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Karjalainen M, Tossavainen H, Hellman M, Permi P. HACANCOi: a new H α-detected experiment for backbone resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:741-752. [PMID: 33118136 PMCID: PMC7701164 DOI: 10.1007/s10858-020-00347-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns timescale dynamics ensures long transverse (T2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. 1Hα-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D 1Hα-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates 1Hαi, 13Cαi, 15Ni and [Formula: see text] spins by transferring the magnetization concomitantly from 13Cαi to 15Ni and [Formula: see text]. The B1 domain of protein G (GB1), and the enteropathogenic E. coli EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.
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Affiliation(s)
- Mikael Karjalainen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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3
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Christensen LF, Staby L, Bugge K, O'Shea C, Kragelund BB, Skriver K. Evolutionary conservation of the intrinsic disorder-based Radical-Induced Cell Death1 hub interactome. Sci Rep 2019; 9:18927. [PMID: 31831797 PMCID: PMC6908617 DOI: 10.1038/s41598-019-55385-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/27/2019] [Indexed: 01/08/2023] Open
Abstract
Radical-Induced Cell Death1 (RCD1) functions as a cellular hub interacting with intrinsically disordered transcription factor regions, which lack a well-defined three-dimensional structure, to regulate plant stress. Here, we address the molecular evolution of the RCD1-interactome. Using bioinformatics, its history was traced back more than 480 million years to the emergence of land plants with the RCD1-binding short linear motif (SLiM) identified from mosses to flowering plants. SLiM variants were biophysically verified to be functional and to depend on the same RCD1 residues as the DREB2A transcription factor. Based on this, numerous additional members may be assigned to the RCD1-interactome. Conservation was further strengthened by similar intrinsic disorder profiles of the transcription factor homologs. The unique structural plasticity of the RCD1-interactome, with RCD1-binding induced α-helix formation in DREB2A, but not detectable in ANAC046 or ANAC013, is apparently conserved. Thermodynamic analysis also indicated conservation with interchangeability between Arabidopsis and soybean RCD1 and DREB2A, although with fine-tuned co-evolved binding interfaces. Interruption of conservation was observed, as moss DREB2 lacked the SLiM, likely reflecting differences in plant stress responses. This whole-interactome study uncovers principles of the evolution of SLiM:hub-interactions, such as conservation of α-helix propensities, which may be paradigmatic for disorder-based interactomes in eukaryotes.
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Affiliation(s)
- Lise Friis Christensen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Lasse Staby
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Katrine Bugge
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Charlotte O'Shea
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Birthe B Kragelund
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.
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4
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Rissel D, Peiter E. Poly(ADP-Ribose) Polymerases in Plants and Their Human Counterparts: Parallels and Peculiarities. Int J Mol Sci 2019; 20:E1638. [PMID: 30986964 PMCID: PMC6479469 DOI: 10.3390/ijms20071638] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/25/2022] Open
Abstract
Poly(ADP-ribosyl)ation is a rapid and transient post-translational protein modification that was described first in mammalian cells. Activated by the sensing of DNA strand breaks, poly(ADP-ribose)polymerase1 (PARP1) transfers ADP-ribose units onto itself and other target proteins using NAD⁺ as a substrate. Subsequently, DNA damage responses and other cellular responses are initiated. In plants, poly(ADP-ribose) polymerases (PARPs) have also been implicated in responses to DNA damage. The Arabidopsis genome contains three canonical PARP genes, the nomenclature of which has been uncoordinated in the past. Albeit assumptions concerning the function and roles of PARP proteins in planta have often been inferred from homology and structural conservation between plant PARPs and their mammalian counterparts, plant-specific roles have become apparent. In particular, PARPs have been linked to stress responses of plants. A negative role under abiotic stress has been inferred from studies in which a genetic or, more commonly, pharmacological inhibition of PARP activity improved the performance of stressed plants; in response to pathogen-associated molecular patterns, a positive role has been suggested. However, reports have been inconsistent, and the effects of PARP inhibitors appear to be more robust than the genetic abolition of PARP gene expression, indicating the presence of alternative targets of those drugs. Collectively, recent evidence suggests a conditionality of stress-related phenotypes of parp mutants and calls for a reconsideration of PARP inhibitor studies on plants. This review critically summarizes our current understanding of poly(ADP-ribosylation) and PARP proteins in plants, highlighting similarities and differences to human PARPs, areas of controversy, and requirements for future studies.
