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Schröder GC, O’Dell WB, Swartz PD, Meilleur F. Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions. Acta Crystallogr F Struct Biol Commun 2021; 77:128-133. [PMID: 33830078 PMCID: PMC8034432 DOI: 10.1107/s2053230x21002399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 11/10/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper-oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William B. O’Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul D. Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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2
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Potor L, Sikura KÉ, Hegedűs H, Pethő D, Szabó Z, Szigeti ZM, Pócsi I, Trencsényi G, Szikra D, Garai I, Gáll T, Combi Z, Kappelmayer J, Balla G, Balla J. The Fungal Iron Chelator Desferricoprogen Inhibits Atherosclerotic Plaque Formation. Int J Mol Sci 2020; 21:ijms21134746. [PMID: 32635347 PMCID: PMC7369830 DOI: 10.3390/ijms21134746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Hemoglobin, heme and iron are implicated in the progression of atherosclerosis. Therefore, we investigated whether the hydrophobic fungal iron chelator siderophore, desferricoprogen (DFC) inhibits atherosclerosis. DFC reduced atherosclerotic plaque formation in ApoE-/- mice on an atherogenic diet. It lowered the plasma level of oxidized LDL (oxLDL) and inhibited lipid peroxidation in aortic roots. The elevated collagen/elastin content and enhanced expression of adhesion molecule VCAM-1 were decreased. DFC diminished oxidation of Low-density Lipoprotein (LDL) and plaque lipids catalyzed by heme or hemoglobin. Formation of foam cells, uptake of oxLDL by macrophages, upregulation of CD36 and increased expression of TNF-α were reduced by DFC in macrophages. TNF-triggered endothelial cell activation (vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecules (ICAMs), E-selectin) and increased adhesion of monocytes to endothelium were attenuated. The increased endothelial permeability and intracellular gap formation provoked by TNF-α was also prevented by DFC. DFC acted as a cytoprotectant in endothelial cells and macrophages challenged with a lethal dose of oxLDL and lowered the expression of stress-responsive heme oxygenase-1 as sublethal dose was employed. Saturation of desferrisiderophore with iron led to the loss of the beneficial effects. We demonstrated that DFC accumulated within the atheromas of the aorta in ApoE-/- mice. DFC represents a novel therapeutic approach to control the progression of atherosclerosis.
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Affiliation(s)
- László Potor
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4012 Debrecen, Hungary; (L.P.); (K.É.S.); (T.G.)
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
| | - Katalin Éva Sikura
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4012 Debrecen, Hungary; (L.P.); (K.É.S.); (T.G.)
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
| | - Hajnalka Hegedűs
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
| | - Dávid Pethő
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
| | - Zsuzsa Szabó
- Department of Molecular Biotechnology and Microbiology, Institute of Technology, Faculty of Science and Technology, University of Debrecen, 4012 Debrecen, Hungary; (Z.S.); (Z.M.S.); (I.P.)
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Technology, Faculty of Science and Technology, University of Debrecen, 4012 Debrecen, Hungary; (Z.S.); (Z.M.S.); (I.P.)
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Technology, Faculty of Science and Technology, University of Debrecen, 4012 Debrecen, Hungary; (Z.S.); (Z.M.S.); (I.P.)
| | - György Trencsényi
- Scanomed Ltd., University of Debrecen, 4012 Debrecen, Hungary; (G.T.); (D.S.); (I.G.)
| | - Dezső Szikra
- Scanomed Ltd., University of Debrecen, 4012 Debrecen, Hungary; (G.T.); (D.S.); (I.G.)
| | - Ildikó Garai
- Scanomed Ltd., University of Debrecen, 4012 Debrecen, Hungary; (G.T.); (D.S.); (I.G.)
| | - Tamás Gáll
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4012 Debrecen, Hungary; (L.P.); (K.É.S.); (T.G.)
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
| | - Zsolt Combi
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
| | - János Kappelmayer
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary;
| | - György Balla
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4012 Debrecen, Hungary; (L.P.); (K.É.S.); (T.G.)
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary
- Correspondence: (G.B.); (J.B.)
| | - József Balla
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4012 Debrecen, Hungary; (L.P.); (K.É.S.); (T.G.)
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4012 Debrecen, Hungary; (H.H.); (D.P.); (Z.C.)
- Correspondence: (G.B.); (J.B.)
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Gryz E, Perlińska-Lenart U, Gawarecka K, Jozwiak A, Piłsyk S, Lipko A, Jemiola-Rzeminska M, Bernat P, Muszewska A, Steczkiewicz K, Ginalski K, Długoński J, Strzalka K, Swiezewska E, Kruszewska JS. Poly-Saturated Dolichols from Filamentous Fungi Modulate Activity of Dolichol-Dependent Glycosyltransferase and Physical Properties of Membranes. Int J Mol Sci 2019; 20:ijms20123043. [PMID: 31234450 PMCID: PMC6628320 DOI: 10.3390/ijms20123043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 11/17/2022] Open
Abstract
Mono-saturated polyprenols (dolichols) have been found in almost all Eukaryotic cells, however, dolichols containing additional saturated bonds at the ω-end, have been identified in A. fumigatus and A. niger. Here we confirm using an LC-ESI-QTOF-MS analysis, that poly-saturated dolichols are abundant in other filamentous fungi, Trichoderma reesei, A. nidulans and Neurospora crassa, while the yeast Saccharomyces cerevisiae only contains the typical mono-saturated dolichols. We also show, using differential scanning calorimetry (DSC) and fluorescence anisotropy of 1,6-diphenyl-l,3,5-hexatriene (DPH) that the structure of dolichols modulates the properties of membranes and affects the functioning of dolichyl diphosphate mannose synthase (DPMS). The activity of this enzyme from T. reesei and S. cerevisiae was strongly affected by the structure of dolichols. Additionally, the structure of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) model membranes was more strongly disturbed by the poly-saturated dolichols from Trichoderma than by the mono-saturated dolichols from yeast. By comparing the lipidome of filamentous fungi with that from S. cerevisiae, we revealed significant differences in the PC/PE ratio and fatty acids composition. Filamentous fungi differ from S. cerevisiae in the lipid composition of their membranes and the structure of dolichols. The structure of dolichols profoundly affects the functioning of dolichol-dependent enzyme, DPMS.
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Affiliation(s)
- Elżbieta Gryz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Urszula Perlińska-Lenart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Katarzyna Gawarecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Adam Jozwiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Agata Lipko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Malgorzata Jemiola-Rzeminska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
| | - Jerzy Długoński
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
| | - Kazimierz Strzalka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Joanna S Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
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Karkehabadi S, Hansson H, Mikkelsen NE, Kim S, Kaper T, Sandgren M, Gudmundsson M. Structural studies of a glycoside hydrolase family 3 β-glucosidase from the model fungus Neurospora crassa. Acta Crystallogr F Struct Biol Commun 2018; 74:787-796. [PMID: 30511673 PMCID: PMC6277957 DOI: 10.1107/s2053230x18015662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
The glycoside hydrolase family 3 (GH3) β-glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β-Glucosidases hydrolyse the β-1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported. The structure has been refined to 2.25 Å resolution, with an Rcryst and Rfree of 0.18 and 0.22, respectively. NcCel3A is an extensively N-glycosylated glycoprotein that shares 46% sequence identity with Hypocrea jecorina Cel3A, the structure of which has recently been published, and 61% sequence identity with the thermophilic β-glucosidase from Rasamsonia emersonii. NcCel3A is a three-domain protein with a number of extended loops that deepen the active-site cleft of the enzyme. These structures characterize this subfamily of GH3 β-glucosidases and account for the high cellobiose specificity of this subfamily.
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Affiliation(s)
- Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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5
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Benedetti L, Barentine AES, Messa M, Wheeler H, Bewersdorf J, De Camilli P. Light-activated protein interaction with high spatial subcellular confinement. Proc Natl Acad Sci U S A 2018; 115:E2238-E2245. [PMID: 29463750 PMCID: PMC5877946 DOI: 10.1073/pnas.1713845115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods to acutely manipulate protein interactions at the subcellular level are powerful tools in cell biology. Several blue-light-dependent optical dimerization tools have been developed. In these systems one protein component of the dimer (the bait) is directed to a specific subcellular location, while the other component (the prey) is fused to the protein of interest. Upon illumination, binding of the prey to the bait results in its subcellular redistribution. Here, we compared and quantified the extent of light-dependent dimer occurrence in small, subcellular volumes controlled by three such tools: Cry2/CIB1, iLID, and Magnets. We show that both the location of the photoreceptor protein(s) in the dimer pair and its (their) switch-off kinetics determine the subcellular volume where dimer formation occurs and the amount of protein recruited in the illuminated volume. Efficient spatial confinement of dimer to the area of illumination is achieved when the photosensitive component of the dimerization pair is tethered to the membrane of intracellular compartments and when on and off kinetics are extremely fast, as achieved with iLID or Magnets. Magnets and the iLID variants with the fastest switch-off kinetics induce and maintain protein dimerization in the smallest volume, although this comes at the expense of the total amount of dimer. These findings highlight the distinct features of different optical dimerization systems and will be useful guides in the choice of tools for specific applications.
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Affiliation(s)
- Lorena Benedetti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
| | - Mirko Messa
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Heather Wheeler
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510;
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
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O’Dell WB, Swartz PD, Weiss KL, Meilleur F. Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction. Acta Crystallogr F Struct Biol Commun 2017; 73:70-78. [PMID: 28177316 PMCID: PMC5297926 DOI: 10.1107/s2053230x16020318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/21/2016] [Indexed: 11/11/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bonds via an oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 from Neurospora crassa (NcPMO-2) was heterologously expressed in Pichia pastoris to facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressing NcPMO-2 from a glycoengineered strain of P. pastoris and by the use of crystal seeding methods, respectively. These improvements resulted in high-resolution (1.20 Å) X-ray diffraction data collection at 100 K and the production of a large NcPMO-2 crystal suitable for room-temperature neutron diffraction data collection to 2.12 Å resolution.
