
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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36
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McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A. Structure and membrane remodeling activity of ESCRT-III helical polymers. Science 2015; 350:1548-51. [PMID: 26634441 PMCID: PMC4684769 DOI: 10.1126/science.aad8305] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 01/24/2023]
Abstract
The endosomal sorting complexes required for transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal intralumenal vesicle formation, HIV budding, nuclear envelope closure, and cytokinetic abscission. ESCRT-III subunits perform key roles in these processes by changing conformation and polymerizing into membrane-remodeling filaments. Here, we report the 4 angstrom resolution cryogenic electron microscopy reconstruction of a one-start, double-stranded helical copolymer composed of two different human ESCRT-III subunits, charged multivesicular body protein 1B (CHMP1B) and increased sodium tolerance 1 (IST1). The inner strand comprises "open" CHMP1B subunits that interlock in an elaborate domain-swapped architecture and is encircled by an outer strand of "closed" IST1 subunits. Unlike other ESCRT-III proteins, CHMP1B and IST1 polymers form external coats on positively curved membranes in vitro and in vivo. Our analysis suggests how common ESCRT-III filament architectures could stabilize different degrees and directions of membrane curvature.
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Affiliation(s)
- John McCullough
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Amy K Clippinger
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathaniel Talledge
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA. Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael L Skowyra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marissa G Saunders
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Teresa V Naismith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leremy A Colf
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Pavel Afonine
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Wesley I Sundquist
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.
| | - Phyllis I Hanson
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Adam Frost
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA. Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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37
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LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem 2015; 290:30390-405. [PMID: 26475863 DOI: 10.1074/jbc.m115.689604] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/06/2022] Open
Abstract
Phosphoinositide 3-kinases (PI3Ks) are a family of lipid kinases that are activated by growth factor and G-protein-coupled receptors and propagate intracellular signals for growth, survival, proliferation, and metabolism. p85α, a modular protein consisting of five domains, binds and inhibits the enzymatic activity of class IA PI3K catalytic subunits. Here, we describe the structural states of the p85α dimer, based on data from in vivo and in vitro solution characterization. Our in vitro assembly and structural analyses have been enabled by the creation of cysteine-free p85α that is functionally equivalent to native p85α. Analytical ultracentrifugation studies showed that p85α undergoes rapidly reversible monomer-dimer assembly that is highly exothermic in nature. In addition to the documented SH3-PR1 dimerization interaction, we identified a second intermolecular interaction mediated by cSH2 domains at the C-terminal end of the polypeptide. We have demonstrated in vivo concentration-dependent dimerization of p85α using fluorescence fluctuation spectroscopy. Finally, we have defined solution conditions under which the protein is predominantly monomeric or dimeric, providing the basis for small angle x-ray scattering and chemical cross-linking structural analysis of the discrete dimer. These experimental data have been used for the integrative structure determination of the p85α dimer. Our study provides new insight into the structure and assembly of the p85α homodimer and suggests that this protein is a highly dynamic molecule whose conformational flexibility allows it to transiently associate with multiple binding proteins.
