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Brito AF, Pinney JW. Protein-Protein Interactions in Virus-Host Systems. Front Microbiol 2017; 8:1557. [PMID: 28861068 PMCID: PMC5562681 DOI: 10.3389/fmicb.2017.01557] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/02/2017] [Indexed: 01/10/2023] Open
Abstract
To study virus–host protein interactions, knowledge about viral and host protein architectures and repertoires, their particular evolutionary mechanisms, and information on relevant sources of biological data is essential. The purpose of this review article is to provide a thorough overview about these aspects. Protein domains are basic units defining protein interactions, and the uniqueness of viral domain repertoires, their mode of evolution, and their roles during viral infection make viruses interesting models of study. Mutations at protein interfaces can reduce or increase their binding affinities by changing protein electrostatics and structural properties. During the course of a viral infection, both pathogen and cellular proteins are constantly competing for binding partners. Endogenous interfaces mediating intraspecific interactions—viral–viral or host–host interactions—are constantly targeted and inhibited by exogenous interfaces mediating viral–host interactions. From a biomedical perspective, blocking such interactions is the main mechanism underlying antiviral therapies. Some proteins are able to bind multiple partners, and their modes of interaction define how fast these “hub proteins” evolve. “Party hubs” have multiple interfaces; they establish simultaneous/stable (domain–domain) interactions, and tend to evolve slowly. On the other hand, “date hubs” have few interfaces; they establish transient/weak (domain–motif) interactions by means of short linear peptides (15 or fewer residues), and can evolve faster. Viral infections are mediated by several protein–protein interactions (PPIs), which can be represented as networks (protein interaction networks, PINs), with proteins being depicted as nodes, and their interactions as edges. It has been suggested that viral proteins tend to establish interactions with more central and highly connected host proteins. In an evolutionary arms race, viral and host proteins are constantly changing their interface residues, either to evade or to optimize their binding capabilities. Apart from gaining and losing interactions via rewiring mechanisms, virus–host PINs also evolve via gene duplication (paralogy); conservation (orthology); horizontal gene transfer (HGT) (xenology); and molecular mimicry (convergence). The last sections of this review focus on PPI experimental approaches and their limitations, and provide an overview of sources of biomolecular data for studying virus–host protein interactions.
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Affiliation(s)
- Anderson F Brito
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College LondonLondon, United Kingdom
| | - John W Pinney
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College LondonLondon, United Kingdom
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102
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Baudin M, Hassan JA, Schreiber KJ, Lewis JD. Analysis of the ZAR1 Immune Complex Reveals Determinants for Immunity and Molecular Interactions. PLANT PHYSIOLOGY 2017; 174:2038-2053. [PMID: 28652264 PMCID: PMC5543953 DOI: 10.1104/pp.17.00441] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/22/2017] [Indexed: 05/06/2023]
Abstract
Plants depend on innate immunity to prevent disease. Plant pathogenic bacteria, like Pseudomonas syringae and Xanthomonas campestris, use the type III secretion system as a molecular syringe to inject type III secreted effector (T3SE) proteins in plants. The primary function of most T3SEs is to suppress immunity; however, the plant can evolve nucleotide-binding domain-leucine-rich repeat domain-containing proteins to recognize specific T3SEs. The AtZAR1 NLR induces strong defense responses against P. syringae and X. campestris The P. syringae T3SE HopZ1a is an acetyltransferase that acetylates the pseudokinase AtZED1 and triggers recognition by AtZAR1. However, little is known about the molecular mechanisms that lead to AtZAR1-induced immunity in response to HopZ1a. We established a transient expression system in Nicotiana benthamiana to study detailed interactions among HopZ1a, AtZED1, and AtZAR1. We show that the AtZAR1 immune pathway is conserved in N. benthamiana and identify AtZAR1 domains, and residues in AtZAR1 and AtZED1, that are important for immunity and protein-protein interactions in planta and in yeast (Saccharomyces cerevisiae). We show that the coiled-coil domain of AtZAR1 oligomerizes, and this domain acts as a signal to induce immunity. This detailed analysis of the AtZAR1-AtZED1 protein complex provides a better understanding of the immune signaling hub controlled by AtZAR1.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Karl J Schreiber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
- Plant Gene Expression Center, U.S. Department of Agriculture, Albany, California 94710
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103
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Zhou S, Jiang W, Long F, Cheng S, Yang W, Zhao Y, Zhou DX. Rice Homeodomain Protein WOX11 Recruits a Histone Acetyltransferase Complex to Establish Programs of Cell Proliferation of Crown Root Meristem. THE PLANT CELL 2017; 29:1088-1104. [PMID: 28487409 PMCID: PMC5466029 DOI: 10.1105/tpc.16.00908] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/19/2017] [Accepted: 05/07/2017] [Indexed: 05/05/2023]
Abstract
Shoot-borne crown roots are the major root system in cereals. Previous work has shown that the Wuschel-related homeobox gene WOX11 is necessary and sufficient to promote rice (Oryza sativa) crown root emergence and elongation. Here, we show that WOX11 recruits the ADA2-GCN5 histone acetyltransferase module to activate downstream target genes in crown root meristem. Rice ADA2 and GCN5 genes are highly expressed in root meristem and are shown to be essential for cell division and growth. WOX11 and ADA2-GCN5 commonly target and regulate a set of root-specific genes involved in energy metabolism, cell wall biosynthesis, and hormone response, some of which are known to be important for root development. The results indicate that the recruitment of ADA2-GCN5 by WOX11 establishes gene expression programs of crown root meristem cell division and suggest that permissive chromatin modification involving histone acetylation is a strategy for WOX11 to stimulate root meristem development.
