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Karahoda B, Pfannenstiel BT, Sarikaya-Bayram Ö, Dong Z, Ho Wong K, Fleming AB, Keller NP, Bayram Ö. The KdmB-EcoA-RpdA-SntB (KERS) chromatin regulatory complex controls development, secondary metabolism and pathogenicity in Aspergillus flavus. Fungal Genet Biol 2023; 169:103836. [PMID: 37666447 PMCID: PMC10841535 DOI: 10.1016/j.fgb.2023.103836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
The filamentous fungus Aspergillus flavus is a plant and human pathogen predominantly found in the soil as spores or sclerotia and is capable of producing various secondary metabolites (SM) such as the carcinogenic mycotoxin aflatoxin. Recently, we have discovered a novel nuclear chromatin binding complex (KERS) that contains the JARID1-type histone demethylase KdmB, a putative cohesion acetyl transferase EcoA, a class I type histone deacetylase RpdA and the PHD ring finger reader protein SntB in the model filamentous fungus Aspergillus nidulans. Here, we show the presence of the KERS complex in A. flavus by immunoprecipitation-coupled mass spectrometry and constructed kdmBΔ and rpdAΔ strains to study their roles in fungal development, SM production and histone post-translational modifications (HPTMs). We found that KdmB and RpdA couple the regulation of SM gene clusters with fungal light-responses and HPTMs. KdmB and RpdA have opposing roles in light-induced asexual conidiation, while both factors are positive regulators of sclerotia development through the nsdC and nsdD pathway. KdmB and RpdA are essential for the productions of aflatoxin (similar to findings for SntB) as well as cyclopiazonic acid, ditryptophenaline and leporin B through controlling the respective SM biosynthetic gene clusters. We further show that both KdmB and RpdA regulate H3K4me3 and H3K9me3 levels, while RpdA also acts on H3K14ac levels in nuclear extracts. Therefore, the chromatin modifiers KdmB and RpdA of the KERS complex are key regulators for fungal development and SM metabolism in A. flavus.
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Affiliation(s)
- Betim Karahoda
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Brandon T Pfannenstiel
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | | | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau; Institute of Translational Medicine, University of Macau, Macau; Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau
| | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | - Özgür Bayram
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland.
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Bauer I, Sarikaya Bayram Ö, Bayram Ö. The use of immunoaffinity purification approaches coupled with LC-MS/MS offers a powerful strategy to identify protein complexes in filamentous fungi. Essays Biochem 2023; 67:877-892. [PMID: 37681641 DOI: 10.1042/ebc20220253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Fungi are a diverse group of organisms that can be both beneficial and harmful to mankind. They have advantages such as producing food processing enzymes and antibiotics, but they can also be pathogens and produce mycotoxins that contaminate food. Over the past two decades, there have been significant advancements in methods for studying fungal molecular biology. These advancements have led to important discoveries in fungal development, physiology, pathogenicity, biotechnology, and natural product research. Protein complexes and protein-protein interactions (PPIs) play crucial roles in fungal biology. Various methods, including yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC), are used to investigate PPIs. However, affinity-based PPI methods like co-immunoprecipitation (Co-IP) are highly preferred because they represent the natural conditions of PPIs. In recent years, the integration of liquid chromatography coupled with mass spectrometry (LC-MS/MS) has been used to analyse Co-IPs, leading to the discovery of important protein complexes in filamentous fungi. In this review, we discuss the tandem affinity purification (TAP) method and single affinity purification methods such as GFP, HA, FLAG, and MYC tag purifications. These techniques are used to identify PPIs and protein complexes in filamentous fungi. Additionally, we compare the efficiency, time requirements, and material usage of Sepharose™ and magnetic-based purification systems. Overall, the advancements in fungal molecular biology techniques have provided valuable insights into the complex interactions and functions of proteins in fungi. The methods discussed in this review offer powerful tools for studying fungal biology and will contribute to further discoveries in this field.