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Affiliation(s)
| | - Seung Joong Kim
- the Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, and
| | - Yi Shi
- the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Haiyan Wu
- From the Department of Molecular Pharmacology
| | - Brian T Chait
- the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Andrej Sali
- the Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, and
| | | | | | - Jonathan M Backer
- From the Department of Molecular Pharmacology, Department of Biochemistry,
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38
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Different inhibition of Gβγ-stimulated class IB phosphoinositide 3-kinase (PI3K) variants by a monoclonal antibody. Specific function of p101 as a Gβγ-dependent regulator of PI3Kγ enzymatic activity. Biochem J 2015; 469:59-69. [PMID: 26173259 DOI: 10.1042/bj20150099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Class IB phosphoinositide 3-kinases γ (PI3Kγ) are second-messenger-generating enzymes downstream of signalling cascades triggered by G-protein-coupled receptors (GPCRs). PI3Kγ variants have one catalytic p110γ subunit that can form two different heterodimers by binding to one of a pair of non-catalytic subunits, p87 or p101. Growing experimental data argue for a different regulation of p87-p110γ and p101-p110γ allowing integration into distinct signalling pathways. Pharmacological tools enabling distinct modulation of the two variants are missing. The ability of an anti-p110γ monoclonal antibody [mAb(A)p110γ] to block PI3Kγ enzymatic activity attracted us to characterize this tool in detail using purified proteins. In order to get insight into the antibody-p110γ interface, hydrogen-deuterium exchange coupled to MS (HDX-MS) measurements were performed demonstrating binding of the monoclonal antibody to the C2 domain in p110γ, which was accompanied by conformational changes in the helical domain harbouring the Gβγ-binding site. We then studied the modulation of phospholipid vesicles association of PI3Kγ by the antibody. p87-p110γ showed a significantly reduced Gβγ-mediated phospholipid recruitment as compared with p101-p110γ. Concomitantly, in the presence of mAb(A)p110γ, Gβγ did not bind to p87-p110γ. These data correlated with the ability of the antibody to block Gβγ-stimulated lipid kinase activity of p87-p110γ 30-fold more potently than p101-p110γ. Our data argue for differential regulatory functions of the non-catalytic subunits and a specific Gβγ-dependent regulation of p101 in PI3Kγ activation. In this scenario, we consider the antibody as a valuable tool to dissect the distinct roles of the two PI3Kγ variants downstream of GPCRs.
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39
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Lin J, Lucius AL. Examination of the dynamic assembly equilibrium for E. coli ClpB. Proteins 2015; 83:2008-24. [PMID: 26313457 DOI: 10.1002/prot.24914] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/03/2015] [Accepted: 08/18/2015] [Indexed: 12/17/2022]
Abstract
Escherichia coli ClpB is a heat shock protein that belongs to the AAA+ protein superfamily. Studies have shown that ClpB and its homologue in yeast, Hsp104, can disrupt protein aggregates in vivo. It is thought that ClpB requires binding of nucleoside triphosphate to assemble into hexameric rings with protein binding activity. In addition, it is widely assumed that ClpB is uniformly hexameric in the presence of nucleotides. Here we report, in the absence of nucleotide, that increasing ClpB concentration leads to ClpB hexamer formation, decreasing NaCl concentration stabilizes ClpB hexamers, and the ClpB assembly reaction is best described by a monomer, dimer, tetramer, hexamer equilibrium under the three salt concentrations examined. Further, we found that ClpB oligomers exhibit relatively fast dissociation on the time scale of sedimentation. We anticipate our studies on ClpB assembly to be a starting point to understand how ClpB assembly is linked to the binding and disaggregation of denatured proteins.
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Affiliation(s)
- JiaBei Lin
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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40
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Salvarelli E, Krupka M, Rivas G, Mingorance J, Gómez-Puertas P, Alfonso C, Rico AI. The Cell Division Protein FtsZ from Streptococcus pneumoniae Exhibits a GTPase Activity Delay. J Biol Chem 2015; 290:25081-9. [PMID: 26330552 DOI: 10.1074/jbc.m115.650077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 11/06/2022] Open
Abstract
The cell division protein FtsZ assembles in vitro by a mechanism of cooperative association dependent on GTP, monovalent cations, and Mg(2+). We have analyzed the GTPase activity and assembly dynamics of Streptococcus pneumoniae FtsZ (SpnFtsZ). SpnFtsZ assembled in an apparently cooperative process, with a higher critical concentration than values reported for other FtsZ proteins. It sedimented in the presence of GTP as a high molecular mass polymer with a well defined size and tended to form double-stranded filaments in electron microscope preparations. GTPase activity depended on K(+) and Mg(2+) and was inhibited by Na(+). GTP hydrolysis exhibited a delay that included a lag phase followed by a GTP hydrolysis activation step, until reaction reached the GTPase rate. The lag phase was not found in polymer assembly, suggesting a transition from an initial non-GTP-hydrolyzing polymer that switches to a GTP-hydrolyzing polymer, supporting models that explain FtsZ polymer cooperativity.
