1
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He Y, Wang Z, Cui W, Zhang Q, Zheng M, Li W, Gao J, Yang Z, You J. Comparative quantitative phosphoproteomic and parallel reaction monitoring analysis of soybean roots under aluminum stress identify candidate phosphoproteins involved in aluminum resistance capacity. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135485. [PMID: 39208632 DOI: 10.1016/j.jhazmat.2024.135485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/26/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Aluminum (Al) toxicity adversely impacts soybean (Glycine max) growth in acidic soil. Reversible protein phosphorylation plays an important role in adapting to adverse environmental conditions by regulating multiple physiological processes including signal transduction, energy coupling and metabolism adjustment in higher plant. This study aimed to reveal the Al-responsive phosphoproteins to understand their putative function and involvement in the regulation of Al resistance in soybean root. We used immobilized metal affinity chromatography to enrich the key phosphoproteins from soybean root apices at 0, 4, or 24 h Al exposure. These phosphoproteins were detected using liquid chromatography-tandem mass spectrometry measurement, verified by parallel reaction monitoring (PRM), and functionally characterized via overexpression in soybean hairy roots. A total of 638 and 686 phosphoproteins were identified as differentially enriched between the 4-h and 0-h, and the 24-h and 0-h Al treatment comparison groups, respectively. Typically, the phosphoproteins involved in biological processes including cell wall modification, and RNA and protein metabolic regulation displayed patterns of decreasing enrichment (clusters 3, 5 and 6), however, the phosphoproteins involved in the transport and metabolic processes of various substrates, and signal transduction pathways showed increased enrichment after 24 h of Al treatment. The enrichment of phosphoproteins in organelle organization bottomed after 4 h of Al treatment (cluster 1). Next, we selected 26 phosphoproteins from the phosphoproteomic profiles, assessed their enrichment status using PRM, and detected enrichment patterns similar to those observed via phosphoproteomic analysis. Among them, 15 phosphoproteins were found to reduce the accumulation of Al and callose in Al-stressed soybean root apices when their corresponding genes were individually overexpressed in soybean hairy roots. In summary, the findings of this study facilitated a comprehensive understanding of the protein phosphorylation events involved in Al resistance responses and revealed some critical phosphoproteins that enhance Al resistance in soybean roots.
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Affiliation(s)
- Ying He
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Zhengbiao Wang
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Wenmo Cui
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Qingxiu Zhang
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Meihui Zheng
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Wen Li
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Jie Gao
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Zhenming Yang
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Jiangfeng You
- College of Plant Science, Jilin University, Changchun 130062, China.
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2
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Hewezi T. Phytopathogens Reprogram Host Alternative mRNA Splicing. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:173-192. [PMID: 38691872 DOI: 10.1146/annurev-phyto-121423-041908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Alternative splicing (AS) is an evolutionarily conserved cellular process in eukaryotes in which multiple messenger RNA (mRNA) transcripts are produced from a single gene. The concept that AS adds to transcriptome complexity and proteome diversity introduces a new perspective for understanding how phytopathogen-induced alterations in host AS cause diseases. Recently, it has been recognized that AS represents an integral component of the plant immune system during parasitic, commensalistic, and symbiotic interactions. Here, I provide an overview of recent progress detailing the reprogramming of plant AS by phytopathogens and the functional implications on disease phenotypes. Additionally, I discuss the vital function of AS of immune receptors in regulating plant immunity and how phytopathogens use effector proteins to target key components of the splicing machinery and exploit alternatively spliced variants of immune regulators to negate defense responses. Finally, the functional association between AS and nonsense-mediated mRNA decay in the context of plant-pathogen interface is recapitulated.