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Affiliation(s)
- Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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3
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Study of Humoral Responses against Lomentospora/ Scedosporium spp. and Aspergillus fumigatus to Identify L. prolificans Antigens of Interest for Diagnosis and Treatment. Vaccines (Basel) 2019; 7:vaccines7040212. [PMID: 31835471 PMCID: PMC6963885 DOI: 10.3390/vaccines7040212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/28/2022] Open
Abstract
The high mortality rates of Lomentospora prolificans infections are due, above all, to the tendency of the fungus to infect weakened hosts, late diagnosis and a lack of effective therapeutic treatments. To identify proteins of significance for diagnosis, therapy or prophylaxis, immunoproteomics-based studies are especially important. Consequently, in this study murine disseminated infections were carried out using L. prolificans, Scedosporium aurantiacum, Scedosporium boydii and Aspergillus fumigatus, and their sera used to identify the most immunoreactive proteins of L. prolificans total extract and secreted proteins. The results showed that L. prolificans was the most virulent species and its infections were characterized by a high fungal load in several organs, including the brain. The proteomics study showed a high cross-reactivity between Scedosporium/Lomentospora species, but not with A. fumigatus. Among the antigens identified were, proteasomal ubiquitin receptor, carboxypeptidase, Vps28, HAD-like hydrolase, GH16, cerato-platanin and a protein of unknown function that showed no or low homology with humans. Finally, Hsp70 deserves a special mention as it was the main antigen recognized by Scedosporium/Lomentospora species in both secretome and total extract. In conclusion, this study identifies antigens of L. prolificans that can be considered as potential candidates for use in diagnosis and as therapeutic targets and the production of vaccines.
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Chen D, Ito S, Yuan H, Hyodo T, Kadomatsu K, Hamaguchi M, Senga T. EML4 promotes the loading of NUDC to the spindle for mitotic progression. Cell Cycle 2016; 14:1529-39. [PMID: 25789526 DOI: 10.1080/15384101.2015.1026514] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Echinoderm microtubule-associated protein (EMAP)-like (EML) family proteins are microtubule-associated proteins that have a conserved hydrophobic EMAP-like protein (HELP) domain and multiple WD40 domains. In this study, we examined the role of EML4, which is a member of the EML family, in cell division. Time-lapse microscopy analysis demonstrated that EML4 depletion induced chromosome misalignment during metaphase and delayed anaphase initiation. Further analysis by immunofluorescence showed that EML4 was required for the organization of the mitotic spindle and for the proper attachment of kinetochores to microtubules. We searched for EML4-associating proteins by mass spectrometry analysis and found that the nuclear distribution gene C (NUDC) protein, which is a critical factor for the progression of mitosis, was associated with EML4. This interaction was mediated by the WD40 repeat of EML4 and by the C-terminus of NUDC. In the absence of EML4, NUDC was no longer able to localize to the mitotic spindle, whereas NUDC was dispensable for EML4 localization. Our results show that EML4 is critical for the loading of NUDC onto the mitotic spindle for mitotic progression.
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Affiliation(s)
- Dan Chen
- a Division of Cancer Biology; Nagoya University Graduate School of Medicine ; Nagoya , Japan
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5
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Cruz OHDL, Marchat LA, Guillén N, Weber C, Rosas IL, Díaz-Chávez J, Herrera L, Rojo-Domínguez A, Orozco E, López-Camarillo C. Multinucleation and Polykaryon Formation is Promoted by the EhPC4 Transcription Factor in Entamoeba histolytica. Sci Rep 2016; 6:19611. [PMID: 26792358 PMCID: PMC4726151 DOI: 10.1038/srep19611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/14/2015] [Indexed: 02/01/2023] Open
Abstract
Entamoeba histolytica is the intestinal parasite responsible for human amoebiasis that is a leading cause of death in developing countries. In this protozoan, heterogeneity in DNA content, polyploidy and genome plasticity have been associated to alterations in mechanisms controlling DNA replication and cell division. Studying the function of the transcription factor EhPC4, we unexpectedly found that it is functionally related to DNA replication, and multinucleation. Site-directed mutagenesis on the FRFPKG motif revealed that the K127 residue is required for efficient EhPC4 DNA-binding activity. Remarkably, overexpression of EhPC4 significantly increased cell proliferation, DNA replication and DNA content of trophozoites. A dramatically increase in cell size resulting in the formation of giant multinucleated trophozoites (polykaryon) was also found. Multinucleation event was associated to cytokinesis failure leading to abortion of ongoing cell division. Consistently, genome-wide profiling of EhPC4 overexpressing trophozoites revealed the up-regulation of genes involved in carbohydrates and nucleic acids metabolism, chromosome segregation and cytokinesis. Forced overexpression of one of these genes, EhNUDC (nuclear movement protein), led to alterations in cytokinesis and partially recapitulated the multinucleation phenotype. These data indicate for the first time that EhPC4 is associated with events related to polyploidy and genome stability in E. histolytica.
