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Sun X, LaVoie M, Lefebvre PA, Gallaher SD, Glaesener AG, Strenkert D, Mehta R, Merchant SS, Silflow CD. Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586359. [PMID: 38586028 PMCID: PMC10996464 DOI: 10.1101/2024.03.22.586359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation of HYDA1 transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of the HYDA1 promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termed cehc1-1 , leads to constitutive expression of HYDA1 and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway. CRR1 was required for the constitutive expression of the HYDA1 reporter gene in cehc1-1 mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized in cehc1-1 cells, supporting the conclusion that CEHC1 acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in the CRR1 pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
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Bouraoui A, Louzada RA, Aimeur S, Waeytens J, Wien F, My-Chan Dang P, Bizouarn T, Dupuy C, Baciou L. New insights in the molecular regulation of the NADPH oxidase 2 activity: Negative modulation by Poldip2. Free Radic Biol Med 2023; 199:113-125. [PMID: 36828293 DOI: 10.1016/j.freeradbiomed.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Poldip2 was shown to be involved in oxidative signaling to ensure certain biological functions. It was proposed that, in VSMC, by interaction with the Nox4-associated membrane protein p22phox, Poldip2 stimulates the level of reactive oxygen species (ROS) production. In vitro, with fractionated membranes from HEK393 cells over-expressing Nox4, we confirmed the up-regulation of NADPH oxidase 4 activity by the recombinant and purified Poldip2. Besides Nox4, the Nox1, Nox2, or Nox3 isoforms are also established partners of the p22phox protein raising the question of their regulation by Poldip2 and of the effect in cells expressing simultaneously different Nox isoforms. In this study, we have addressed this issue by investigating the potential regulatory role of Poldip2 on NADPH oxidase 2, present in phagocyte cells. Unexpectedly, the effect of Poldip2 on phagocyte NADPH oxidase 2 was opposite to that observed on NADPH oxidase 4. Using membranes from circulating resting neutrophils, the ROS production rate of NADPH oxidase 2 was down-regulated by Poldip2 (2.5-fold). The down-regulation effect could not be correlated to the interaction of Poldip2 with p22phox but rather, to the interaction of Poldip2 with the p47phox protein, one of the regulatory proteins of the phagocyte NADPH oxidase. Our results show that the interaction of Poldip2 with p47phox constitutes a novel regulatory mechanism that can negatively modulate the activity of NADPH oxidase 2 by trapping the so-called "adaptor" subunit of the complex. Poldip2 could act as a tunable switch capable of specifically regulating the activities of NADPH oxidases. This selective regulatory role of Poldip2, positive for Nox4 or negative for Nox2 could orchestrate the level and the type of ROS generated by Nox enzymes in the cells.
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Affiliation(s)
- Aicha Bouraoui
- Université Paris-Saclay, Institut de Chimie Physique UMR 8000, CNRS, 91405, Orsay Cedex, France
| | - Ruy Andrade Louzada
- Université Paris Saclay, UMR 9019 CNRS, Gustave Roussy, 94800, Villejuif, France
| | - Sana Aimeur
- Université Paris-Saclay, Institut de Chimie Physique UMR 8000, CNRS, 91405, Orsay Cedex, France
| | - Jehan Waeytens
- Université Paris-Saclay, Institut de Chimie Physique UMR 8000, CNRS, 91405, Orsay Cedex, France; Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium
| | - Frank Wien
- DISCO beamline, Synchrotron SOLEIL, Campus Paris-Saclay, 91192, Gif-sur-Yvette Cedex, France
| | - Pham My-Chan Dang
- INSERM U1149, CNRS ERL8252, Centre de Recherche sur l'Inflammation, Université de Paris, Laboratoire d'Excellence Inflamex, Faculté de Médecine, Site Xavier Bichat, Paris, F-75018, France
| | - Tania Bizouarn
- Université Paris-Saclay, Institut de Chimie Physique UMR 8000, CNRS, 91405, Orsay Cedex, France
| | - Corinne Dupuy
- Université Paris Saclay, UMR 9019 CNRS, Gustave Roussy, 94800, Villejuif, France
| | - Laura Baciou
- Université Paris-Saclay, Institut de Chimie Physique UMR 8000, CNRS, 91405, Orsay Cedex, France.