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Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA;
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3
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Ahsan N, Kataya ARA, Rao RSP, Swatek KN, Wilson RS, Meyer LJ, Tovar-Mendez A, Stevenson S, Maszkowska J, Dobrowolska G, Yao Q, Xu D, Thelen JJ. Decoding Arabidopsis thaliana CPK/SnRK Superfamily Kinase Client Signaling Networks Using Peptide Library and Mass Spectrometry. PLANTS (BASEL, SWITZERLAND) 2024; 13:1481. [PMID: 38891291 PMCID: PMC11174488 DOI: 10.3390/plants13111481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Members of the calcium-dependent protein kinase (CDPK/CPK) and SNF-related protein kinase (SnRK) superfamilies are commonly found in plants and some protists. Our knowledge of client specificity of the members of this superfamily is fragmentary. As this family is represented by over 30 members in Arabidopsis thaliana, the identification of kinase-specific and overlapping client relationships is crucial to our understanding the nuances of this large family of kinases as directed towards signal transduction pathways. Herein, we used the kinase client (KiC) assay-a relative, quantitative, high-throughput mass spectrometry-based in vitro phosphorylation assay-to identify and characterize potential CPK/SnRK targets of Arabidopsis. Eight CPKs (1, 3, 6, 8, 17, 24, 28, and 32), four SnRKs (subclass 1 and 2), and PPCK1 and PPCK2 were screened against a synthetic peptide library that contains 2095 peptides and 2661 known phosphorylation sites. A total of 625 in vitro phosphorylation sites corresponding to 203 non-redundant proteins were identified. The most promiscuous kinase, CPK17, had 105 candidate target proteins, many of which had already been discovered. Sequence analysis of the identified phosphopeptides revealed four motifs: LxRxxS, RxxSxxR, RxxS, and LxxxxS, that were significantly enriched among CPK/SnRK clients. The results provide insight into both CPK- and SnRK-specific and overlapping signaling network architectures and recapitulate many known in vivo relationships validating this large-scale approach towards discovering kinase targets.
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Affiliation(s)
- Nagib Ahsan
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Chemistry and Biochemistry, Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK 73019, USA
| | - Amr R. A. Kataya
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - R. Shyama Prasad Rao
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru 575018, India
| | - Kirby N. Swatek
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rashaun S. Wilson
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Arvinas, Inc., New Haven, CT 06511, USA
| | - Louis J. Meyer
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Bayer Crop Science, St. Louis, MO 63141, USA
| | - Alejandro Tovar-Mendez
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Elemental Enzymes, St. Louis, MO 63132, USA
| | - Severin Stevenson
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Justyna Maszkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland (G.D.)
| | - Grazyna Dobrowolska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland (G.D.)
| | - Qiuming Yao
- Department of Electrical Engineering & Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Electrical Engineering & Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jay J. Thelen
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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4
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Demko V, Belova T, Messerer M, Hvidsten TR, Perroud PF, Ako AE, Johansen W, Mayer KFX, Olsen OA, Lang D. Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens. Commun Biol 2024; 7:261. [PMID: 38438476 PMCID: PMC10912778 DOI: 10.1038/s42003-024-05933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.
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Affiliation(s)
- Viktor Demko
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84104, Bratislava, Slovakia
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dubravska cesta 9, 84104, Bratislava, Slovakia
| | - Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Ako Eugene Ako
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, NG25 0QF, UK
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, 85354, Freising, Germany
| | - Odd-Arne Olsen
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Daniel Lang
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Bundeswehr Institute of Microbiology, Microbial Genomics and Bioforensics, 80937, Munich, Germany.