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Affiliation(s)
| | - Laurence A. Marchat
- National Polytechnic Institute, National School of Medicine and Homeopathy, Institutional Program of Molecular Biomedicine, Biotechnology Program, Mexico City, Mexico
| | - Nancy Guillén
- Institut Pasteur, Cellular Biology of Parasitism Unit, Paris, France
- INSERM U786, Paris, France
| | - Christian Weber
- Institut Pasteur, Cellular Biology of Parasitism Unit, Paris, France
- INSERM U786, Paris, France
| | - Itzel López Rosas
- Universidad Autonoma de la Ciudad de Mexico, Genomics Sciences Program, Mexico City, Mexico
| | - José Díaz-Chávez
- National Institute of Cancerology, Carcinogenesis Laboratory, Mexico City, Mexico
| | - Luis Herrera
- National Institute of Cancerology, Carcinogenesis Laboratory, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Metropolitan Autonomous University, Natural Sciences Department, Mexico City, Mexico
| | - Esther Orozco
- Center for Research and Advanced Studies of the National Polytechnic Institute, Department of Infectomics and Molecular Pathogenesis, Mexico City, Mexico
| | - César López-Camarillo
- Universidad Autonoma de la Ciudad de Mexico, Genomics Sciences Program, Mexico City, Mexico
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6
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Beckmann EA, Köhler AM, Meister C, Christmann M, Draht OW, Rakebrandt N, Valerius O, Braus GH. Integration of the catalytic subunit activates deneddylase activity in vivo as final step in fungal COP9 signalosome assembly. Mol Microbiol 2015; 97:110-24. [PMID: 25846252 DOI: 10.1111/mmi.13017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2015] [Indexed: 12/23/2022]
Abstract
The eight-subunit COP9 signalosome (CSN) is conserved from filamentous fungi to humans and functions at the interface between cellular signalling and protein half-life control. CSN consists of six PCI and two MPN domain proteins and forms a scaffold for additional interacting proteins. CSN controls protein stability in the ubiquitin-proteasome system where the MPN domain CSN5/CsnE subunit inactivates cullin-RING ligases. The CSN5/CsnE isopeptidase functions as deneddylase and removes the ubiquitin-like protein Nedd8. The six PCI domain proteins of human CSN form a horseshoe-like ring and all eight subunits are connected by a bundle of C-terminal α-helices. We show that single deletions of any csn subunit of Aspergillus nidulans resulted in the lack of deneddylase activity and identical defects in the coordination of development and secondary metabolism. The CSN1/CsnA N-terminus is dispensable for deneddylase activity but required for asexual spore formation. Complex analyses in mutant strains revealed the presence of a seven-subunit pre-CSN without catalytic activity. Reconstitution experiments with crude extracts of deletion strains and recombinant proteins allowed the integration of CSN5/CsnE into pre-CSN resulting in an active deneddylase. This supports a stable seven subunit pre-CSN intermediate where deneddylase activation in vivo can be controlled by CSN5/CsnE integration as final assembly step.