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Affiliation(s)
- William B. O’Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Paul D. Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
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Zanphorlin LM, Lima TB, Wong MJ, Balbuena TS, Minetti CASA, Remeta DP, Young JC, Barbosa LRS, Gozzo FC, Ramos CHI. Heat Shock Protein 90 kDa (Hsp90) Has a Second Functional Interaction Site with the Mitochondrial Import Receptor Tom70. J Biol Chem 2016; 291:18620-31. [PMID: 27402847 PMCID: PMC5009240 DOI: 10.1074/jbc.m115.710137] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 07/07/2016] [Indexed: 12/19/2022] Open
Abstract
To accomplish its crucial role, mitochondria require proteins that are produced in the cytosol, delivered by cytosolic Hsp90, and translocated to its interior by the translocase outer membrane (TOM) complex. Hsp90 is a dimeric molecular chaperone and its function is modulated by its interaction with a large variety of co-chaperones expressed within the cell. An important family of co-chaperones is characterized by the presence of one TPR (tetratricopeptide repeat) domain, which binds to the C-terminal MEEVD motif of Hsp90. These include Tom70, an important component of the TOM complex. Despite a wealth of studies conducted on the relevance of Tom70·Hsp90 complex formation, there is a dearth of information regarding the exact molecular mode of interaction. To help fill this void, we have employed a combined experimental strategy consisting of cross-linking/mass spectrometry to investigate binding of the C-terminal Hsp90 domain to the cytosolic domain of Tom70. This approach has identified a novel region of contact between C-Hsp90 and Tom70, a finding that is confirmed by probing the corresponding peptides derived from cross-linking experiments via isothermal titration calorimetry and mitochondrial import assays. The data generated in this study are combined to input constraints for a molecular model of the Hsp90/Tom70 interaction, which has been validated by small angle x-ray scattering, hydrogen/deuterium exchange, and mass spectrometry. The resultant model suggests that only one of the MEEVD motifs within dimeric Hsp90 contacts Tom70. Collectively, our findings provide significant insight on the mechanisms by which preproteins interact with Hsp90 and are translocated via Tom70 to the mitochondria.
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Affiliation(s)
- Leticia M Zanphorlin
- From the Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970, Brazil
| | - Tatiani B Lima
- From the Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970, Brazil
| | - Michael J Wong
- the Department of Biochemistry, McGill University, Groupe de Recherche Axé sur la Structure des Protéines, Montreal, QC H3G 0B1, Canada
| | - Tiago S Balbuena
- the College of Agricultural and Veterinary Sciences, State University of Sao Paulo, Jaboticabal, Sao Paulo, 14884-900 Brazil
| | - Conceição A S A Minetti
- the Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, and
| | - David P Remeta
- the Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, and
| | - Jason C Young
- the Department of Biochemistry, McGill University, Groupe de Recherche Axé sur la Structure des Protéines, Montreal, QC H3G 0B1, Canada
| | - Leandro R S Barbosa
- the Instituto de Fisica, Universidade de Sao Paulo USP, Sao Paulo SP, 05508-090 Brazil
| | - Fabio C Gozzo
- From the Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970, Brazil
| | - Carlos H I Ramos
- From the Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970, Brazil,
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8
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Vela-Corcía D, Romero D, Torés JA, De Vicente A, Pérez-García A. Transient transformation of Podosphaera xanthii by electroporation of conidia. BMC Microbiol 2015. [PMID: 25651833 DOI: 10.1186/s12866-014-0338-338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Powdery mildew diseases are a major phytosanitary issue causing important yield and economic losses in agronomic, horticultural and ornamental crops. Powdery mildew fungi are obligate biotrophic parasites unable to grow on culture media, a fact that has significantly limited their genetic manipulation. In this work, we report a protocol based on the electroporation of fungal conidia, for the transient transformation of Podosphaera fusca (synonym Podosphaera xanthii), the main causal agent of cucurbit powdery mildew. RESULTS To introduce DNA into P. xanthii conidia, we applied two square-wave pulses of 1.7 kV for 1 ms with an interval of 5 s. We tested these conditions with several plasmids bearing as selective markers hygromycin B resistance (hph), carbendazim resistance (TUB2) or GFP (gfp) under control of endogenous regulatory elements from Aspergillus nidulans, Neurospora crassa or P. xanthii to drive their expression. An in planta selection procedure using the MBC fungicide carbendazim permitted the propagation of transformants onto zucchini cotyledons and avoided the phytotoxicity associated with hygromycin B. CONCLUSION This is the first report on the transformation of P. xanthii and the transformation of powdery mildew fungi using electroporation. Although the transformants are transient, this represents a feasible method for the genetic manipulation of this important group of plant pathogens.
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Affiliation(s)
- David Vela-Corcía
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
| | - Juan Antonio Torés
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750 Algarrobo-Costa, Málaga, Spain.
| | - Antonio De Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
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9
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Hu W, Song H, Sae Her A, Bak DW, Naowarojna N, Elliott SJ, Qin L, Chen X, Liu P. Bioinformatic and biochemical characterizations of C-S bond formation and cleavage enzymes in the fungus Neurospora crassa ergothioneine biosynthetic pathway. Org Lett 2014; 16:5382-5. [PMID: 25275953 PMCID: PMC4201327 DOI: 10.1021/ol502596z] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 01/03/2023]
Abstract
Ergothioneine is a histidine thiol derivative. Its mycobacterial biosynthetic pathway has five steps (EgtA-E catalysis) with two novel reactions: a mononuclear nonheme iron enzyme (EgtB) catalyzed oxidative C-S bond formation and a PLP-mediated C-S lyase (EgtE) reaction. Our bioinformatic and biochemical analyses indicate that the fungus Neurospora crassa has a more concise ergothioneine biosynthetic pathway because its nonheme iron enzyme, Egt1, makes use of cysteine instead of γ-Glu-Cys as the substrate. Such a change of substrate preference eliminates the competition between ergothioneine and glutathione biosyntheses. In addition, we have identified the N. crassa C-S lyase (NCU11365) and reconstituted its activity in vitro, which makes the future ergothioneine production through metabolic engineering feasible.
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Affiliation(s)
- Wen Hu
- State
Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou, P. R. China
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Heng Song
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ampon Sae Her
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Daniel W. Bak
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Sean J. Elliott
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Li Qin
- State
Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou, P. R. China
| | - Xiaoping Chen
- State
Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou, P. R. China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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10
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Gao W, Wang Z, Wang Y. [LAH-3, a transcriptional factor involved in osmotic regulation in Neurospora crassa]. Wei Sheng Wu Xue Bao 2014; 54:984-991. [PMID: 25522587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
[OBJECTIVE] In order to identify the function of lah-3 in osmotic regulation, we generated lah-3 deletion strain and analyzed its phenotype by osmostress treatment. [METHODS] We used homologous recombination to replace lah-3gene by hph gene and treated these cells with 4% NaCl and 1 M sorbitol to analyze the phenotype. Northern blot was used to detect the expressions of osmoresponsing genes. Western blot was used to examine the phosphorylation level of LAH-3 and OS-2 and the expression of OS-2. [RESULTS] In the deletion strain of transcription factor lah-3 gene, the expressions of osmoresponsing genes gcy-1, stl-1 and pck-1 were significantly reduced. Besides, the phosphorylation level of LAH-3 protein increased under the osmostress treatment. The phosphorylation of LAH-3 was not mediated by OS-2. The deletion of lah-3 did not affect the os-2 expression and the phosphorylation level of OS-2 upon osmostress. [ CONCLUSION] LAH-3 involved in osmoresponsing was independent of OS-2 MAPK pathway.
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11
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Raffelberg S, Gutt A, Gärtner W, Mandalari C, Abbruzzetti S, Viappiani C, Losi A. The amino acids surrounding the flavin 7a-methyl group determine the UVA spectral features of a LOV protein. Biol Chem 2014; 394:1517-28. [PMID: 23828427 DOI: 10.1515/hsz-2013-0163] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/01/2013] [Indexed: 11/15/2022]
Abstract
Flavin-binding light, oxygen, and voltage (LOV) domains are UVA/blue-light-sensing protein units that form a reversible flavin mononucleotide-cysteine adduct upon light induction. In their dark-adapted state, LOV domains exhibit the typical spectral features of fully oxidized riboflavin derivatives. A survey on the absorption spectra of various LOV domains revealed that the UVA spectral range is the most variable region (whereas the absorption band at 450 nm is virtually unchanged), showing essentially two distinct patterns found in plant phototropin LOV1 and LOV2 domains, respectively. In this work, we have identified a residue directly interacting with the isoalloxazine methyl group at C(7a) as the major UVA spectral tuner. In YtvA from Bacillus subtilis, this amino acid is threonine 30, and its mutation into apolar residues converts the LOV2-like spectrum of native YtvA into a LOV1-like pattern. Mutation T30A also accelerates the photocycle ca. 4-fold. Together with control mutations at different positions, our results experimentally confirm the previously calculated direction of the transition dipole moment for the UVA ππ* state and identify the mechanisms underlying spectral tuning in the LOV domains.