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5
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Mihiret YE, Schaaf G, Kamleitner M. Protein pyrophosphorylation by inositol phosphates: a novel post-translational modification in plants? FRONTIERS IN PLANT SCIENCE 2024; 15:1347922. [PMID: 38455731 PMCID: PMC10917965 DOI: 10.3389/fpls.2024.1347922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Inositol pyrophosphates (PP-InsPs) are energy-rich molecules harboring one or more diphosphate moieties. PP-InsPs are found in all eukaryotes evaluated and their functional versatility is reflected in the various cellular events in which they take part. These include, among others, insulin signaling and intracellular trafficking in mammals, as well as innate immunity and hormone and phosphate signaling in plants. The molecular mechanisms by which PP-InsPs exert such functions are proposed to rely on the allosteric regulation via direct binding to proteins, by competing with other ligands, or by protein pyrophosphorylation. The latter is the focus of this review, where we outline a historical perspective surrounding the first findings, almost 20 years ago, that certain proteins can be phosphorylated by PP-InsPs in vitro. Strikingly, in vitro phosphorylation occurs by an apparent enzyme-independent but Mg2+-dependent transfer of the β-phosphoryl group of an inositol pyrophosphate to an already phosphorylated serine residue at Glu/Asp-rich protein regions. Ribosome biogenesis, vesicle trafficking and transcription are among the cellular events suggested to be modulated by protein pyrophosphorylation in yeast and mammals. Here we discuss the latest efforts in identifying targets of protein pyrophosphorylation, pointing out the methodological challenges that have hindered the full understanding of this unique post-translational modification, and focusing on the latest advances in mass spectrometry that finally provided convincing evidence that PP-InsP-mediated pyrophosphorylation also occurs in vivo. We also speculate about the relevance of this post-translational modification in plants in a discussion centered around the protein kinase CK2, whose activity is critical for pyrophosphorylation of animal and yeast proteins. This enzyme is widely present in plant species and several of its functions overlap with those of PP-InsPs. Until now, there is virtually no data on pyrophosphorylation of plant proteins, which is an exciting field that remains to be explored.
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Affiliation(s)
| | | | - Marília Kamleitner
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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6
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Fuji S, Yamauchi S, Sugiyama N, Kohchi T, Nishihama R, Shimazaki KI, Takemiya A. Light-induced stomatal opening requires phosphorylation of the C-terminal autoinhibitory domain of plasma membrane H +-ATPase. Nat Commun 2024; 15:1195. [PMID: 38378726 PMCID: PMC10879506 DOI: 10.1038/s41467-024-45236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Plasma membrane H+-ATPase provides the driving force for light-induced stomatal opening. However, the mechanisms underlying the regulation of its activity remain unclear. Here, we show that the phosphorylation of two Thr residues in the C-terminal autoinhibitory domain is crucial for H+-ATPase activation and stomatal opening in Arabidopsis thaliana. Using phosphoproteome analysis, we show that blue light induces the phosphorylation of Thr-881 within the C-terminal region I, in addition to penultimate Thr-948 in AUTOINHIBITED H+-ATPASE 1 (AHA1). Based on site-directed mutagenesis experiments, phosphorylation of both Thr residues is essential for H+ pumping and stomatal opening in response to blue light. Thr-948 phosphorylation is a prerequisite for Thr-881 phosphorylation by blue light. Additionally, red light-driven guard cell photosynthesis induces Thr-881 phosphorylation, possibly contributing to red light-dependent stomatal opening. Our findings provide mechanistic insights into H+-ATPase activation that exploits the ion transport across the plasma membrane and light signalling network in guard cells.
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Affiliation(s)
- Saashia Fuji
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan
| | - Shota Yamauchi
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Naoyuki Sugiyama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Ken-Ichiro Shimazaki
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Atsushi Takemiya
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan.
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7
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Wang Y, Wakelam MJO, Bankaitis VA, McDermott MI. The wide world of non-mammalian phospholipase D enzymes. Adv Biol Regul 2024; 91:101000. [PMID: 38081756 DOI: 10.1016/j.jbior.2023.101000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 02/25/2024]
Abstract
Phospholipase D (PLD) hydrolyses phosphatidylcholine (PtdCho) to produce free choline and the critically important lipid signaling molecule phosphatidic acid (PtdOH). Since the initial discovery of PLD activities in plants and bacteria, PLDs have been identified in a diverse range of organisms spanning the taxa. While widespread interest in these proteins grew following the discovery of mammalian isoforms, research into the PLDs of non-mammalian organisms has revealed a fascinating array of functions ranging from roles in microbial pathogenesis, to the stress responses of plants and the developmental patterning of flies. Furthermore, studies in non-mammalian model systems have aided our understanding of the entire PLD superfamily, with translational relevance to human biology and health. Increasingly, the promise for utilization of non-mammalian PLDs in biotechnology is also being recognized, with widespread potential applications ranging from roles in lipid synthesis, to their exploitation for agricultural and pharmaceutical applications.