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Affiliation(s)
- Elena A Beckmann
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Anna M Köhler
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Cindy Meister
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Martin Christmann
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Oliver W Draht
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Nikolas Rakebrandt
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Oliver Valerius
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Gerhard H Braus
- Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
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7
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Christmann M, Schmaler T, Gordon C, Huang X, Bayram Ö, Schinke J, Stumpf S, Dubiel W, Braus GH. Control of multicellular development by the physically interacting deneddylases DEN1/DenA and COP9 signalosome. PLoS Genet 2013; 9:e1003275. [PMID: 23408908 PMCID: PMC3567183 DOI: 10.1371/journal.pgen.1003275] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 12/11/2012] [Indexed: 11/18/2022] Open
Abstract
Deneddylases remove the ubiquitin-like protein Nedd8 from modified proteins. An increased deneddylase activity has been associated with various human cancers. In contrast, we show here that a mutant strain of the model fungus Aspergillus nidulans deficient in two deneddylases is viable but can only grow as a filament and is highly impaired for multicellular development. The DEN1/DenA and the COP9 signalosome (CSN) deneddylases physically interact in A. nidulans as well as in human cells, and CSN targets DEN1/DenA for protein degradation. Fungal development responds to light and requires both deneddylases for an appropriate light reaction. In contrast to CSN, which is necessary for sexual development, DEN1/DenA is required for asexual development. The CSN-DEN1/DenA interaction that affects DEN1/DenA protein levels presumably balances cellular deneddylase activity. A deneddylase disequilibrium impairs multicellular development and suggests that control of deneddylase activity is important for multicellular development. The family of small ubiquitin-like (Ubl) proteins plays a major role in the control of stability, activity, or localization of modified target proteins in a eukaryotic cell. Lysine side chains are modified by covalent Ubl attachment, and this process can be reversed by specific proteases. Nedd8 is the closest relative to ubiquitin in the Ubl family. We describe here a novel, conserved interplay between two physically interacting deneddylases that are specific for Nedd8. Increased deneddylase activity had been shown to be associated with human cancers. We convey here specific distinct developmental functions of the two deneddylases in multicellular differentiation of the filamentous fungus Aspergillus nidulans. The physical interaction between both proteins affects protein stability and therefore cellular deneddylase activity. The equilibrium between the two deneddylases and their physical interaction are conserved from fungi to human and seem to be important for normal development of a multicellular organism. These findings open a different angle for future studies of tumor formation in humans.
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Affiliation(s)
- Martin Christmann
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Tilo Schmaler
- Department of General, Visceral, Vascular and Thoracic Surgery, Division of Molecular Biology, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Colin Gordon
- Medical Research Council, Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Xiaohua Huang
- Department of General, Visceral, Vascular and Thoracic Surgery, Division of Molecular Biology, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Josua Schinke
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Sina Stumpf
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Wolfgang Dubiel
- Department of General, Visceral, Vascular and Thoracic Surgery, Division of Molecular Biology, Charité–Universitätsmedizin Berlin, Berlin, Germany
- * E-mail: (WD); (GHB)
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail: (WD); (GHB)
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8
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Live-cell visualization of intracellular interaction between a nuclear migration protein (hNUDC) and the thrombopoietin receptor (Mpl). PLoS One 2012; 7:e51849. [PMID: 23284788 PMCID: PMC3524126 DOI: 10.1371/journal.pone.0051849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 11/07/2012] [Indexed: 11/29/2022] Open
Abstract
We previously demonstrated that endogenous hNUDC and Mpl co-localized in the perinuclear and cytoplasmic regions of megakaryocyte cells by indirect immunofluorescence. We further reported that hNUDC accumulated in the Golgi when NIH 3T3 cells were transfected with an hNUDC expression vector alone. However, co-transfection with hNUDC and Mpl expression vectors caused both proteins to co-localize predominantly in the cytosol. These observations led us to hypothesize that a complex containing hNUDC and Mpl may alter hNUDC subcellular location and induce its secretion. In the present study, we test this hypothesis by employing bimolecular fluorescence complementation (BiFC) to detect and visualize the complex formation of hNUDC/Mpl in living cells. We further examined in detail the subcellular locations of the hNUDC/Mpl complex by co-transfection of BiFC chimeras with known subcellular markers. The distribution of hNUDC/Mpl in the endoplasmic reticulum (ER), Golgi and cell surface was determined. Furthermore, the N-terminal 159 amino acids of hNUDC, but not C-terminal half, bound to Mpl in vivo and exhibited a similar localization pattern to that of full-length hNUDC in Cos-1 cells. Adenovirus-mediated overexpression of hNUDC or its N-terminal 159 residues in a human megakaryocyte cell line (Dami) resulted in increased levels of hNUDC or hNUDC(1-159) secretion. In contrast, depletion of Mpl by transfecting Dami cells with adenovirus bearing Mpl-targeting siRNA significantly blocked hNUDC secretion. Thus, we provide the first evidence that the N-terminal region of hNUDC contains all of the necessary information to complex with Mpl and traffic through the secretory pathway.