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Affiliation(s)
- Dagmar Rissel
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany.
- Agrochemisches Institut Piesteritz e.V. (AIP), Möllensdorfer Strasse 13, 06886 Lutherstadt Wittenberg, Germany.
- Institute for Plant Protection in Field Crops and Grassland, Julius Kühn-Institut (JKI), 38104 Braunschweig, Germany.
| | - Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany.
- Agrochemisches Institut Piesteritz e.V. (AIP), Möllensdorfer Strasse 13, 06886 Lutherstadt Wittenberg, Germany.
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5
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Shapiguzov A, Vainonen JP, Hunter K, Tossavainen H, Tiwari A, Järvi S, Hellman M, Aarabi F, Alseekh S, Wybouw B, Van Der Kelen K, Nikkanen L, Krasensky-Wrzaczek J, Sipari N, Keinänen M, Tyystjärvi E, Rintamäki E, De Rybel B, Salojärvi J, Van Breusegem F, Fernie AR, Brosché M, Permi P, Aro EM, Wrzaczek M, Kangasjärvi J. Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 2019; 8:43284. [PMID: 30767893 PMCID: PMC6414205 DOI: 10.7554/elife.43284] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/14/2019] [Indexed: 01/17/2023] Open
Abstract
Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles. Most plant cells contain two types of compartments, the mitochondria and the chloroplasts, which work together to supply the chemical energy required by life processes. Genes located in another part of the cell, the nucleus, encode for the majority of the proteins found in these compartments. At any given time, the mitochondria and the chloroplasts send specific, ‘retrograde’ signals to the nucleus to turn on or off the genes they need. For example, mitochondria produce molecules known as reactive oxygen species (ROS) if they are having problems generating energy. These molecules activate several regulatory proteins that move into the nucleus and switch on MDS genes, a set of genes which helps to repair the mitochondria. Chloroplasts also produce ROS that can act as retrograde signals. It is still unclear how the nucleus integrates signals from both chloroplasts and mitochondria to ‘decide’ which genes to switch on, but a protein called RCD1 may play a role in this process. Indeed, previous studies have found that Arabidopsis plants that lack RCD1 have defects in both their mitochondria and chloroplasts. In these mutant plants, the MDS genes are constantly active and the chloroplasts have problems making ROS. To investigate this further, Shapiguzov, Vainonen et al. use biochemical and genetic approaches to study RCD1 in Arabidopsis. The experiments confirm that this protein allows a dialog to take place between the retrograde signals of both mitochondria and chloroplasts. On one hand, RCD1 binds to and inhibits the regulatory proteins that usually activate the MDS genes under the control of mitochondria. This explains why, in the absence of RCD1, the MDS genes are always active, which is ultimately disturbing how these compartments work. On the other hand, RCD1 is also found to be sensitive to the ROS that chloroplasts produce. This means that chloroplasts may be able to affect when mitochondria generate energy by regulating the protein. Finally, further experiments show that MDS genes can affect both mitochondria and chloroplasts: by influencing how these genes are regulated, RCD1 therefore acts on the two types of compartments. Overall, the work by Shapiguzov, Vainonen et al. describes a new way Arabidopsis coordinates its mitochondria and chloroplasts. Further studies will improve our understanding of how plants regulate these compartments in different environments to produce the energy they need. In practice, this may also help plant breeders create new varieties of crops that produce energy more efficiently and which better resist to stress.
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Affiliation(s)
- Alexey Shapiguzov
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Julia P Vainonen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Kerri Hunter
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Arjun Tiwari
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Sari Järvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Fayezeh Aarabi
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Brecht Wybouw
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lauri Nikkanen
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Krasensky-Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Nina Sipari
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Eevi Rintamäki
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Eva-Mari Aro
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
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