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Kulik AA, Maruszczak KK, Thomas DC, Nabi-Aldridge NLA, Carr M, Bingham RJ, Cooper CDO. Crystal structure and molecular dynamics of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability. Protein Sci 2021; 30:1196-1209. [PMID: 33884680 PMCID: PMC8138528 DOI: 10.1002/pro.4085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 01/02/2023]
Abstract
Polymerase δ‐interacting protein 2 (POLDIP2, PDIP38) is a multifaceted, “moonlighting” protein, involved in binding protein partners from many different cellular processes, including mitochondrial metabolism and DNA replication and repair. How POLDIP2 interacts with many different proteins is unknown. Towards this goal, we present the crystal structure of POLDIP2 to 2.8 Å, which exhibited a compact two‐domain β‐strand‐rich globular structure, confirmed by circular dichroism and small angle X‐ray scattering approaches. POLDIP2 comprised canonical DUF525 and YccV domains, but with a conserved domain linker packed tightly, resulting in an “extended” YccV module. A central channel was observed, which we hypothesize could influence structural changes potentially mediated by redox conditions, following observation of a modified cysteine residue in the channel. Unstructured regions were rebuilt by ab initio modelling to generate a model of full‐length POLDIP2. Molecular dynamics simulations revealed a highly dynamic N‐terminal region tethered to the YccV‐domain by an extended linker, potentially facilitating interactions with distal binding partners. Models of POLDIP2 complexed with two of its partners, PrimPol and PCNA, indicated that dynamic flexibility of the POLDIP2 N‐terminus and loop regions likely mediate protein interactions. PDB Code(s): 6Z9C;
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Affiliation(s)
- Anastasija A Kulik
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
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A Multifunctional Protein PolDIP2 in DNA Translesion Synthesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:35-45. [PMID: 32383114 DOI: 10.1007/978-3-030-41283-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Polymerase δ-interacting protein 2 (PolDIP2) is involved in the multiple protein-protein interactions and plays roles in many cellular processes including regulation of the nuclear redox environment, organization of the mitotic spindle and chromosome segregation, pre-mRNA processing, mitochondrial morphology and functions, cell migration and cellular adhesion. PolDIP2 is also a binding partner of high-fidelity DNA polymerase delta, PCNA and a number of translesion and repair DNA polymerases. The growing evidence suggests that PolDIP2 is a general regulatory protein in DNA damage response. However PolDIP2 functions in DNA translesion synthesis and repair are not fully understood. In this review, we address the functional interaction of PolDIP2 with human DNA polymerases and discuss the possible functions in DNA damage response.
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Bogdanović X, Palm GJ, Schwenteit J, Singh RK, Gudmundsdóttir BK, Hinrichs W. Structural evidence of intramolecular propeptide inhibition of the aspzincin metalloendopeptidase AsaP1. FEBS Lett 2016; 590:3280-94. [DOI: 10.1002/1873-3468.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Xenia Bogdanović
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Biochemistry and Molecular Biology; ZBMZ; Medical Faculty; University of Freiburg; Freiburg im Breisgau Germany
| | - Gottfried J. Palm
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | - Johanna Schwenteit
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Experimental Pathology; University of Iceland, Keldur; Reykjavík Iceland
| | - Rajesh K. Singh
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | | | - Winfried Hinrichs
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
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Krzysiak TC, Chen BB, Lear T, Mallampalli RK, Gronenborn AM. Crystal structure and interaction studies of the human FBxo3 ApaG domain. FEBS J 2016; 283:2091-101. [PMID: 27010866 DOI: 10.1111/febs.13721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 12/17/2022]
Abstract