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Affiliation(s)
- Y Wang
- Department of Cell Biology & Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA; Department of Microbiology, University of Washington, Seattle, WA98109, USA
| | - M J O Wakelam
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - V A Bankaitis
- Department of Cell Biology & Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA; Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA; Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - M I McDermott
- Department of Cell Biology & Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA.
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8
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Smith MA, Benidickson KH, Plaxton WC. In Vivo Phosphorylation of the Cytosolic Glucose-6-Phosphate Dehydrogenase Isozyme G6PD6 in Phosphate-Resupplied Arabidopsis thaliana Suspension Cells and Seedlings. PLANTS (BASEL, SWITZERLAND) 2023; 13:31. [PMID: 38202338 PMCID: PMC10780934 DOI: 10.3390/plants13010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) catalyzes the first committed step of the oxidative pentose phosphate pathway (OPPP). Our recent phosphoproteomics study revealed that the cytosolic G6PD6 isozyme became hyperphosphorylated at Ser12, Thr13 and Ser18, 48 h following phosphate (Pi) resupply to Pi-starved (-Pi) Arabidopsis thaliana cell cultures. The aim of the present study was to assess whether G6PD6 phosphorylation also occurs in shoots or roots following Pi resupply to -Pi Arabidopsis seedlings, and to investigate its relationship with G6PD activity. Interrogation of phosphoproteomic databases indicated that N-terminal, multi-site phosphorylation of G6PD6 and its orthologs is quite prevalent. However, the functions of these phosphorylation events remain unknown. Immunoblotting with an anti-(pSer18 phosphosite-specific G6PD6) antibody confirmed that G6PD6 from Pi-resupplied, but not -Pi, Arabidopsis cell cultures or seedlings (i.e., roots) was phosphorylated at Ser18; this correlated with a significant increase in extractable G6PD activity, and biomass accumulation. Peptide kinase assays of Pi-resupplied cell culture extracts indicated that G6PD6 phosphorylation at Ser18 is catalyzed by a Ca2+-dependent protein kinase (CDPK), which correlates with the 'CDPK-like' targeting motif that flanks Ser18. Our results support the hypothesis that N-terminal phosphorylation activates G6PD6 to enhance OPPP flux and thus the production of reducing power (i.e., NADPH) and C-skeletons needed to establish the rapid resumption of growth that ensures Pi-resupply to -Pi Arabidopsis.
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Affiliation(s)
| | | | - William C. Plaxton
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (M.A.S.); (K.H.B.)
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9
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Šafranek M, Shumbusho A, Johansen W, Šarkanová J, Voško S, Bokor B, Jásik J, Demko V. Membrane-anchored calpains - hidden regulators of growth and development beyond plants? FRONTIERS IN PLANT SCIENCE 2023; 14:1289785. [PMID: 38173928 PMCID: PMC10762896 DOI: 10.3389/fpls.2023.1289785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Calpains are modulatory proteases that modify diverse cellular substrates and play essential roles in eukaryots. The best studied are animal cytosolic calpains. Here, we focus on enigmatic membrane-anchored calpains, their structural and functional features as well as phylogenetic distribution. Based on domain composition, we identified four types of membrane-anchored calpains. Type 1 and 2 show broad phylogenetic distribution among unicellular protists and streptophytes suggesting their ancient evolutionary origin. Type 3 and 4 diversified early and are present in brown algae and oomycetes. The plant DEK1 protein is the only representative of membrane-anchored calpains that has been functionally studied. Here, we present up to date knowledge about its structural features, putative regulation, posttranslational modifications, and biological role. Finally, we discuss potential model organisms and available tools for functional studies of membrane-anchored calpains with yet unknown biological role. Mechanistic understanding of membrane-anchored calpains may provide important insights into fundamental principles of cell polarization, cell fate control, and morphogenesis beyond plants.