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12
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Quester K, Avalos-Borja M, Vilchis-Nestor AR, Camacho-López MA, Castro-Longoria E. SERS properties of different sized and shaped gold nanoparticles biosynthesized under different environmental conditions by Neurospora crassa extract. PLoS One 2013; 8:e77486. [PMID: 24130891 PMCID: PMC3793955 DOI: 10.1371/journal.pone.0077486] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/06/2013] [Indexed: 11/25/2022] Open
Abstract
Surface-enhanced Raman scattering (SERS) is a surface-sensitive technique that enhances Raman scattering by molecules adsorbed on rough metal surfaces. It is known that metal nanoparticles, especially gold and silver nanoparticles, exhibit great SERS properties, which make them very attractive for the development of biosensors and biocatalysts. On the other hand, the development of ecofriendly methods for the synthesis of metallic nanostructures has become the focus of research in several countries, and many microorganisms and plants have already been used to biosynthesize metallic nanostructures. However, the majority of these are pathogenic to plants or humans. Here, we report gold nanoparticles with good SERS properties, biosynthesized by Neurospora crassa extract under different environmental conditions, increasing Raman signals up to 40 times using methylene blue as a target molecule. Incubation of tetrachloroauric acid solution with the fungal extract at 60°C and a pH value of a) 3, b) 5.5, and c) 10 resulted in the formation of gold nanoparticles of a) different shapes like triangles, hexagons, pentagons etc. in a broad size range of about 10-200 nm, b) mostly quasi-spheres with some different shapes in a main size range of 6-23 nm, and c) only quasi-spheres of 3-12 nm. Analyses included TEM, HRTEM, and EDS in order to corroborate the shape and the elemental character of the gold nanoparticles, respectively. The results presented here show that these ‘green’ synthesized gold nanoparticles might have potential applicability in the field of biological sensing.
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Affiliation(s)
- Katrin Quester
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., Mexico
| | - Miguel Avalos-Borja
- Centro de Nanociencias y Nanotecnologia (CNyN), Universidad Nacional Autónoma de México (UNAM), Ensenada, Mexico
| | | | - Marco Antonio Camacho-López
- Laboratorio de Investigación y Desarollo de Materiales Avanzados, Sección de Espectroscopía, Raman, Facultad de Química, UAEMex, Toluca, Estado de México, Mexico.
| | - Ernestina Castro-Longoria
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., Mexico
- * E-mail:
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13
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Araujo-Palomares CL, Richthammer C, Seiler S, Castro-Longoria E. Functional characterization and cellular dynamics of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. PLoS One 2011; 6:e27148. [PMID: 22087253 PMCID: PMC3210136 DOI: 10.1371/journal.pone.0027148] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/11/2011] [Indexed: 11/18/2022] Open
Abstract
Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 – RAC – CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.
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Affiliation(s)
- Cynthia L. Araujo-Palomares
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada Baja California, México
| | - Corinna Richthammer
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany
| | - Stephan Seiler
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany
- * E-mail: (SS); (EC-L)
| | - Ernestina Castro-Longoria
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada Baja California, México
- * E-mail: (SS); (EC-L)
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Costantino V, Mangoni A, Teta R, Kra-Oz G, Yarden O. Neurosporaside, a tetraglycosylated sphingolipid from Neurospora crassa. J Nat Prod 2011; 74:554-558. [PMID: 21425845 DOI: 10.1021/np1009493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The new tetraglycosylceramide neurosporaside (1a) has been isolated from the fungus Neurospora crassa. Neurosporaside is a tetraglycosylated glycosphingolipid characterized by a sugar chain unprecedented among natural glycoconjugates. The structure of neurosporaside was elucidated by extensive spectroscopic analysis and microscale degradation analysis, which allowed full structure elucidation using less than 1 mg of compound.
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Affiliation(s)
- Valeria Costantino
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
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15
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Wang J, Hu Q, Chen H, Zhou Z, Li W, Wang Y, Li S, He Q. Role of individual subunits of the Neurospora crassa CSN complex in regulation of deneddylation and stability of cullin proteins. PLoS Genet 2010; 6:e1001232. [PMID: 21151958 PMCID: PMC2996332 DOI: 10.1371/journal.pgen.1001232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 11/01/2010] [Indexed: 11/18/2022] Open
Abstract
The Cop9 signalosome (CSN) is an evolutionarily conserved multifunctional complex that controls ubiquitin-dependent protein degradation in eukaryotes. We found seven CSN subunits in Neurospora crassa in a previous study, but only one subunit, CSN-2, was functionally characterized. In this study, we created knockout mutants for the remaining individual CSN subunits in N. crassa. By phenotypic observation, we found that loss of CSN-1, CSN-2, CSN-4, CSN-5, CSN-6, or CSN-7 resulted in severe defects in growth, conidiation, and circadian rhythm; the defect severity was gene-dependent. Unexpectedly, CSN-3 knockout mutants displayed the same phenotype as wild-type N. crassa. Consistent with these phenotypic observations, deneddylation of cullin proteins in csn-1, csn-2, csn-4, csn-5, csn-6, or csn-7 mutants was dramatically impaired, while deletion of csn-3 did not cause any alteration in the neddylation/deneddylation state of cullins. We further demonstrated that CSN-1, CSN-2, CSN-4, CSN-5, CSN-6, and CSN-7, but not CSN-3, were essential for maintaining the stability of Cul1 in SCF complexes and Cul3 and BTB proteins in Cul3-BTB E3s, while five of the CSN subunits, but not CSN-3 and CSN-5, were also required for maintaining the stability of SKP-1 in SCF complexes. All seven CSN subunits were necessary for maintaining the stability of Cul4-DDB1 complexes. In addition, CSN-3 was also required for maintaining the stability of the CSN-2 subunit and FWD-1 in the SCFFWD-1 complex. Together, these results not only provide functional insights into the different roles of individual subunits in the CSN complex, but also establish a functional framework for understanding the multiple functions of the CSN complex in biological processes. Protein degradation is precisely controlled in cells. The ubiquitin-mediated protein degradation pathway is highly conserved in eukaryotes, and the activity of ubiquitin ligases is regulated by the Cop9 signalosome (CSN), a multisubunit complex that is evolutionarily conserved from yeast to humans. Determining how the CSN complex functions biologically is crucial for understanding regulation of the ubiquitin-mediated protein degradation pathway. The filamentous fungus N. crassa is commonly used to study protein degradation. Its CSN complex contains seven subunits (CSN-1 to CSN-7). In this study, we generated knockout mutants of individual CSN subunits and observed the phenotypes of each mutant. We demonstrated that six of the seven CSN subunits were essential for cleaving the ubiquitin-like protein Nedd8 from cullin proteins (which act as scaffolds for ubiquitin ligases). In contrast, loss of the CSN-3 subunit had no effect on cullin neddylation. We also found that each CSN subunit had distinct roles in maintaining the stability of key components of cullin-based ubiquitin ligases. In summary, we systematically investigated the unequal contributions of CSN subunits to deneddylation and the maintenance of cullin-based ubiquitin ligases in N. crassa. Our work establishes a framework for understanding the function of CSN subunits in other eukaryotes.
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Affiliation(s)
- Jiyong Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiwen Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huijie Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhipeng Zhou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Weihua Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Ying Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shaojie Li
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (Q. He); (S. Li)
| | - Qun He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail: (Q. He); (S. Li)
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16
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Lamb JS, Zoltowski BD, Pabit SA, Li L, Crane BR, Pollack L. Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering. J Mol Biol 2009; 393:909-19. [PMID: 19712683 PMCID: PMC2858630 DOI: 10.1016/j.jmb.2009.08.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 08/14/2009] [Accepted: 08/18/2009] [Indexed: 02/04/2023]
Abstract
The PAS-LOV domain is a signal-transducing component found in a large variety of proteins that is responsible for sensing different stimuli such as light, oxygen, and voltage. The LOV protein VVD regulates blue light responses in the filamentous fungi Neurospora crassa. Using photocoupled, time-resolved small-angle X-ray scattering, we extract the solution protein structure in both dark-adapted and light-activated states. Two distinct dark-adapted conformations are detected in the wild-type protein: a compact structure that corresponds to the crystal structure of the dark-state monomer as well as an extended structure that is well modeled by introducing conformational disorder at the N-terminus of the protein. These conformations are accentuated in carefully selected variants, in which a key residue for propagating structural transitions, Cys71, has been mutated or oxidized. Despite different dark-state conformations, all proteins form a common dimer in response to illumination. Taken together, these data support a reaction scheme that describes the mechanism for light-induced dimerization of VVD. Envelope reconstructions of the transient light-state dimer reveal structures that are best described by a parallel arrangement of subunits that have significantly changed conformation compared to the crystal structure.
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Affiliation(s)
- Jessica S Lamb
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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Sandmann G, Takaichi S, Fraser PD. C(35)-apocarotenoids in the yellow mutant Neurospora crassa YLO. Phytochemistry 2008; 69:2886-2890. [PMID: 19007949 DOI: 10.1016/j.phytochem.2008.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 05/27/2023]
Abstract
The Neurospora crassa mutant YLO exhibits a yellow phenotype instead of the red-orange pigmentation of the wild type. Recently, it was shown that the mutant YLO is defective in a specific aldehyde dehydrogenase which catalyses the last step of carotenogenesis to the formation of neurosporaxanthin [Estrada, A.F., Youssar, L., Scherzinger, D., Al-Babili, S., Avalos, J., 2008. The ylo-1 gene encodes an aldehyde dehydrogenase responsible for the last reaction in the Neurospora carotenoid pathway. Mol. Microbiol. 69, 1207-1220]. Since different carotenoid compositions between wild type and YLO have been reported in earlier publications, the carotenoids of YLO were analyzed and unknown carotenoids identified. Fractionation of carotenoid extracts from YLO revealed in the less polar fraction two major carotenoids of low polarity which were found only in trace amounts in the wild type. Both carotenoids could be hydrolyzed with KOH to more polar products indicating the presence of fatty acid esters. The fatty acid moiety was identified as myristic acid by gas chromatography. Optical and mass spectra as well as co-chromatography with a synthesized authentic standard identified the free alcohols as 4'-apolycopene-4'-ol and 4'-apo-gamma-carotene-4'-ol which assigns the dominating carotenoids in the YLO mutant as 4'-apolycopene-4'-myristate and 4'-apo-gamma-carotene-4'-myristate. We can attribute the accumulation of these two carotenoids in YLO to the substantial mutation of the neurosporaxanthin-forming aldehyde dehydrogenase. However, the aldehyde intermediates 4'-apo-gamma-carotene-4'-al and 4'-apo-lycopene-4'-al do not accumulate substantially but are reduced instead to the corresponding alcohols, 4'-apolycopene-4'-ol and 4'-apo-gamma-carotene-4'-ol, and both further esterified with mainly myristic acid yielding 4'-apolycopene-4'-myristate and 4'-apo-gamma-carotene-4'-myristate.