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Affiliation(s)
- Estefanía Salvarelli
- From the Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid, Spain, Biomol-Informatics S.L., Universidad Autónoma, 28049 Madrid, Spain,
| | | | - Germán Rivas
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Jesus Mingorance
- From the Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid, Spain
| | - Paulino Gómez-Puertas
- Biomol-Informatics S.L., Universidad Autónoma, 28049 Madrid, Spain, the Molecular Modelling Group, Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain, and
| | - Carlos Alfonso
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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41
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Abstract
The ATPases associated with diverse cellular activities (AAA+) is a large superfamily of proteins involved in a broad array of biological processes. Many members of this family require nucleotide binding to assemble into their final active hexameric form. We have been studying two example members, Escherichia coli ClpA and ClpB. These two enzymes are active as hexameric rings that both require nucleotide binding for assembly. Our studies have shown that they both reside in a monomer, dimer, tetramer, and hexamer equilibrium, and this equilibrium is thermodynamically linked to nucleotide binding. Moreover, we are finding that the kinetics of the assembly reaction are very different for the two enzymes. Here, we present our strategy for determining the self-association constants in the absence of nucleotide to set the stage for the analysis of nucleotide binding from other experimental approaches including analytical ultracentrifugation.
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Affiliation(s)
- JiaBei Lin
- Department of Chemistry, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Aaron L Lucius
- Department of Chemistry, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
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42
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Pearson JZ, Krause F, Haffke D, Demeler B, Schilling K, Cölfen H. Next-Generation AUC Adds a Spectral Dimension: Development of Multiwavelength Detectors for the Analytical Ultracentrifuge. Methods Enzymol 2015; 562:1-26. [PMID: 26412645 DOI: 10.1016/bs.mie.2015.06.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe important advances in analytical ultracentrifugation (AUC) hardware, which add new information to the hydrodynamic information observed in traditional AUC instruments. In contrast to the Beckman-Coulter XLA UV/visible detector, multiwavelength (MWL) detection is able to collect sedimentation data not just for one wavelength, but for a large wavelength range in a single experiment. The additional dimension increases the data density by orders of magnitude, significantly improving the statistics of the measurement and adding important information to the experiment since an additional dimension of spectral characterization is now available to complement the hydrodynamic information. The new detector avoids tedious repeats of experiments at different wavelengths and opens up new avenues for the solution-based investigation of complex mixtures. In this chapter, we describe the capabilities, characteristics, and applications of the new detector design with biopolymers as the focus of study. We show data from two different MWL detectors and discuss strengths and weaknesses of differences in the hardware and different data acquisition modes. Also, difficulties with fiber optic applications in the UV are discussed. Data quality is compared across platforms.
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Affiliation(s)
- Joseph Z Pearson
- Physical Chemistry, Department of Chemistry, University of Konstanz, Konstanz, Germany
| | | | - Dirk Haffke
- Physical Chemistry, Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | - Helmut Cölfen
- Physical Chemistry, Department of Chemistry, University of Konstanz, Konstanz, Germany.