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Affiliation(s)
- Shaoli Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wei Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Fei Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Saifeng Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wenjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
- Institute Plant Science Paris-Saclay (IPS2), CNRS, INRA, Université Paris-sud 11, Université Paris-Saclay, 91405 Orsay, France
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104
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Sklodowski K, Riedelsberger J, Raddatz N, Riadi G, Caballero J, Chérel I, Schulze W, Graf A, Dreyer I. The receptor-like pseudokinase MRH1 interacts with the voltage-gated potassium channel AKT2. Sci Rep 2017; 7:44611. [PMID: 28300158 PMCID: PMC5353636 DOI: 10.1038/srep44611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/25/2017] [Indexed: 12/23/2022] Open
Abstract
The potassium channel AKT2 plays important roles in phloem loading and unloading. It can operate as inward-rectifying channel that allows H+-ATPase-energized K+ uptake. Moreover, through reversible post-translational modifications it can also function as an open, K+-selective channel, which taps a 'potassium battery', providing additional energy for transmembrane transport processes. Knowledge about proteins involved in the regulation of the operational mode of AKT2 is very limited. Here, we employed a large-scale yeast two-hybrid screen in combination with fluorescence tagging and null-allele mutant phenotype analysis and identified the plasma membrane localized receptor-like kinase MRH1/MDIS2 (AT4G18640) as interaction partner of AKT2. The phenotype of the mrh1-1 knockout plant mirrors that of akt2 knockout plants in energy limiting conditions. Electrophysiological analyses showed that MRH1/MDIS2 failed to exert any functional regulation on AKT2. Using structural protein modeling approaches, we instead gathered evidence that the putative kinase domain of MRH1/MDIS2 lacks essential sites that are indispensable for a functional kinase suggesting that MRH1/MDIS2 is a pseudokinase. We propose that MRH1/MDIS2 and AKT2 are likely parts of a bigger protein complex. MRH1 might help to recruit other, so far unknown partners, which post-translationally regulate AKT2. Additionally, MRH1 might be involved in the recognition of chemical signals.
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Affiliation(s)
- Kamil Sklodowski
- Heisenberg Group of Biophysics and Molecular Plant Biology, Institute of Biochemistry and Biology, Molecular Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
- ETH Zürich, Department of Biology, CH-8092 Zürich, Switzerland
| | - Janin Riedelsberger
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Natalia Raddatz
- Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), E-28223 Pozuelo de Alarcón (Madrid), Spain
- Instituto de Biología Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, E-41092 Sevilla, Spain
| | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Isabelle Chérel
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5004, Institut National de la Recherche Agronomique U386, Montpellier SupAgro, Université Montpellier II, F-34060 Montpellier cedex 2, France
| | - Waltraud Schulze
- Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
- Department of Plant Systems Biology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Alexander Graf
- Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Ingo Dreyer
- Heisenberg Group of Biophysics and Molecular Plant Biology, Institute of Biochemistry and Biology, Molecular Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
- Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), E-28223 Pozuelo de Alarcón (Madrid), Spain
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105
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Xing S, Mehlhorn DG, Wallmeroth N, Asseck LY, Kar R, Voss A, Denninger P, Schmidt VAF, Schwarzländer M, Stierhof YD, Grossmann G, Grefen C. Loss of GET pathway orthologs in Arabidopsis thaliana causes root hair growth defects and affects SNARE abundance. Proc Natl Acad Sci U S A 2017; 114:E1544-E1553. [PMID: 28096354 PMCID: PMC5338382 DOI: 10.1073/pnas.1619525114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins are key players in cellular trafficking and coordinate vital cellular processes, such as cytokinesis, pathogen defense, and ion transport regulation. With few exceptions, SNAREs are tail-anchored (TA) proteins, bearing a C-terminal hydrophobic domain that is essential for their membrane integration. Recently, the Guided Entry of Tail-anchored proteins (GET) pathway was described in mammalian and yeast cells that serve as a blueprint of TA protein insertion [Schuldiner M, et al. (2008) Cell 134(4):634-645; Stefanovic S, Hegde RS (2007) Cell 128(6):1147-1159]. This pathway consists of six proteins, with the cytosolic ATPase GET3 chaperoning the newly synthesized TA protein posttranslationally from the ribosome to the endoplasmic reticulum (ER) membrane. Structural and biochemical insights confirmed the potential of pathway components to facilitate membrane insertion, but the physiological significance in multicellular organisms remains to be resolved. Our phylogenetic analysis of 37 GET3 orthologs from 18 different species revealed the presence of two different GET3 clades. We identified and analyzed GET pathway components in Arabidopsis thaliana and found reduced root hair elongation in Atget lines, possibly as a result of reduced SNARE biogenesis. Overexpression of AtGET3a in a receptor knockout (KO) results in severe growth defects, suggesting presence of alternative insertion pathways while highlighting an intricate involvement for the GET pathway in cellular homeostasis of plants.