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von Zeska Kress MR, Harting R, Bayram Ö, Christmann M, Irmer H, Valerius O, Schinke J, Goldman GH, Braus GH. The COP9 signalosome counteracts the accumulation of cullin SCF ubiquitin E3 RING ligases during fungal development. Mol Microbiol 2012; 83:1162-77. [PMID: 22329854 DOI: 10.1111/j.1365-2958.2012.07999.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Defects in the COP9 signalosome (CSN) impair multicellular development, including embryonic plant or animal death or a block in sexual development of the fungus Aspergillus nidulans. CSN deneddylates cullin-RING ligases (CRLs), which are activated by covalent linkage to ubiquitin-like NEDD8. Deneddylation allows CRL disassembly for subsequent reassembly. An attractive hypothesis is a consecutive order of CRLs for development, which demands repeated cycles of neddylation and deneddylation for reassembling CRLs. Interruption of these cycles could explain developmental blocks caused by csn mutations. This predicts an accumulation of neddylated CRLs exhibiting developmental functions when CSN is dysfunctional. We tested this hypothesis in A. nidulans, which tolerates reduced levels of neddylation for growth. We show that only genes for CRL subunits or neddylation are essential, whereas CSN is primarily required for development. We used functional tagged NEDD8, recruiting all three fungal cullins. Cullins are associated with the CSN1/CsnA subunit when deneddylation is defective. Two CRLs were identified which are specifically involved in differentiation and accumulate during the developmental block. This suggests that an active CSN complex is required to counteract the accumulation of specific CRLs during development.
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Affiliation(s)
- Marcia Regina von Zeska Kress
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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10
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Identification of protein complexes from filamentous fungi with tandem affinity purification. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 944:191-205. [PMID: 23065618 DOI: 10.1007/978-1-62703-122-6_14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fungal molecular biology has benefited from the enormous advances in understanding protein-protein interactions in prokaryotic or eukaryotic organisms of the past decade. Tandem affinity purification (TAP) allows the enrichment of native protein complexes from cell extracts under mild conditions. We codon-optimized tags and established TAP, previously not applicable to filamentous fungi, for the model organism Aspergillus nidulans. We could identify by this method the trimeric Velvet complex VelB/VeA/LaeA or the eight subunit COP9 signalosome. Here, we describe an optimized protocol for A. nidulans which can also be adapted to other filamentous fungi.
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11
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Zheng M, Cierpicki T, Burdette AJ, Utepbergenov D, Janczyk PŁ, Derewenda U, Stukenberg PT, Caldwell KA, Derewenda ZS. Structural features and chaperone activity of the NudC protein family. J Mol Biol 2011; 409:722-41. [PMID: 21530541 DOI: 10.1016/j.jmb.2011.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/07/2011] [Accepted: 04/07/2011] [Indexed: 11/19/2022]
Abstract
The NudC family consists of four conserved proteins with representatives in all eukaryotes. The archetypal nudC gene from Aspergillus nidulans is a member of the nud gene family that is involved in the maintenance of nuclear migration. This family also includes nudF, whose human orthologue, Lis1, codes for a protein essential for brain cortex development. Three paralogues of NudC are known in vertebrates: NudC, NudC-like (NudCL), and NudC-like 2 (NudCL2). The fourth distantly related member of the family, CML66, contains a NudC-like domain. The three principal NudC proteins have no catalytic activity but appear to play as yet poorly defined roles in proliferating and dividing cells. We present crystallographic and NMR studies of the human NudC protein and discuss the results in the context of structures recently deposited by structural genomics centers (i.e., NudCL and mouse NudCL2). All proteins share the same core CS domain characteristic of proteins acting either as cochaperones of Hsp90 or as independent small heat shock proteins. However, while NudC and NudCL dimerize via an N-terminally located coiled coil, the smaller NudCL2 lacks this motif and instead dimerizes as a result of unique domain swapping. We show that NudC and NudCL, but not NudCL2, inhibit the aggregation of several target proteins, consistent with an Hsp90-independent heat shock protein function. Importantly, and in contrast to several previous reports, none of the three proteins is able to form binary complexes with Lis1. The availability of structural information will be of help in further studies on the cellular functions of the NudC family.