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43
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Hernández-Rocamora VM, Alfonso C, Margolin W, Zorrilla S, Rivas G. Evidence That Bacteriophage λ Kil Peptide Inhibits Bacterial Cell Division by Disrupting FtsZ Protofilaments and Sequestering Protein Subunits. J Biol Chem 2015; 290:20325-35. [PMID: 26124275 DOI: 10.1074/jbc.m115.653329] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/06/2022] Open
Abstract
The effects of Kil peptide from bacteriophage λ on the assembly of Escherichia coli FtsZ into one subunit thick protofilaments were studied using combined biophysical and biochemical methods. Kil peptide has recently been identified as the factor from bacteriophage λ responsible for the inhibition of bacterial cell division during lytic cycle, targeting FtsZ polymerization. Here, we show that this antagonist blocks FtsZ assembly into GTP-dependent protofilaments, producing a wide distribution of smaller oligomers compared with the average size of the intact protofilaments. The shortening of FtsZ protofilaments by Kil is detectable at concentrations of the peptide in the low micromolar range, the mid-point of the inhibition being close to its apparent affinity for GDP-bound FtsZ. This antagonist not only interferes with FtsZ assembly but also reverses the polymerization reaction. The negative regulation by Kil significantly reduces the GTPase activity of FtsZ protofilaments, and FtsZ polymers assembled in guanosine-5'-[(α,β)-methyleno]triphosphate are considerably less sensitive to Kil. Our results suggest that, at high concentrations, Kil may use an inhibition mechanism involving the sequestration of FtsZ subunits, similar to that described for other inhibitors like the SOS response protein SulA or the moonlighting enzyme OpgH. This mechanism is different from those employed by the division site selection antagonists MinC and SlmA. This work provides new insight into the inhibition of FtsZ assembly by phages, considered potential tools against bacterial infection.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
| | - Carlos Alfonso
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
| | - William Margolin
- the Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas 77030
| | - Silvia Zorrilla
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
| | - Germán Rivas
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
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44
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Brautigam CA. Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data. Methods Enzymol 2015; 562:109-33. [PMID: 26412649 DOI: 10.1016/bs.mie.2015.05.001] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The analysis of analytical ultracentrifugation (AUC) data has been greatly facilitated by the advances accumulated in recent years. These improvements include refinements in AUC-based binding isotherms, advances in the fitting of both sedimentation velocity (SV) and sedimentation equilibrium (SE) data, and innovations in calculations related to posttranslationally modified proteins and to proteins with a large amount of associated cosolute, e.g., detergents. To capitalize on these advances, the experimenter often must prepare and collate multiple data sets and parameters for subsequent analyses; these tasks can be cumbersome and unclear, especially for new users. Examples are the sorting of concentration-profile scans for SE data, the integration of sedimentation velocity distributions (c(s)) to arrive at weighted-average binding isotherms, and the calculations to determine the oligomeric state of glycoproteins and membrane proteins. The significant organizational and logistical hurdles presented by these approaches are streamlined by the software described herein, called GUSSI. GUSSI also creates publication-quality graphics for documenting and illustrating AUC and other biophysical experiments with minimal effort on the user's part. The program contains three main modules, allowing for plotting and calculations on c(s) distributions, SV signal versus radius data, and general data/fit/residual plots.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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45
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Alfonso C, del Castillo U, Martín I, Muga A, Rivas G. Sedimentation Equilibrium Analysis of ClpB Self-Association in Diluted and Crowded Solutions. Methods Enzymol 2015; 562:135-60. [PMID: 26412650 DOI: 10.1016/bs.mie.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ClpB belongs to the Hsp100 family of ring-forming heat-shock proteins involved in degradation of unfolded/misfolded proteins and in reactivation of protein aggregates. ClpB monomers reversibly associate to form the hexameric molecular chaperone that, together with the DnaK system, has the ability to disaggregate stress-denatured proteins. Here, we summarize the use of sedimentation equilibrium approaches, complemented with sedimentation velocity and composition-gradient static light scattering measurements, to study the self-association properties of ClpB in dilute and crowded solutions. As the functional unit of ClpB is the hexamer, we study the effect of environmental factors, i.e., ionic strength and natural ligands, in the association equilibrium of ClpB as well as the role of the flexible N-terminal and M domains of the protein in the self-association process. The application of the nonideal sedimentation equilibrium technique to measure the effects of volume exclusion, reproducing in part the natural crowded conditions inside a cell, on the self-association and on the stability of the oligomeric species of the disaggregase will be described. Finally, the biochemical and physiological implications of these studies and future experimental challenges to eventually reconstitute minimal disaggregating machineries will be discussed.