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Affiliation(s)
- Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, J. W. Goethe Universität, Frankfurt, Germany.
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18
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Rasmussen CG, Morgenstein RM, Peck S, Glass NL. Lack of the GTPase RHO-4 in Neurospora crassa causes a reduction in numbers and aberrant stabilization of microtubules at hyphal tips. Fungal Genet Biol 2008; 45:1027-39. [PMID: 18387834 DOI: 10.1016/j.fgb.2008.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 02/14/2008] [Accepted: 02/15/2008] [Indexed: 01/12/2023]
Abstract
The multinucleate hyphae of the filamentous ascomycete fungus Neurospora crassa grow by polarized hyphal tip extension. Both the actin and microtubule cytoskeleton are required for maximum hyphal extension, in addition to other vital processes. Previously, we have shown that the monomeric GTPase encoded by the N. crassa rho-4 locus is required for actin ring formation during the process of septation; rho-4 mutants lack septa. However, other phenotypic aspects of the rho-4 mutant, such as slow growth and cytoplasmic bleeding, led us to examine the hypothesis that the microtubule (MT) cytoskeleton of the rho-4 mutant was affected in morphology and dynamics. Unlike a wild-type strain, the rho-4 mutant had few MTs and these few MTs originated from nuclear spindle pole bodies. rho-4 mutants and rho-4 strains containing a GTP-locked (activated) rho-4 allele showed a reduction in numbers of cytoplasmic MTs and microtubule stabilization at hyphal tips. Strains containing a GDP-biased (negative) allele of rho-4 showed normal numbers of MTs and minor effects on microtubule stabilization. An examination of nuclear dynamics revealed that rho-4 mutants have large, and often, stretched or broken nuclei. These observations indicate that RHO-4 plays important roles in regulating both the actin and MT cytoskeleton, which are essential for optimal hyphal tip growth and in nuclear distribution and morphology.
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Affiliation(s)
- Carolyn G Rasmussen
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
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Uchida M, Mouriño-Pérez RR, Freitag M, Bartnicki-García S, Roberson RW. Microtubule dynamics and the role of molecular motors in Neurospora crassa. Fungal Genet Biol 2007; 45:683-92. [PMID: 18069024 DOI: 10.1016/j.fgb.2007.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 10/15/2007] [Accepted: 10/19/2007] [Indexed: 11/17/2022]
Abstract
Live-cell imaging methods were used to study microtubule dynamics in the apical regions of leading hyphae and germ tubes of Neurospora crassa expressing beta-tubulin-GFP. Microtubule polymerization rates in hyphae of N. crassa were much faster than those previously reported in any other eukaryotic organism. In order to address the roles of motor proteins in microtubule dynamic instability in N. crassa, the microtubule-motor mutant strains, Deltankin and ro-1, were examined. Polymerization and depolymerization rates in leading hyphae of these strains were reduced by one half relative to the wild type. Furthermore, microtubules in germ tubes of wild type and microtubule-motor mutants exhibited similar dynamic characteristics as those in hyphae of mutant strains. Small microtubule fragments exhibiting anterograde and retrograde motility were present in leading hyphae of all strains and germ tubes of wild-type strains. Our data suggest that microtubule motors play important roles in regulating microtubule dynamic instability in leading hyphae but not in germ tubes.
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Affiliation(s)
- Maho Uchida
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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Abstract
The absolute configurations of the enacyloxins, a series of polyhydroxylated polyene antibiotics from Frateuria species, were determined. The so far elusive (13'R,14'R,15'S)-configuration was assigned to enacycloxin IVa (1) by means of 'J-resolved HMBC-1' and NOESY NMR methods.
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Affiliation(s)
- Hiroyuki Furukawa
- Laboratory of Applied Bioorganic Chemistry, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiya, Aoba-ku, Sendai 981-8555, Japan
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21
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Abstract
The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).
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Affiliation(s)
- Brian D. Zoltowski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Joanne Widom
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer J. Loros
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Alexandrine M. Bilwes
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jay C. Dunlap
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- To whom correspondence should be addressed.
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22
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Rauch G, Ehammer H, Bornemann S, Macheroux P. Mutagenic analysis of an invariant aspartate residue in chorismate synthase supports its role as an active site base. Biochemistry 2007; 46:3768-74. [PMID: 17326665 DOI: 10.1021/bi602420u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chorismate synthase catalyzes the anti-1,4-elimination of the 3-phosphate and the C(6proR) hydrogen from 5-enolpyruvylshikimate 3-phosphate (EPSP) to generate chorismate, the final product of the common shikimate pathway and a precursor for the biosynthesis of aromatic compounds. The enzyme has an absolute requirement for reduced FMN, which is thought to facilitate cleavage of C-O bonds by transiently donating an electron to the substrate. The crystal structure of the enzyme revealed that EPSP is bound near the flavin isoalloxazine ring with several invariant amino acid residues in contact with the substrate and/or cofactor. Here, we report the results of a mutagenesis study in which an invariant aspartate residue at position 367 of the Neurospora crassa chorismate synthase was replaced with alanine and asparagine. Both single mutant proteins (Asp367Ala and Asp367Asn) were comparable to the wild-type enzyme with respect to substrate and cofactor binding, indicating that Asp367 is not required for binding of either the flavin or the substrate. In sharp contrast to these results, the activity of both single mutant proteins was found to be 620 and 310 times lower for the Asp367Ala and Asp367Asn mutant proteins, respectively. This finding provides strong evidence that the carboxylate group of Asp367 plays a major role during the catalytic reaction. On the basis of the structure of the enzyme, our data provide the first experimental evidence that the carboxylate group of aspartate 367 participates in the deprotonation of N(5) of the reduced flavin cofactor, which in turn abstracts the C(6proR) hydrogen yielding chorismate as the product.
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Affiliation(s)
- Gernot Rauch
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
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23
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Marques I, Ushakova AV, Duarte M, Videira A. Role of the Conserved Cysteine Residues of the 11.5 kDa Subunit in Complex I Catalytic Properties. J Biochem 2007; 141:489-93. [PMID: 17261544 DOI: 10.1093/jb/mvm049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial complex I exists as a mixture of two inter-convertible forms: active (A) and de-activated (D), the latter being sensitive to SH-modifying compounds. To investigate if the conserved cysteine-rich 11.5 kDa subunit of Neurospora crassa complex I is involved in this process, we subjected the corresponding genomic DNA to site-directed mutagenesis. The four cysteine residues of the subunit were separately substituted with serine residues and the resulting proteins were independently expressed in a null-mutant strain. All of the obtained mutant strains were able to assemble a complex I with similar kinetic properties to those observed in the wild-type enzyme, indicating that none of the cysteine residues of the 11.5 kDa protein is individually relevant for the A/D transition process. Diminished amounts of assembled complex I seem to be the major effect of these specific mutations. The cysteine residues are likely important to the acquisition and stabilization of the correct 11.5 kDa protein conformation and this is reflected in the assembly/stability of complex I.
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Affiliation(s)
- Isabel Marques
- IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, Porto, Portugal.
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24
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Abstract
The direction of translocation of microtubules on a surface coated with kinesin is usually random. Here we demonstrate and quantify the rate at which externally applied electric fields can direct moving microtubules parallel to the field by deflecting their leading end toward the anode. Effects of electric field strength, kinesin surface density, and microtubule translocation speed on the rate of redirection of microtubules were analyzed statistically. Furthermore, we demonstrated that microtubules can be steered in any desired direction via manipulation of externally applied E-fields.
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Affiliation(s)
- Taesung Kim
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan 48109, USA
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25
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Tralau T, Lanthaler K, Robson GD, Crosthwaite SK. Circadian rhythmicity during prolonged chemostat cultivation of Neurospora crassa. Fungal Genet Biol 2006; 44:754-63. [PMID: 17196855 DOI: 10.1016/j.fgb.2006.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 11/06/2006] [Accepted: 11/07/2006] [Indexed: 10/23/2022]
Abstract
Following exposure to light and attainment of steady-state in the chemostat, Neurospora was grown in constant conditions of darkness at 25 degrees C for 6 days. Biomass samples were taken every 4h for the extraction of RNA and protein, and the state of the circadian clock was assessed by assaying the levels of three rhythmically expressed mRNAs; frequency (frq), antisense frq (qrf) and clock-controlled gene-14 (ccg-14), and by monitoring the clock-controlled rhythm of sporulation. Our results indicate that the Neurospora clock continued to run in the chemostat. This is the longest reported time that Neurospora has been grown in a chemostat in filamentous form and opens up the possibility of studying the response of Neurospora to a range of stimuli in the absence of confounding effects due to; alterations in growth rate, aging, and changing conditions of the growth medium.
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Affiliation(s)
- Tewes Tralau
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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26
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Hizlan D, Mishima M, Tittmann P, Gross H, Glotzer M, Hoenger A. Structural analysis of the ZEN-4/CeMKLP1 motor domain and its interaction with microtubules. J Struct Biol 2006; 153:73-84. [PMID: 16361109 DOI: 10.1016/j.jsb.2005.10.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 10/17/2005] [Accepted: 10/27/2005] [Indexed: 11/25/2022]
Abstract
The centralspindlin complex is required for the assembly and maintenance of the central spindle during late anaphase and the completion of cytokinesis. It is composed of two copies each of the kinesin-like protein ZEN-4, a Caenorhabditis elegans MKLP-1 (Kinesin-6 family), and the RhoGAP CYK-4. By using cryo-electron microscopy and helical 3D reconstruction, we are investigating the structural features of the interactions between monomeric and dimeric motor domain constructs of ZEN-4 and microtubules. We have calculated helically averaged 3D maps of microtubules decorated with ZEN-4 motor domain in the presence of AMP-PNP, ADP, ADP-AlF(4)(-), and nucleotide-free conditions. We used statistical difference mapping to compare these maps among each other and to related maps obtained from microtubules decorated with a well-characterized Kinesin-1 motor domain from Neurospora crassa. Thereby, we found distinct structural features in microtubule-ZEN-4 complexes that may directly relate to the functional properties of ZEN-4 and centralspindlin. Furthermore, we investigated the location, structure, and function of a highly conserved extension of approximately 50 residues unique to the Kinesin-6 subfamily, located in the motor core loop6/beta4 region.