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Affiliation(s)
- Meiying Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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12
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Helmstaedt K, Schwier EU, Christmann M, Nahlik K, Westermann M, Harting R, Grond S, Busch S, Braus GH. Recruitment of the inhibitor Cand1 to the cullin substrate adaptor site mediates interaction to the neddylation site. Mol Biol Cell 2010; 22:153-64. [PMID: 21119001 PMCID: PMC3016973 DOI: 10.1091/mbc.e10-08-0732] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cand1 inhibits cullin RING ubiquitin ligases by binding unneddylated cullins. The Cand1 N-terminus blocks the cullin neddylation site, whereas the C-terminus inhibits cullin adaptor interaction. These Cand1 binding sites can be separated into two functional polypeptides which bind sequentially. C-terminal Cand1 can directly bind to unneddylated cullins in the nucleus without blocking the neddylation site. The smaller N-terminal Cand1 cannot bind to the cullin neddylation region without C-terminal Cand1. The separation of a single cand1 into two independent genes represents the in vivo situation of the fungus Aspergillus nidulans, where C-terminal Cand1 recruits smaller N-terminal Cand1 in the cytoplasm. Either deletion results in an identical developmental and secondary metabolism phenotype in fungi, which resembles csn mutants deficient in the COP9 signalosome (CSN) deneddylase. We propose a two-step Cand1 binding to unneddylated cullins which initiates at the adaptor binding site and subsequently blocks the neddylation site after CSN has left.
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Affiliation(s)
- Kerstin Helmstaedt
- Institute of Microbiology and Genetics, Georg-August-Universität, D-37077 Göttingen, Germany
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13
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Valinluck M, Ahlgren S, Sawada M, Locken K, Banuett F. Role of the nuclear migration protein Lis1 in cell morphogenesis in Ustilago maydis. Mycologia 2010; 102:493-512. [PMID: 20524583 DOI: 10.3852/09-193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ustilago maydis is a basidiomycete fungus that exhibits a yeast-like and a filamentous form. Growth of the fungus in the host leads to additional morphological transitions. The different morphologies are characterized by distinct nuclear movements. Dynein and alpha-tubulin are required for nuclear movements and for cell morphogenesis of the yeast-like form. Lis1 is a microtubule plus-end tracking protein (+TIPs) conserved in eukaryotes and required for nuclear migration and spindle positioning. Defects in nuclear migration result in altered cell fate and aberrant development in metazoans, slow growth in fungi and disease in humans (e.g. lissencephaly). Here we investigate the role of the human LIS1 homolog in U. maydis and demonstrate that it is essential for cell viability, not previously seen in other fungi. With a conditional null mutation we show that lis1 is necessary for nuclear migration in the yeast-like cell and during the dimorphic transition. Studies of asynchronous exponentially growing cells and time-lapse microscopy uncovered novel functions of lis1: It is necessary for cell morphogenesis, positioning of the septum and cell wall integrity. lis1-depleted cells exhibit altered axes of growth and loss of cell polarity leading to grossly aberrant cells with clusters of nuclei and morphologically altered buds devoid of nuclei. Altered septum positioning and cell wall deposition contribute to the aberrant morphology. lis1-depleted cells lyse, indicative of altered cell wall properties or composition. We also demonstrate, with indirect immunofluorescence to visualize tubulin, that lis1 is necessary for the normal organization of the microtubule cytoskeleton: lis1-depleted cells contain more and longer microtubules that can form coils perpendicular to the long axis of the cell. We propose that lis1 controls microtubule dynamics and thus the regulated delivery of vesicles to growth sites and other cell domains that govern nuclear movements.