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Affiliation(s)
- Carlos Alfonso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Urko del Castillo
- Unidad de Biofísica (CSIC/UPV-EHU), Departamento de Bioquímica y Biología Molecular, Universidad de País Vasco-Euskal Herriko Unibertsitatea (UPV-EHU), Bilbao, Biscay, Spain
| | - Ianire Martín
- Unidad de Biofísica (CSIC/UPV-EHU), Departamento de Bioquímica y Biología Molecular, Universidad de País Vasco-Euskal Herriko Unibertsitatea (UPV-EHU), Bilbao, Biscay, Spain
| | - Arturo Muga
- Unidad de Biofísica (CSIC/UPV-EHU), Departamento de Bioquímica y Biología Molecular, Universidad de País Vasco-Euskal Herriko Unibertsitatea (UPV-EHU), Bilbao, Biscay, Spain.
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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46
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The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PLoS One 2015; 10:e0118606. [PMID: 25897750 PMCID: PMC4405576 DOI: 10.1371/journal.pone.0118606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/21/2015] [Indexed: 11/19/2022] Open
Abstract
Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct(6)A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct(6)A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct(6)A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct(6)A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct(6)A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.
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47
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Clinton TR, Weinstock MT, Jacobsen MT, Szabo-Fresnais N, Pandya MJ, Whitby FG, Herbert AS, Prugar LI, McKinnon R, Hill CP, Welch BD, Dye JM, Eckert DM, Kay MS. Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets. Protein Sci 2015; 24:446-63. [PMID: 25287718 PMCID: PMC4380977 DOI: 10.1002/pro.2578] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/01/2014] [Indexed: 01/07/2023]
Abstract
Ebolaviruses are highly lethal filoviruses that cause hemorrhagic fever in humans and nonhuman primates. With no approved treatments or preventatives, the development of an anti-ebolavirus therapy to protect against natural infections and potential weaponization is an urgent global health need. Here, we describe the design, biophysical characterization, and validation of peptide mimics of the ebolavirus N-trimer, a highly conserved region of the GP2 fusion protein, to be used as targets to develop broad-spectrum inhibitors of ebolavirus entry. The N-trimer region of GP2 is 90% identical across all ebolavirus species and forms a critical part of the prehairpin intermediate that is exposed during viral entry. Specifically, we fused designed coiled coils to the N-trimer to present it as a soluble trimeric coiled coil as it appears during membrane fusion. Circular dichroism, sedimentation equilibrium, and X-ray crystallography analyses reveal the helical, trimeric structure of the designed N-trimer mimic targets. Surface plasmon resonance studies validate that the N-trimer mimic binds its native ligand, the C-peptide region of GP2. The longest N-trimer mimic also inhibits virus entry, thereby confirming binding of the C-peptide region during viral entry and the presence of a vulnerable prehairpin intermediate. Using phage display as a model system, we validate the suitability of the N-trimer mimics as drug screening targets. Finally, we describe the foundational work to use the N-trimer mimics as targets in mirror-image phage display, which will be used to identify D-peptide inhibitors of ebolavirus entry.