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Affiliation(s)
- Dilem Hizlan
- European Molecular Biology Laboratory, Structural Biology and Biocomputing Programme, Heidelberg, Germany
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27
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Kwan AHY, Winefield RD, Sunde M, Matthews JM, Haverkamp RG, Templeton MD, Mackay JP. Structural basis for rodlet assembly in fungal hydrophobins. Proc Natl Acad Sci U S A 2006; 103:3621-6. [PMID: 16537446 PMCID: PMC1533775 DOI: 10.1073/pnas.0505704103] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class I hydrophobins are a unique family of fungal proteins that form a polymeric, water-repellent monolayer on the surface of structures such as spores and fruiting bodies. Similar monolayers are being discovered on an increasing range of important microorganisms. Hydrophobin monolayers are amphipathic and particularly robust, and they reverse the wettability of the surface on which they are formed. There are also significant similarities between these polymers and amyloid-like fibrils. However, structural information on these proteins and the rodlets they form has been elusive. Here, we describe the three-dimensional structure of the monomeric form of the class I hydrophobin EAS. EAS forms a beta-barrel structure punctuated by several disordered regions and displays a complete segregation of charged and hydrophobic residues on its surface. This structure is consistent with its ability to form an amphipathic polymer. By using this structure, together with data from mutagenesis and previous biophysical studies, we have been able to propose a model for the polymeric rodlet structure adopted by these proteins. X-ray fiber diffraction data from EAS rodlets are consistent with our model. Our data provide molecular insight into the nature of hydrophobin rodlet films and extend our understanding of the fibrillar beta-structures that continue to be discovered in the protein world.
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Affiliation(s)
- A. H. Y. Kwan
- *School of Molecular and Microbial Biosciences, University of Sydney, Sydney 2006, Australia
| | - R. D. Winefield
- Horticultural and Food Research Institute of New Zealand, Mount Albert Research Centre, Auckland, New Zealand; and
- Institute of Technology and Engineering, Massey University, Palmerston North, New Zealand
| | - M. Sunde
- *School of Molecular and Microbial Biosciences, University of Sydney, Sydney 2006, Australia
| | - J. M. Matthews
- *School of Molecular and Microbial Biosciences, University of Sydney, Sydney 2006, Australia
| | - R. G. Haverkamp
- Institute of Technology and Engineering, Massey University, Palmerston North, New Zealand
| | - M. D. Templeton
- Horticultural and Food Research Institute of New Zealand, Mount Albert Research Centre, Auckland, New Zealand; and
- To whom correspondence may be addressed at:
Bioprotection Group, The Horticulture and Food Research Institute of New Zealand, Private Bag 92-169, Auckland, New Zealand. E-mail:
| | - J. P. Mackay
- *School of Molecular and Microbial Biosciences, University of Sydney, Sydney 2006, Australia
- To whom correspondence may be addressed. E-mail:
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28
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Runke G, Maier E, Summers WAT, Bay DC, Benz R, Court DA. Deletion variants of Neurospora mitochondrial porin: electrophysiological and spectroscopic analysis. Biophys J 2006; 90:3155-64. [PMID: 16500966 PMCID: PMC1432131 DOI: 10.1529/biophysj.105.072520] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial porins are predicted to traverse the outer membrane as a series of beta-strands, but the precise structure of the resulting beta-barrel has remained elusive. Toward determining the positions of the membrane-spanning segments, a series of small deletions was introduced into several of the predicted beta-strands of the Neurospora crassa porin. Overall, three classes of porin variants were identified: i), those producing large, stable pores, indicating deletions likely outside of beta-strands; ii), those with minimal pore-forming ability, indicating disruptions in key beta-strands or beta-turns; and iii), those that formed small unstable pores with a variety of gating and ion-selectivity properties. The latter class presumably results from a subset of proteins that adopt an alternative barrel structure upon the loss of stabilizing residues. Some variants were not sufficiently stable in detergent for structural analysis; circular dichroism spectropolarimetry of those that were did not reveal significant differences in the overall structural composition among the detergent-solubilized porin variants and the wild-type protein. Several of the variants displayed altered tryptophan fluorescence profiles, indicative of differing microenvironments surrounding these residues. Based on these results, modifications to the existing models for porin structure are proposed.
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Affiliation(s)
- Greg Runke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
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29
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Froehlich AC, Noh B, Vierstra RD, Loros J, Dunlap JC. Genetic and molecular analysis of phytochromes from the filamentous fungus Neurospora crassa. Eukaryot Cell 2006; 4:2140-52. [PMID: 16339731 PMCID: PMC1317490 DOI: 10.1128/ec.4.12.2140-2152.2005] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Phytochromes (Phys) comprise a superfamily of red-/far-red-light-sensing proteins. Whereas higher-plant Phys that control numerous growth and developmental processes have been well described, the biochemical characteristics and functions of the microbial forms are largely unknown. Here, we describe analyses of the expression, regulation, and activities of two Phys in the filamentous fungus Neurospora crassa. In addition to containing the signature N-terminal domain predicted to covalently associate with a bilin chromophore, PHY-1 and PHY-2 contain C-terminal histidine kinase and response regulator motifs, implying that they function as hybrid two-component sensor kinases activated by light. A bacterially expressed N-terminal fragment of PHY-2 covalently bound either biliverdin or phycocyanobilin in vitro, with the resulting holoprotein displaying red-/far-red-light photochromic absorption spectra and a photocycle in vitro. cDNA analysis of phy-1 and phy-2 revealed two splice isoforms for each gene. The levels of the phy transcripts are not regulated by light, but the abundance of the phy-1 mRNAs is under the control of the circadian clock. Phosphorylated and unphosphorylated forms of PHY-1 were detected; both species were found exclusively in the cytoplasm, with their relative abundances unaffected by light. Strains containing deletions of phy-1 and phy-2, either singly or in tandem, were not compromised in any known photoresponses in Neurospora, leaving their function(s) unclear.
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MESH Headings
- Alternative Splicing
- Amino Acid Motifs
- Amino Acid Sequence
- Base Sequence
- Chromosome Mapping
- Chromosomes, Fungal
- Circadian Rhythm
- Cytoplasm/metabolism
- DNA, Complementary/analysis
- DNA, Complementary/genetics
- DNA, Fungal
- Escherichia coli/genetics
- Exons
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/isolation & purification
- Fungal Proteins/metabolism
- Gene Deletion
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Genetic Linkage
- Genome, Fungal
- Histidine Kinase
- Introns
- Kinetics
- Light
- Molecular Sequence Data
- Neurospora crassa/chemistry
- Neurospora crassa/genetics
- Neurospora crassa/growth & development
- Neurospora crassa/metabolism
- Neurospora crassa/radiation effects
- Open Reading Frames
- Phosphorylation
- Phytochrome/chemistry
- Phytochrome/genetics
- Phytochrome/isolation & purification
- Phytochrome/metabolism
- Pigments, Biological/chemistry
- Pigments, Biological/genetics
- Pigments, Biological/isolation & purification
- Pigments, Biological/metabolism
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Kinases/chemistry
- Protein Kinases/genetics
- Protein Kinases/isolation & purification
- Protein Kinases/metabolism
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Sequence Homology, Amino Acid
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Affiliation(s)
- Allan C Froehlich
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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30
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Schmitt S, Prokisch H, Schlunck T, Camp DG, Ahting U, Waizenegger T, Scharfe C, Meitinger T, Imhof A, Neupert W, Oefner PJ, Rapaport D. Proteome analysis of mitochondrial outer membrane fromNeurospora crassa. Proteomics 2006; 6:72-80. [PMID: 16294304 DOI: 10.1002/pmic.200402084] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mitochondrial outer membrane mediates numerous interactions between the metabolic and genetic systems of mitochondria and the rest of the eukaryotic cell. We performed a proteomic study to discover novel functions of components of the mitochondrial outer membrane. Proteins of highly pure outer membrane vesicles (OMV) from Neurospora crassa were identified by a combination of LC-MS/MS of tryptic peptide digests and gel electrophoresis of solubilized OMV proteins, followed by their identification using MALDI-MS PMF. Among the 30 proteins found in at least three of four separate analyses were 23 proteins with known functions in the outer membrane. These included components of the import machinery (the TOM and TOB complexes), a pore-forming component (porin), and proteins that control fusion and fission of the organelle. In addition, proteins playing a role in various biosynthetic pathways, whose intracellular location had not been established previously, could be localized to the mitochondrial outer membrane. Thus, the proteome of the outer membrane can help in identifying new mitochondria-related functions.
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Affiliation(s)
- Simone Schmitt
- Institute for Physiological Chemistry, Ludwig-Maximillians-Universität, Butenandstrasse 5, 81377 Munich, Germany
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31
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Becker L, Bannwarth M, Meisinger C, Hill K, Model K, Krimmer T, Casadio R, Truscott KN, Schulz GE, Pfanner N, Wagner R. Preprotein translocase of the outer mitochondrial membrane: reconstituted Tom40 forms a characteristic TOM pore. J Mol Biol 2005; 353:1011-20. [PMID: 16213519 DOI: 10.1016/j.jmb.2005.09.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2005] [Revised: 09/06/2005] [Accepted: 09/07/2005] [Indexed: 11/23/2022]
Abstract
Tom40 is the central pore-forming component of the translocase of the outer mitochondrial membrane (TOM complex). Different views exist about the secondary structure and electrophysiological characteristics of Tom40 from Saccharomyces cerevisiae and Neurospora crassa. We have directly compared expressed and renatured Tom40 from both species and find a high content of beta-structure in circular dichroism measurements in agreement with refined secondary structure predictions. The electrophysiological characterization of renatured Tom40 reveals the same characteristics as the purified TOM complex or mitochondrial outer membrane vesicles, with two exceptions. The total conductance of the TOM complex and outer membrane vesicles is twofold higher than the total conductance of renatured Tom40, consistent with the presence of two TOM pores. TOM complex and outer membrane vesicles possess a strongly enhanced sensitivity to a mitochondrial presequence compared to Tom40 alone, in agreement with the presence of several presequence binding sites in the TOM complex, suggesting a role of the non-channel Tom proteins in regulating channel activity.