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Affiliation(s)
- Michael Valinluck
- Department of Biological Sciences, California State University, 1250 Bellflower Boulevard, Long Beach, California 90840 USA
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Cao Z, Jia Z, Liu Y, Wang M, Zhao J, Zheng J, Wang G. Constitutive expression of ZmsHSP in Arabidopsis enhances their cytokinin sensitivity. Mol Biol Rep 2010; 37:1089-97. [PMID: 19821154 DOI: 10.1007/s11033-009-9848-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 09/28/2009] [Indexed: 01/15/2023]
Abstract
A small HSP gene, ZmsHSP, was isolated from Zea mays. Sequence analysis revealed that the open reading frame of ZmsHSP was 477 bp and that it encodes a protein composed of 159 amino acid residues with a calculated molecular mass of 18.17 kD and a predicated isoelectric point (pI) of 5.63. ZmsHSP contains a CS domain (p23-like domain) and shares similarity with the HSP90 co-chaperone p23. The expression level of ZmsHSP was different among various tissues with the highest expression in leaves and the lowest in silks. Results also showed that the expression of ZmsHSP in maize was significantly up-regulated by dehydration. Transgenic Arabidopsis plants overexpressing ZmsHSP under the control of the CaMV 35S promoter had lower endogenous cytokinin content and showed more sensitivity to cytokinin during the germination and early seedling stage than wild-type plants, suggesting that ZmsHSP might has a function in cytokinin response in Zea mays.
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Affiliation(s)
- Zuping Cao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
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Jurkuta RJ, Kaplinsky NJ, Spindel JE, Barton MK. Partitioning the apical domain of the Arabidopsis embryo requires the BOBBER1 NudC domain protein. THE PLANT CELL 2009; 21:1957-71. [PMID: 19648297 PMCID: PMC2729608 DOI: 10.1105/tpc.108.065284] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 06/24/2009] [Accepted: 07/09/2009] [Indexed: 05/20/2023]
Abstract
The apical domain of the embryo is partitioned into distinct regions that will give rise to the cotyledons and the shoot apical meristem. In this article, we describe a novel screen to identify Arabidopsis thaliana embryo arrest mutants that are defective in this partitioning, and we describe the phenotype of one such mutant, bobber1. bobber1 mutants arrest at the globular stage of development, they express the meristem-specific SHOOTMERISTEMLESS gene throughout the top half of the embryo, and they fail to express the AINTEGUMENTA transcript normally found in cotyledons. Thus, BOBBER1 is required to limit the extent of the meristem domain and/or to promote the development of the cotyledon domains. Based on expression of early markers for apical development, bobber1 mutants differentiate protodermis and undergo normal early apical development. Consistent with a role for auxin in cotyledon development, BOBBER1 mutants fail to express localized maxima of the DR5:green fluorescent protein reporter. BOBBER1 encodes a protein with homology to the Aspergillus nidulans protein NUDC that has similarity to protein chaperones, indicating a possible role for BOBBER1 in synthesis or transport of proteins involved in patterning the Arabidopsis embryo.
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Affiliation(s)
- Rebecca Joy Jurkuta
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
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Riera J, Lazo PS. The mammalian NudC-like genes: a family with functions other than regulating nuclear distribution. Cell Mol Life Sci 2009; 66:2383-90. [PMID: 19381437 PMCID: PMC11115750 DOI: 10.1007/s00018-009-0025-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/25/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022]
Abstract
Nuclear distribution gene C homolog (NudC) is a highly conserved gene. It has been identified in different species from fungi to mammals. The high degree of conservation, in special in the nudC domain, suggests that they are genes with essential functions. Most of the identified genes in the family have been implicated in cell division through the regulation of cytoplasmic dynein. As for mammalian genes, human NUDC has been implicated in the migration and proliferation of tumor cells and has therefore been considered a possible therapeutic target. There is evidence suggesting that mammalian NudC is also implicated in the regulation of the inflammatory response and in thrombopoiesis. The presence of these other functions not related to the interaction with molecular motors agrees with that these genes and their products are larger in size than their microbial orthologous, indicating that they have evolved to convey additional features.
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Affiliation(s)
- José Riera
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Campus del Cristo, 33071 Oviedo, Spain
| | - Pedro S. Lazo
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Campus del Cristo, 33071 Oviedo, Spain
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