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Affiliation(s)
- Tracy R Clinton
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650
| | - Matthew T Weinstock
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650
| | - Michael T Jacobsen
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650
| | - Nicolas Szabo-Fresnais
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650,Cardiology Section, Department of Internal Medicine, University of Utah School of MedicineSalt Lake City, Utah, 84148
| | - Maya J Pandya
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort DetrickFrederick, Maryland, 21702-5011
| | - Laura I Prugar
- U.S. Army Medical Research Institute of Infectious Diseases, Fort DetrickFrederick, Maryland, 21702-5011
| | - Rena McKinnon
- D-Peptide Research Division, Navigen, Inc.Salt Lake City, Utah, 84108
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650
| | - Brett D Welch
- D-Peptide Research Division, Navigen, Inc.Salt Lake City, Utah, 84108
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Fort DetrickFrederick, Maryland, 21702-5011
| | - Debra M Eckert
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650,*Correspondence to: Debra M. Eckert; Department of Biochemistry, University of Utah School of Medicine, 15 N. Medical Drive East, Rm 4100, Salt Lake City, UT 84112. E-mail: or Michael S. Kay; Department of Biochemistry, University of Utah School of Medicine, 15 N. Medical Drive East, Rm 4100, Salt Lake City, UT 84112. E-mail:
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of MedicineSalt Lake City, Utah, 84112-5650,*Correspondence to: Debra M. Eckert; Department of Biochemistry, University of Utah School of Medicine, 15 N. Medical Drive East, Rm 4100, Salt Lake City, UT 84112. E-mail: or Michael S. Kay; Department of Biochemistry, University of Utah School of Medicine, 15 N. Medical Drive East, Rm 4100, Salt Lake City, UT 84112. E-mail:
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48
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Vander Linden RT, Hemmis CW, Schmitt B, Ndoja A, Whitby FG, Robinson H, Cohen RE, Yao T, Hill CP. Structural basis for the activation and inhibition of the UCH37 deubiquitylase. Mol Cell 2015; 57:901-911. [PMID: 25702872 DOI: 10.1016/j.molcel.2015.01.016] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
Abstract
The UCH37 deubiquitylase functions in two large and very different complexes, the 26S proteasome and the INO80 chromatin remodeler. We have performed biochemical characterization and determined crystal structures of UCH37 in complexes with RPN13 and NFRKB, which mediate its recruitment to the proteasome and INO80, respectively. RPN13 and NFRKB make similar contacts to the UCH37 C-terminal domain but quite different contacts to the catalytic UCH domain. RPN13 can activate UCH37 by disrupting dimerization, although physiologically relevant activation likely results from stabilization of a surface competent for ubiquitin binding and modulation of the active-site crossover loop. In contrast, NFRKB inhibits UCH37 by blocking the ubiquitin-binding site and by disrupting the enzyme active site. These findings reveal remarkable commonality in mechanisms of recruitment, yet very different mechanisms of regulating enzyme activity, and provide a foundation for understanding the roles of UCH37 in the unrelated proteasome and INO80 complexes.
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Affiliation(s)
- Ryan T Vander Linden
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Casey W Hemmis
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Benjamin Schmitt
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Ada Ndoja
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Frank G Whitby
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Howard Robinson
- Biology Department Brookhaven National Laboratory, Upton, NY, 11973 USA
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Christopher P Hill
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
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49
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Martín I, Celaya G, Alfonso C, Moro F, Rivas G, Muga A. Crowding activates ClpB and enhances its association with DnaK for efficient protein aggregate reactivation. Biophys J 2014; 106:2017-27. [PMID: 24806934 DOI: 10.1016/j.bpj.2014.03.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/24/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022] Open
Abstract
Reactivation of intracellular protein aggregates after a severe stress is mandatory for cell survival. In bacteria, this activity depends on the collaboration between the DnaK system and ClpB, which in vivo occurs in a highly crowded environment. The reactivation reaction includes two steps: extraction of unfolded monomers from the aggregate and their subsequent refolding into the native conformation. Both steps might be compromised by excluded volume conditions that would favor aggregation of unstable protein folding intermediates. Here, we have investigated whether ClpB and the DnaK system are able to compensate this unproductive effect and efficiently reactivate aggregates of three different substrate proteins under crowding conditions. To this aim, we have compared the association equilibrium, biochemical properties, stability, and chaperone activity of the disaggregase ClpB in the absence and presence of an inert macromolecular crowding agent. Our data show that crowding i), increases three to four orders of magnitude the association constant of the functional hexamer; ii), shifts the conformational equilibrium of the protein monomer toward a compact state; iii), stimulates its ATPase activity; and iv), favors association of the chaperone with substrate proteins and with aggregate-bound DnaK. These effects strongly enhance protein aggregate reactivation by the DnaK-ClpB network, highlighting the importance of volume exclusion in complex processes in which several proteins have to work in a sequential manner.