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Affiliation(s)
- Lars Becker
- Biophysik, Universität Osnabrück, FB Biologie/Chemie, D-49034 Osnabrück, Germany
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32
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Bathe F, Hahlen K, Dombi R, Driller L, Schliwa M, Woehlke G. The complex interplay between the neck and hinge domains in kinesin-1 dimerization and motor activity. Mol Biol Cell 2005; 16:3529-37. [PMID: 15901834 PMCID: PMC1182295 DOI: 10.1091/mbc.e04-11-0957] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Kinesin-1 dimerizes via the coiled-coil neck domain. In contrast to animal kinesins, neck dimerization of the fungal kinesin-1 NcKin requires additional residues from the hinge. Using chimeric constructs containing or lacking fungal-specific elements, the proximal part of the hinge was shown to stabilize the neck coiled-coil conformation in a complex manner. The conserved fungal kinesin hinge residue W384 caused neck coiled-coil formation in a chimeric NcKin construct, including parts of the human kinesin-1 stalk. The stabilizing effect was retained in a NcKinW384F mutant, suggesting important pi-stacking interactions. Without the stalk, W384 was not sufficient to induce coiled-coil formation, indicating that W384 is part of a cluster of several residues required for neck coiled-coil folding. A W384-less chimera of NcKin and human kinesin possessed a non-coiled-coil neck conformation and showed inhibited activity that could be reactivated when artificial interstrand disulfide bonds were used to stabilize the neck coiled-coil conformation. On the basis of yeast two-hybrid data, we propose that the proximal hinge can bind kinesin's cargo-free tail domain and causes inactivation of kinesin by disrupting the neck coiled-coil conformation.
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Affiliation(s)
- Friederike Bathe
- Department of Cell Biology, Adolf-Butenandt-Institute, University of Munich, D-80336 Munich, Germany
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33
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Park C, Bennion B, François IEJA, Ferket KKA, Cammue BPA, Thevissen K, Levery SB. Neutral glycolipids of the filamentous fungus Neurospora crassa: altered expression in plant defensin-resistant mutants. J Lipid Res 2005; 46:759-68. [PMID: 15654124 DOI: 10.1194/jlr.m400457-jlr200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To defend themselves against fungal pathogens, plants produce numerous antifungal proteins and peptides, including defensins, some of which have been proposed to interact with fungal cell surface glycosphingolipid components. Although not known as a phytopathogen, the filamentous fungus Neurospora crassa possesses numerous genes similar to those required for plant pathogenesis identified in fungal pathogens (Galagan, J. E., et al. 2003. Nature 422: 859-868), and it has been used as a model for studying plant-phytopathogen interactions targeting fungal membrane components (Thevissen, K., et al. 2003. Peptides. 24: 1705-1712). For this study, neutral glycolipid components were extracted from wild-type and plant defensin-resistant mutant strains of N. crassa. The structures of purified components were elucidated by NMR spectroscopy and mass spectrometry. Neutral glycosphingolipids of both wild-type and mutant strains were characterized as beta-glucopyranosylceramides, but those of the mutants were found with structurally altered ceramides. Although the wild type expressed a preponderance of N-2'-hydroxy-(E)-Delta3-octadecenoate as the fatty-N-acyl component attached to the long-chain base (4E,8E)-9-methyl-4,8-sphingadienine, the mutant ceramides were found with mainly N-2'-hydroxyhexadecanoate instead. In addition, the mutant strains expressed highly increased levels of a sterol glucoside identified as ergosterol-beta-glucoside. The potential implications of these findings with respect to defensin resistance in the N. crassa mutants are discussed.
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Affiliation(s)
- Chaeho Park
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
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34
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Yang J, Wang Y, Woolridge EM, Arora V, Petsko GA, Kozarich JW, Ringe D. Crystal structure of 3-carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida, a fumarase class II type cycloisomerase: enzyme evolution in parallel pathways. Biochemistry 2004; 43:10424-34. [PMID: 15301541 DOI: 10.1021/bi036205c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Carboxy-cis,cis-muconate lactonizing enzymes (CMLEs), the key enzymes in the protocatechuate branch of the beta-ketoadipate pathway in microorganisms, catalyze the conversion of 3-carboxy-cis,cis-muconate to muconolactones. We have determined the crystal structure of the prokaryotic Pseudomonas putida CMLE (PpCMLE) at 2.6 A resolution. PpCMLE is a homotetramer and belongs to the fumarase class II superfamily. The active site of PpCMLE is formed largely by three regions, which are moderately conserved in the fumarase class II superfamily, from three respective monomers. It has been proposed that residue His141, which is highly conserved in all fumarase class II enzymes and forms a charge relay with residue Glu275 (both His141 and Glu275 are in adenylosuccinate lyase numbering), acts as the general base in most fumarase class II superfamily members. However, this charge relay pair is broken in PpCMLE. The residues corresponding to His141 and Glu275 are Trp153 and Ala289, respectively, in PpCMLE. The structures of prokaryotic MLEs and that of CMLE from the eukaryotic Neurospora crassa are completely different from that of PpCMLE, indicating MLEs and CMLEs, as well as the prokaryotic and eukaryotic CMLEs, evolved from distinct ancestors, although they catalyze similar reactions. The structural differences may be related to recognition by substrates and to differences in the mechanistic pathways by which these enzymes catalyze their respective reactions.
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Affiliation(s)
- Jian Yang
- Rosenstiel Basic Medical Sciences Research Center and Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA
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35
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Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 2004; 68:1-108. [PMID: 15007097 PMCID: PMC362109 DOI: 10.1128/mmbr.68.1.1-108.2004] [Citation(s) in RCA: 434] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
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Affiliation(s)
- Katherine A Borkovich
- Department of Plant Pathology, University of California, Riverside, California 92521, USA. Katherine/
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36
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Abstract
Microtubules are highly dynamic components of the cytoskeleton. They are important for cell movement and they are involved in a variety of transport processes together with motor proteins, such as kinesin. The exact mechanism of these transport processes is not known and so far the focus has been on structural changes within the motor domains, but not within the underlying microtubule structure. Here we investigated the interaction between kinesin and tubulin and our experimental data show that microtubules themselves are changing structure during that process. We studied unstained, vitrified samples of microtubules composed of 15 protofilaments using cryo electron microscopy and helical image analysis. 3D maps of plain microtubules and microtubules decorated with kinesin have been reconstructed to approximately 17A resolution. The alphabeta-tubulin dimer could be identified and, according to our data, alpha- and beta-tubulin adopt different conformations in plain microtubules. Significant differences were detected between maps of plain microtubules and microtubule-kinesin complexes. Most pronounced is the continuous axial inter-dimer contact in the microtubule-kinesin complex, suggesting stabilized protofilaments along the microtubule axis. It seems, that mainly structural changes within alpha-tubulin are responsible for this observation. Lateral effects are less pronounced. Following our data, we believe, that microtubules play an active role in intracellular transport processes through modulations of their core structure.
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Affiliation(s)
- A Krebs
- European Molecular Biology Laboratory, Meyerhofstrasse1, 69117, Heidelberg, Germany.
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Ciccarelli FD, Izaurralde E, Bork P. The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. BMC Bioinformatics 2003; 4:64. [PMID: 14687415 PMCID: PMC319699 DOI: 10.1186/1471-2105-4-64] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Accepted: 12/19/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence. RESULTS We identified a new module, the PAM domain (PCI/PINT associated module), present in single subunits of well characterized multiprotein complexes, like the regulatory lid of the 26S proteasome, the COP-9 signalosome and the Sac3-Thp1 complex. This module is an around 200 residue long domain with a predicted TPR-like all-alpha-helical fold. CONCLUSIONS The occurrence of the PAM domain in specific subunits of multimeric protein complexes, together with the role of other all-alpha-helical folds in protein-protein interactions, suggest a function for this domain in mediating transient binding to diverse target proteins.
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Affiliation(s)
- Francesca D Ciccarelli
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 Heidelberg, Germany
- Max-Delbrueck-Centrum, PO Box 740238, D-13092 Berlin, Germany
| | - Elisa Izaurralde
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 Heidelberg, Germany
- Max-Delbrueck-Centrum, PO Box 740238, D-13092 Berlin, Germany
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38
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Paschen SA, Waizenegger T, Stan T, Preuss M, Cyrklaff M, Hell K, Rapaport D, Neupert W. Evolutionary conservation of biogenesis of β-barrel membrane proteins. Nature 2003; 426:862-6. [PMID: 14685243 DOI: 10.1038/nature02208] [Citation(s) in RCA: 330] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2003] [Accepted: 10/30/2003] [Indexed: 11/08/2022]
Abstract
The outer membranes of mitochondria and chloroplasts are distinguished by the presence of beta-barrel membrane proteins. The outer membrane of Gram-negative bacteria also harbours beta-barrel proteins. In mitochondria these proteins fulfil a variety of functions such as transport of small molecules (porin/VDAC), translocation of proteins (Tom40) and regulation of mitochondrial morphology (Mdm10). These proteins are encoded by the nucleus, synthesized in the cytosol, targeted to mitochondria as chaperone-bound species, recognized by the translocase of the outer membrane, and then inserted into the outer membrane where they assemble into functional oligomers. Whereas some knowledge has been accumulated on the pathways of insertion of proteins that span cellular membranes with alpha-helical segments, very little is known about how beta-barrel proteins are integrated into lipid bilayers and assembled into oligomeric structures. Here we describe a protein complex that is essential for the topogenesis of mitochondrial outer membrane beta-barrel proteins (TOB). We present evidence that important elements of the topogenesis of beta-barrel membrane proteins have been conserved during the evolution of mitochondria from endosymbiotic bacterial ancestors.