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Affiliation(s)
- Shuping Xing
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany
| | - Dietmar Gerald Mehlhorn
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany
| | - Niklas Wallmeroth
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany
| | - Lisa Yasmin Asseck
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany
| | - Ritwika Kar
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany
| | - Alessa Voss
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany
| | - Philipp Denninger
- Centre for Organismal Studies, CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany
| | - Vanessa Aphaia Fiona Schmidt
- Centre for Organismal Studies, CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany
| | - Markus Schwarzländer
- Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - York-Dieter Stierhof
- Centre for Plant Molecular Biology, Microscopy, University of Tübingen, 72076 Tuebingen, Germany
| | - Guido Grossmann
- Centre for Organismal Studies, CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christopher Grefen
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076 Tuebingen, Germany;
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106
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Lynch MJ, Levenson R, Kim EA, Sircar R, Blair DF, Dahlquist FW, Crane BR. Co-Folding of a FliF-FliG Split Domain Forms the Basis of the MS:C Ring Interface within the Bacterial Flagellar Motor. Structure 2017; 25:317-328. [PMID: 28089452 DOI: 10.1016/j.str.2016.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/21/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
The interface between the membrane (MS) and cytoplasmic (C) rings of the bacterial flagellar motor couples torque generation to rotation within the membrane. The structure of the C-terminal helices of the integral membrane protein FliF (FliFC) bound to the N terminal domain of the switch complex protein FliG (FliGN) reveals that FliGN folds around FliFC to produce a topology that closely resembles both the middle and C-terminal domains of FliG. The interface is consistent with solution-state nuclear magnetic resonance, small-angle X-ray scattering, in vivo interaction studies, and cellular motility assays. Co-folding with FliFC induces substantial conformational changes in FliGN and suggests that FliF and FliG have the same stoichiometry within the rotor. Modeling the FliFC:FliGN complex into cryo-electron microscopy rotor density updates the architecture of the middle and upper switch complex and shows how domain shuffling of a conserved interaction module anchors the cytoplasmic rotor to the membrane.
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Affiliation(s)
- Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Robert Levenson
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ria Sircar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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107
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Zhang B, Karnik R, Waghmare S, Donald N, Blatt MR. VAMP721 Conformations Unmask an Extended Motif for K+ Channel Binding and Gating Control. PLANT PHYSIOLOGY 2017; 173:536-551. [PMID: 27821719 PMCID: PMC5210753 DOI: 10.1104/pp.16.01549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/04/2016] [Indexed: 05/20/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play a major role in membrane fusion and contribute to cell expansion, signaling, and polar growth in plants. The SNARE SYP121 of Arabidopsis thaliana that facilitates vesicle fusion at the plasma membrane also binds with, and regulates, K+ channels already present at the plasma membrane to affect K+ uptake and K+-dependent growth. Here, we report that its cognate partner VAMP721, which assembles with SYP121 to drive membrane fusion, binds to the KAT1 K+ channel via two sites on the protein, only one of which contributes to channel-gating control. Binding to the VAMP721 SNARE domain suppressed channel gating. By contrast, interaction with the amino-terminal longin domain conferred specificity on VAMP721 binding without influencing gating. Channel binding was defined by a linear motif within the longin domain. The SNARE domain is thought to wrap around this structure when not assembled with SYP121 in the SNARE complex. Fluorescence lifetime analysis showed that mutations within this motif, which suppressed channel binding and its effects on gating, also altered the conformational displacement between the VAMP721 SNARE and longin domains. The presence of these two channel-binding sites on VAMP721, one also required for SNARE complex assembly, implies a well-defined sequence of events coordinating K+ uptake and the final stages of vesicle traffic. It suggests that binding begins with VAMP721, and subsequently with SYP121, thereby coordinating K+ channel gating during SNARE assembly and vesicle fusion. Thus, our findings also are consistent with the idea that the K+ channels are nucleation points for SNARE complex assembly.
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Affiliation(s)
- Ben Zhang
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Rucha Karnik
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Sakharam Waghmare
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Naomi Donald
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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108
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Husbands AY, Aggarwal V, Ha T, Timmermans MCP. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. THE PLANT CELL 2016; 28:1783-94. [PMID: 27385814 PMCID: PMC5006705 DOI: 10.1105/tpc.16.00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/03/2016] [Indexed: 05/12/2023]
Abstract
Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205 Howard Hughes Medical Institute, Baltimore, Maryland 21205
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
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