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Affiliation(s)
- Ianire Martín
- Unidad de Biofísica (Consejo Superior de Investigaciones Científicas/Universidad del País Vasco-Euskal Herriko Unibertsitatea) and Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Apartado 644, Bilbao 48080, Spain
| | - Garbiñe Celaya
- Unidad de Biofísica (Consejo Superior de Investigaciones Científicas/Universidad del País Vasco-Euskal Herriko Unibertsitatea) and Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Apartado 644, Bilbao 48080, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Fernando Moro
- Unidad de Biofísica (Consejo Superior de Investigaciones Científicas/Universidad del País Vasco-Euskal Herriko Unibertsitatea) and Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Apartado 644, Bilbao 48080, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Arturo Muga
- Unidad de Biofísica (Consejo Superior de Investigaciones Científicas/Universidad del País Vasco-Euskal Herriko Unibertsitatea) and Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Apartado 644, Bilbao 48080, Spain.
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50
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Ramachandran G, Singh PK, Luque-Ortega JR, Yuste L, Alfonso C, Rojo F, Wu LJ, Meijer WJJ. A complex genetic switch involving overlapping divergent promoters and DNA looping regulates expression of conjugation genes of a gram-positive plasmid. PLoS Genet 2014; 10:e1004733. [PMID: 25340403 PMCID: PMC4207663 DOI: 10.1371/journal.pgen.1004733] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 09/03/2014] [Indexed: 11/22/2022] Open
Abstract
Plasmid conjugation plays a significant role in the dissemination of antibiotic resistance and pathogenicity determinants. Understanding how conjugation is regulated is important to gain insights into these features. Little is known about regulation of conjugation systems present on plasmids from Gram-positive bacteria. pLS20 is a native conjugative plasmid from the Gram-positive bacterium Bacillus subtilis. Recently the key players that repress and activate pLS20 conjugation have been identified. Here we studied in detail the molecular mechanism regulating the pLS20 conjugation genes using both in vivo and in vitro approaches. Our results show that conjugation is subject to the control of a complex genetic switch where at least three levels of regulation are integrated. The first of the three layers involves overlapping divergent promoters of different strengths regulating expression of the conjugation genes and the key transcriptional regulator RcoLS20. The second layer involves a triple function of RcoLS20 being a repressor of the main conjugation promoter and an activator and repressor of its own promoter at low and high concentrations, respectively. The third level of regulation concerns formation of a DNA loop mediated by simultaneous binding of tetrameric RcoLS20 to two operators, one of which overlaps with the divergent promoters. The combination of these three layers of regulation in the same switch allows the main conjugation promoter to be tightly repressed during conditions unfavorable to conjugation while maintaining the sensitivity to accurately switch on the conjugation genes when appropriate conditions occur. The implications of the regulatory switch and comparison with other genetic switches involving DNA looping are discussed. Plasmids are extrachromosomal, autonomously replicating units that are harbored by many bacteria. Many plasmids encode transfer function allowing them to be transferred into plasmid-free bacteria by a process named conjugation. Since many of them also carry antibiotic resistance genes, plasmid-mediated conjugation is a major mechanism in the dissemination of antibiotic resistance. In depth knowledge on the regulation of conjugation genes is a prerequisite to design measures interfering with the spread of antibiotic resistance. pLS20 is a conjugative plasmid of the soil bacterium Bacillus subtilis, which is also a gut commensal in animals and humans. Here we describe in detail the molecular mechanism by which the key transcriptional regulator tightly represses the conjugation genes during conditions unfavorable to conjugation without compromising the ability to switch on accurately the conjugation genes when appropriate. We found that conjugation is subject to the control of a unique genetic switch where at least three levels of regulation are integrated. The first level involves overlapping divergent promoters of different strengths. The second layer involves a triple function of the transcriptional regulator. And the third level of regulation concerns formation of a DNA loop mediated by the transcriptional regulator.
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Affiliation(s)
- Gayetri Ramachandran
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Praveen K. Singh
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Luis Yuste
- Centro Nacional de Biotecnología (CSIC), Canto Blanco, Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Fernando Rojo
- Centro Nacional de Biotecnología (CSIC), Canto Blanco, Madrid, Spain
| | - Ling J. Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
- * E-mail:
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