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Affiliation(s)
- Stefan A Paschen
- Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, D-81377 München, Germany
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Britton ME, Kapoor M. The oligomeric state, complex formation, and chaperoning activity of hsp70 and hsp80 of Neurospora crassa. Biochem Cell Biol 2003; 80:797-809. [PMID: 12555813 DOI: 10.1139/o02-166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Molecular chaperones perform vital cellular functions under normal growth conditions and protect cells against stress-induced damage. The stress proteins Hsp70 and Hsp80 of Neurospora crassa were extracted from heat-shocked mycelium, purified to near homogeneity, and examined with respect to their oligomeric state, complex formation, and chaperoning properties. Their oligomeric state was assessed by dynamic light-scattering measurements, and both Hsp70 and Hsp80 were observed to form a range of soluble, high-molecular-mass protein aggregates. Direct interaction between Hsp70 and Hsp80 was studied by partial tryptic digestion and surface plasmon resonance (SPR). Hsp70 was immobilized on the sensor chip surface, and the binding of Hsp80 in solution was followed in real time. Proteolytic digestion revealed that Hsp70-Hsp80 complex formation results in conformational changes in both proteins. The data from SPR studies yielded an equilibrium dissociation constant, KD, of 8.5 x 10(-9) M. The chaperoning ability of Hsp70, Hsp80, and Hsp70-Hsp80 was monitored in vitro by the protection of citrate synthase from thermal aggregation. The binding of nucleotides modulates the oligomeric state, chaperoning function, and hetero-oligomeric complex formation of Hsp70 and Hsp80.
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Affiliation(s)
- M E Britton
- Cellular, Molecular, and Microbial Biology Division, Department of Biological Sciences, The University of Calgary, Calgary, AB T2N 1N4, Canada
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40
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Zhang X, Zhu D, Wang D, Lin J, Qu Y, Yu S. [Study on xylose fermentation by Neurospora crassa]. Wei Sheng Wu Xue Bao 2003; 43:466-72. [PMID: 16276921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The influence of oxygen limitation and medium initial pH on xylose fermentation by Neurospora crassa AS 3.1602 was investigated. N. crassa AS 3.1602 has high ability of xylose fermentation producing ethanol and xylitol. Oxygen limitation has big influence on ethanol and xylitol production. The maximum conversion rate of ethanol was 63.2% obtained under semi-aerobic conditions. The maximum conversion rate of xylitol was 31.8% obtained under micro-aerobic conditions. Xylitol accumulation is behind the accumulation of ethanol. The optimal pH is 5.0 for ethanol fermentation, and 4.0 for xylitol fermentation, respectively. Xylose fermentation is greatly inhibited at high pH. The yields of ethanol and xylitol are greatly influenced by the initial concentration of xylose. The addition of glucose inhibits both the xylose utilization and the ethanol and xylitol production.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
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41
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Abstract
The effects of cold-shock on Neurospora crassa was here investigated. In cold-shock treated hyphae (6 h at 4 degrees C) the branching pattern was changed and dichotomy as well as a fan-like-pattern structure were temporarily detected at the tips. When exogenous Ca(2+) (500 mM) was added to the hyphae, these morphological alterations were not detected. In addition, the protein electrophoretic profile of cultures submitted to cold-shock was different from that of cultures kept at 30 degrees C. After 1 and 2 hours at 4 degrees C at least 5 bands were more intense than at 30 degrees C. The results suggest that cold-shock temporarily increases the synthesis of some proteins probably involved in the acclimatization process at 4 degrees C, and that the effects on morphology are probably due to damage to calcium influx.
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Affiliation(s)
- Cristina Yoshiko Kawano
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, CEP 14040-903--Ribeirão Preto--SP--Brasil
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42
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Schäfer F, Deluca D, Majdic U, Kirchner J, Schliwa M, Moroder L, Woehlke G. A conserved tyrosine in the neck of a fungal kinesin regulates the catalytic motor core. EMBO J 2003; 22:450-8. [PMID: 12554646 PMCID: PMC140721 DOI: 10.1093/emboj/cdg036] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The neck domain of fungal conventional kinesins displays characteristic properties which are reflected in a specific sequence pattern. The exchange of the strictly conserved Tyr 362, not present in animals, into Lys, Cys or Phe leads to a failure to dimerize. The destabilizing effect is confirmed by a lower coiled-coil propensity of mutant peptides. Whereas the Phe substitution has only a structural effect, the Lys and Cys replacements lead to dramatic kinetic changes. The steady state ATPase is 4- to 7-fold accelerated, which may be due to a faster microtubule-stimulated ADP release rate. These data suggest that an inhibitory effect of the fungal neck domain on the motor core is mediated by direct interaction of the aromatic ring of Tyr 362 with the head, whereas the OH group is essential for dimerization. This is the first demonstration of a direct influence of the kinesin neck region in regulation of the catalytic activity.
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Affiliation(s)
| | - Dominga Deluca
- Adolf Butenandt Institute, Cell Biology, University of Munich, Schillerstraße 42, D-80336 Munich and
Max Planck Institute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany Corresponding author e-mail:
| | | | | | | | - Luis Moroder
- Adolf Butenandt Institute, Cell Biology, University of Munich, Schillerstraße 42, D-80336 Munich and
Max Planck Institute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany Corresponding author e-mail:
| | - Günther Woehlke
- Adolf Butenandt Institute, Cell Biology, University of Munich, Schillerstraße 42, D-80336 Munich and
Max Planck Institute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany Corresponding author e-mail:
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43
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Taylor RD, McHale BJ, Nargang FE. Characterization of Neurospora crassa Tom40-deficient mutants and effect of specific mutations on Tom40 assembly. J Biol Chem 2003; 278:765-75. [PMID: 12399467 DOI: 10.1074/jbc.m208083200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The TOM complex (Translocase of the Outer mitochondrial Membrane) is responsible for the recognition of mitochondrial preproteins synthesized in the cytosol and for their translocation across or into the outer mitochondrial membrane. Tom40 is the major component of the TOM complex and forms the translocation pore. We have created a tom40 mutant of Neurospora crassa and have demonstrated that the gene is essential for the viability of the organism. Mitochondria with reduced levels of Tom40 were deficient for import of mitochondrial preproteins and contained reduced levels of the TOM complex components Tom22 and Tom6, suggesting that the import and/or stability of these proteins is dependent on the presence of Tom40. Mutant Tom40 preproteins were analyzed for their ability to be assembled into the TOM complex. In vitro import assays revealed that conserved regions near the N terminus (residues 51-60) and the C terminus (residues 321-323) of the 349-amino acid protein were required for assembly beyond a 250-kDa intermediate form. Mutant strains expressing Tom40 with residues 51-60 deleted were viable but exhibited growth defects. Slow growing mutants expressing Tom40, where residues 321-323 were changed to Ala residues, were isolated but showed TOM complex defects, whereas strains in which residues 321-323 were deleted could not be isolated. Analysis of the assembly of mutant Tom40 precursors in vitro supported a previous model in which Tom40 precursors progress from the 250-kDa intermediate to a 100-kDa form and then assemble into the 400-kDa TOM complex. Surprisingly, when wild type mitochondria containing Tom40 precursors arrested at the 250-kDa intermediate were treated with sodium carbonate, further assembly of intermediates into the TOM complex occurred, suggesting that disruption of protein-protein interactions may facilitate assembly. Import of wild type Tom40 precursor into mitochondria containing a mutant Tom40 lacking residues 40-48 revealed an alternate assembly pathway and demonstrated that the N-terminal region of pre-existing Tom40 molecules in the TOM complex plays a role in the assembly of incoming Tom40 molecules.
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Affiliation(s)
- Rebecca D Taylor
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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44
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Harrison KA, Marzluf GA. Characterization of DNA binding and the cysteine rich region of SRE, a GATA factor in Neurospora crassa involved in siderophore synthesis. Biochemistry 2002; 41:15288-95. [PMID: 12484767 DOI: 10.1021/bi0204995] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several homologous genes encoding proteins involved in regulating siderophore synthesis in fungi have been isolated, including the sre gene from the filamentous fungus Neurospora crassa. We present data that further characterize SRE and provide new insights into the regulation of iron homeostasis in Neurospora. SRE is a member of the GATA factor family, which is comprised of transcription factors that contain either one or two zinc finger motifs that recognize and bind to GATA-containing DNA sequences. Results from electrophoretic mobility shift assays demonstrate that SRE binds with high affinity to a DNA probe containing the iron response element from the sid1 promoter from Ustilago. SRE binding to DNA was demonstrated to be zinc-dependent. Moreover, changes in the spacing between two GATA sites altered the DNA binding affinity of SRE. Mutants of highly conserved cysteine residues present in SRE and homologous proteins were created by site-directed mutagenesis. The combined results of mobility shift assays, siderophore synthesis assays, and ornithine oxygenase enzyme activity determinations demonstrate that these mutants with cysteine substitutions have a dominant repressor phenotype.