UNLABELLED Transcriptional activation of proinflammatory cytokines, mediated by tumor necrosis factor receptor-associated factors (TRAFs), is in part triggered by the degradation of the F-box protein, FBxl2, via an E3 ligase that contains another F-box protein, FBxo3. The ApaG domain of FBxo3 is required for the interaction with and degradation of FBxl2 [Mallampalli RK et al., (2013) J Immunol 191, 5247-5255]. Here, we report the X-ray structure of the human FBxo3 ApaG domain, residues 278-407, at 2.0 Å resolution. Like bacterial ApaG proteins, this domain is characterized by a classic Immunoglobin/Fibronectin III-type fold, comprising a seven-stranded β-sheet core, surrounded by four extended loops. Although cation binding had been proposed for bacterial ApaG proteins, no interactions with Mg(2+) or Co(2+) were detected for the human ApaG domain. In addition, dinucleotide polyphosphates, which have been reported to be second messengers in the inflammation response and targets of the bacterial apaG-containing operon, are not bound by the human ApaG domain. In the context of the full-length protein, loop 1, comprising residues 294-303, is critical for the interaction with FBxl2. However, titration of the individual ApaG domain with a 15-mer FBxl2 peptide that was phosphorylated on the crucial T404, as well as the inability of the ApaG domain to interact with full-length FBxl2, assessed by coimmunoprecipitation, indicate that the ApaG domain alone is necessary, but not sufficient for binding and degradation of FBxl2. DATABASE PDB ID (5HDW).
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Affiliation(s)
- Troy C Krzysiak
- Department of Structural Biology, Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, PA, USA
| | - Bill B Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, USA.,Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine, PA, USA
| | - Travis Lear
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, USA.,Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine, PA, USA.,Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, PA, USA
| | - Rama K Mallampalli
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, USA.,Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine, PA, USA.,Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, PA, USA.,Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, PA, USA
| | - Angela M Gronenborn
- Department of Structural Biology, Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, PA, USA
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Bodelón G, Palomino C, Fernández LÁ. Immunoglobulin domains inEscherichia coliand other enterobacteria: from pathogenesis to applications in antibody technologies. FEMS Microbiol Rev 2013; 37:204-50. [DOI: 10.1111/j.1574-6976.2012.00347.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/07/2012] [Accepted: 06/14/2012] [Indexed: 11/28/2022] Open
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Paek S, Kawai F, Choi KJ, Yeo HJ. Crystal structure of the Campylobacter jejuni Cj0090 protein reveals a novel variant of the immunoglobulin fold among bacterial lipoproteins. Proteins 2012; 80:2804-9. [PMID: 22987763 DOI: 10.1002/prot.24182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 08/28/2012] [Accepted: 09/03/2012] [Indexed: 11/09/2022]
Abstract
Bacterial lipoproteins play an important role in bacterial pathogenesis and physiology. The genome of Campylobacter jejuni, a major foodborn pathogen, is predicted to contain over 20 lipoproteins. However, the functions of the majority of C. jejuni lipoproteins remain unknown. The Cj0090 protein is encoded by a lipoprotein operon composed of cj0089, cj0090, and cj0091. Here, we report the crystal structure of Cj0090 at 1.9 Å resolution, revealing a novel variant of the immunoglobulin fold with β-sandwich architecture. The structure suggests that Cj0090 may be involved in protein-protein interactions, consistent with a possible role for bacterial lipoproteins.
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Affiliation(s)
- Seonghee Paek
- Department of Biology and Biochemistry, University of Houston, TX 77204, USA
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A new member of the ribbon-helix-helix transcription factor superfamily from the plant pathogen Xanthomonas axonopodis pv. citri. J Struct Biol 2010; 170:21-31. [DOI: 10.1016/j.jsb.2009.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 11/11/2009] [Accepted: 12/22/2009] [Indexed: 11/19/2022]
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Falconi M, Oteri F, Eliseo T, Cicero DO, Desideri A. MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation. Biophys J 2008; 95:1108-17. [PMID: 18487311 PMCID: PMC2479573 DOI: 10.1529/biophysj.108.130849] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Accepted: 04/01/2008] [Indexed: 11/18/2022] Open
Abstract
The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.
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Affiliation(s)
- M Falconi
- Department of Biology and Center of Biostatistics and Bioinformatics, University of Rome Tor Vergata, Rome, Italy
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