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Affiliation(s)
- Kelly A Harrison
- The Ohio State Biochemistry Program and Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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45
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Collett MA, Garceau N, Dunlap JC, Loros JJ. Light and clock expression of the Neurospora clock gene frequency is differentially driven by but dependent on WHITE COLLAR-2. Genetics 2002; 160:149-58. [PMID: 11805052 PMCID: PMC1461937 DOI: 10.1093/genetics/160.1.149] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Visible light is thought to reset the Neurospora circadian clock by acting through heterodimers of the WHITE COLLAR-1 and WHITE COLLAR-2 proteins to induce transcription of the frequency gene. To characterize this photic entrainment we examined frq expression in constant light, under which condition the mRNA and protein of this clock gene were strongly induced. In continuous illumination FRQ accumulated in a highly phosphorylated state similar to that seen at subjective dusk, the time at which a step from constant light to darkness sets the clock. Examination of frq expression in several wc-2 mutant alleles surprisingly revealed differential regulation when frq expression was compared between constant light, following a light pulse, and darkness (clock-driven expression). Construction of a wc-2 null strain then demonstrated that WC-2 is absolutely required for both light and clock-driven frq expression, in contrast to previous expectations based on presumptive nulls containing altered Zn-finger function. Additionally, we found that frq light signal transduction differs from that of other light-regulated genes. Thus clock and light-driven frq expression is differentially regulated by, but dependent on, WC-2.
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Affiliation(s)
- Michael A Collett
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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46
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47
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Song YH, Marx A, Müller J, Woehlke G, Schliwa M, Krebs A, Hoenger A, Mandelkow E. Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules. EMBO J 2001; 20:6213-25. [PMID: 11707393 PMCID: PMC125725 DOI: 10.1093/emboj/20.22.6213] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ordered and enables one to describe the complete nucleotide-binding pocket, including three inter-switch salt bridges between switch 1 and 2. (ii) Loop 9 in the switch 1 region bends outwards, making the nucleotide-binding pocket very wide. The displacement in switch 1 resembles that of the G-protein ras complexed with its guanosine nucleotide exchange factor. (iii) Loop 5 in the entrance to the nucleotide-binding pocket is remarkably long and interacts with the ribose of ATP. (iv) The linker and neck region is not well defined, indicating that it is mobile. (v) Image reconstructions of ice-embedded microtubules decorated with NcKin show that it interacts with several tubulin subunits, including a central beta-tubulin monomer and the two flanking alpha-tubulin monomers within the microtubule protofilament. Comparison of NcKin with other kinesins, myosin and G-proteins suggests that the rate-limiting step of ADP release is accelerated in the fungal kinesin and accounts for the unusually high velocity and ATPase activity.
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Affiliation(s)
- Y.-H. Song
- Max-Planck Unit for Structural Molecular Biology, D-22607 Hamburg,
Department of Cell Biology, Ludwig-Maximilians-University, D-80336 München and EMBL, D-69117 Heidelberg, Germany Corresponding authors e-mail: or
| | | | | | - G. Woehlke
- Max-Planck Unit for Structural Molecular Biology, D-22607 Hamburg,
Department of Cell Biology, Ludwig-Maximilians-University, D-80336 München and EMBL, D-69117 Heidelberg, Germany Corresponding authors e-mail: or
| | - M. Schliwa
- Max-Planck Unit for Structural Molecular Biology, D-22607 Hamburg,
Department of Cell Biology, Ludwig-Maximilians-University, D-80336 München and EMBL, D-69117 Heidelberg, Germany Corresponding authors e-mail: or
| | - A. Krebs
- Max-Planck Unit for Structural Molecular Biology, D-22607 Hamburg,
Department of Cell Biology, Ludwig-Maximilians-University, D-80336 München and EMBL, D-69117 Heidelberg, Germany Corresponding authors e-mail: or
| | - A. Hoenger
- Max-Planck Unit for Structural Molecular Biology, D-22607 Hamburg,
Department of Cell Biology, Ludwig-Maximilians-University, D-80336 München and EMBL, D-69117 Heidelberg, Germany Corresponding authors e-mail: or
| | - E. Mandelkow
- Max-Planck Unit for Structural Molecular Biology, D-22607 Hamburg,
Department of Cell Biology, Ludwig-Maximilians-University, D-80336 München and EMBL, D-69117 Heidelberg, Germany Corresponding authors e-mail: or
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48
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Kallipolitou A, Deluca D, Majdic U, Lakämper S, Cross R, Meyhöfer E, Moroder L, Schliwa M, Woehlke G. Unusual properties of the fungal conventional kinesin neck domain from Neurospora crassa. EMBO J 2001; 20:6226-35. [PMID: 11707394 PMCID: PMC125726 DOI: 10.1093/emboj/20.22.6226] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fungal conventional kinesins are unusually fast microtubule motor proteins. To compare the functional organization of fungal and animal conventional kinesins, a set of C-terminal deletion mutants of the Neurospora crassa conventional kinesin, NcKin, was investigated for its biochemical and biophysical properties. While the shortest, monomeric construct comprising the catalytic core and the neck-linker (NcKin343) displays very high steady-state ATPase (k(cat) = 260/s), constructs including both the full neck and adjacent hinge domains (NcKin400, NcKin433 and NcKin480) show wild-type behaviour: they are dimeric, show fast gliding and slower ATP turnover rates (k(cat) = 60-84/s), and are chemically processive. Unexpectedly, a construct (NcKin378, corresponding to Drosophila KHC381) that includes just the entire coiled-coil neck is a monomer. Its ATPase activity is slow (k(cat) = 27/s), and chemical processivity is abolished. Together with a structural analysis of synthetic neck peptides, our data demonstrate that the NcKin neck domain behaves differently from that of animal conventional kinesins and may be tuned to drive fast, processive motility.
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Affiliation(s)
| | - Dominga Deluca
- Adolf-Butenandt-Institute, Cell Biology 1b, Universität München, Schillerstrasse 42, D-80336 Munich,
Max-Planck-Insitiute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Institute for Molecular and Cellular Physiology, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany and Molecular Motors Group, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Corresponding author e-mail:
| | | | - Stefan Lakämper
- Adolf-Butenandt-Institute, Cell Biology 1b, Universität München, Schillerstrasse 42, D-80336 Munich,
Max-Planck-Insitiute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Institute for Molecular and Cellular Physiology, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany and Molecular Motors Group, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Corresponding author e-mail:
| | - Robert Cross
- Adolf-Butenandt-Institute, Cell Biology 1b, Universität München, Schillerstrasse 42, D-80336 Munich,
Max-Planck-Insitiute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Institute for Molecular and Cellular Physiology, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany and Molecular Motors Group, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Corresponding author e-mail:
| | - Edgar Meyhöfer
- Adolf-Butenandt-Institute, Cell Biology 1b, Universität München, Schillerstrasse 42, D-80336 Munich,
Max-Planck-Insitiute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Institute for Molecular and Cellular Physiology, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany and Molecular Motors Group, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Corresponding author e-mail:
| | - Luis Moroder
- Adolf-Butenandt-Institute, Cell Biology 1b, Universität München, Schillerstrasse 42, D-80336 Munich,
Max-Planck-Insitiute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Institute for Molecular and Cellular Physiology, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany and Molecular Motors Group, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Corresponding author e-mail:
| | | | - Günther Woehlke
- Adolf-Butenandt-Institute, Cell Biology 1b, Universität München, Schillerstrasse 42, D-80336 Munich,
Max-Planck-Insitiute for Biochemistry, Department of Bioorganic Chemistry, Am Klopferspitz 18a, D-82152 Martinsried, Institute for Molecular and Cellular Physiology, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany and Molecular Motors Group, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK Corresponding author e-mail:
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Mackay JP, Matthews JM, Winefield RD, Mackay LG, Haverkamp RG, Templeton MD. The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures. Structure 2001; 9:83-91. [PMID: 11250193 DOI: 10.1016/s0969-2126(00)00559-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Fungal hydrophobin proteins have the remarkable ability to self-assemble into polymeric, amphipathic monolayers on the surface of aerial structures such as spores and fruiting bodies. These monolayers are extremely resistant to degradation and as such offer the possibility of a range of biotechnological applications involving the reversal of surface polarity. The molecular details underlying the formation of these monolayers, however, have been elusive. We have studied EAS, the hydrophobin from the ascomycete Neurospora crassa, in an effort to understand the structural aspects of hydrophobin polymerization. RESULTS We have purified both wild-type and uniformly 15N-labeled EAS from N. crassa conidia, and used a range of physical methods including multidimensional NMR spectroscopy to provide the first high resolution structural information on a member of the hydrophobin family. We have found that EAS is monomeric but mostly unstructured in solution, except for a small region of antiparallel beta sheet that is probably stabilized by four intramolecular disulfide bonds. Polymerised EAS appears to contain substantially higher amounts of beta sheet structure, and shares many properties with amyloid fibers, including a characteristic gold-green birefringence under polarized light in the presence of the dye Congo Red. CONCLUSIONS EAS joins an increasing number of proteins that undergo a disorder-->order transition in carrying out their normal function. This report is one of the few examples where an amyloid-like state represents the wild-type functional form. Thus the mechanism of amyloid formation, now thought to be a general property of polypeptide chains, has actually been applied in nature to form these remarkable structures.
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Affiliation(s)
- J P Mackay
- Department of Biochemistry, University of Sydney, NSW 2006, Sydney, Australia.
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Michiels PJ, Schouten CH, Hilbers CW, Heus HA. Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site. RNA 2000; 6:1821-32. [PMID: 11142381 PMCID: PMC1370051 DOI: 10.1017/s1355838200001394] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The cleavage site of the Neurospora VS RNA ribozyme is located in a separate hairpin domain containing a hexanucleotide internal loop with an A-C mismatch and two adjacent G-A mismatches. The solution structure of the internal loop and helix la of the ribozyme substrate hairpin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The 2 nt in the internal loop, flanking the cleavage site, a guanine and adenine, are involved in two sheared G.A base pairs similar to the magnesium ion-binding site of the hammerhead ribozyme. Adjacent to the tandem G.A base pairs, the adenine and cytidine, which are important for cleavage, form a noncanonical wobble A+-C base pair. The dynamic properties of the internal loop and details of the high-resolution structure support the view that the hairpin structure represents a ground state, which has to undergo a conformational change prior to cleavage. Results of chemical modification and mutagenesis data of the Neurospora VS RNA ribozyme can be explained in context with the present three-dimensional structure.
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Affiliation(s)
- P J Michiels
- NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands
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