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Affiliation(s)
- Martin Šafranek
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alain Shumbusho
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Wenche Johansen
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Júlia Šarkanová
- Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Stanislav Voško
- Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Boris Bokor
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ján Jásik
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Viktor Demko
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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10
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Yu G, Mou Y, Shoaib N, He X, Liu L, Di R, Mughal N, Zhang N, Huang Y. Serine 31 Phosphorylation-Driven Regulation of AGPase Activity: Potential Implications for Enhanced Starch Yields in Crops. Int J Mol Sci 2023; 24:15283. [PMID: 37894964 PMCID: PMC10607544 DOI: 10.3390/ijms242015283] [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: 09/15/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
ADP-Glc pyrophosphorylase (AGPase), which catalyzes the transformation of ATP and glucose-1-phosphate (Glc-1-P) into adenosine diphosphate glucose (ADP-Glc), acts as a rate-limiting enzyme in crop starch biosynthesis. Prior research has hinted at the regulation of AGPase by phosphorylation in maize. However, the identification and functional implications of these sites remain to be elucidated. In this study, we identified the phosphorylation site (serine at the 31st position of the linear amino acid sequence) of the AGPase large subunit (Sh2) using iTRAQTM. Subsequently, to ascertain the impact of Sh2 phosphorylation on AGPase, we carried out site-directed mutations creating Sh2-S31A (serine residue replaced with alanine) to mimic dephosphorylation and Sh2-S31D (serine residue replaced with aspartic acid) or Sh2-S31E (serine residue replaced with glutamic acid) to mimic phosphorylation. Preliminary investigations were performed to determine Sh2 subcellular localization, its interaction with Bt2, and the resultant AGPase enzymatic activity. Our findings indicate that phosphorylation exerts no impact on the stability or localization of Sh2. Furthermore, none of these mutations at the S31 site of Sh2 seem to affect its interaction with Bt2 (smaller subunit). Intriguingly, all S31 mutations in Sh2 appear to enhance AGPase activity when co-transfected with Bt2, with Sh2-S31E demonstrating a substantial five-fold increase in AGPase activity compared to Sh2. These novel insights lay a foundational groundwork for targeted improvements in AGPase activity, thus potentially accelerating the production of ADP-Glc (the primary substrate for starch synthesis), promising implications for improved starch biosynthesis, and holding the potential to significantly impact agricultural practices.
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Affiliation(s)
- Guowu Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
- National Demonstration Center for Experimental Crop Science Education, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuewei Mou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
- National Demonstration Center for Experimental Crop Science Education, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Noman Shoaib
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
- National Demonstration Center for Experimental Crop Science Education, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewu He
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China;
| | - Lun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
| | - Runze Di
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
| | - Nishbah Mughal
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
| | - Na Zhang
- College of Science, Sichuan Agricultural University, Chengdu 611130, China;
| | - Yubi Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (N.S.); (L.L.); (R.D.); (N.M.); (Y.H.)
- National Demonstration Center for Experimental Crop Science Education, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
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11
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Qu L, Liu M, Zheng L, Wang X, Xue H. Data-independent acquisition-based global phosphoproteomics reveal the diverse roles of casein kinase 1 in plant development. Sci Bull (Beijing) 2023; 68:2077-2093. [PMID: 37599176 DOI: 10.1016/j.scib.2023.08.017] [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: 06/02/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Casein kinase 1 (CK1) is serine/threonine protein kinase highly conserved among eukaryotes, and regulates multiple developmental and signaling events through phosphorylation of target proteins. Arabidopsis early flowering 1 (EL1)-like (AELs) are plant-specific CK1s with varied functions, but identification and validation of their substrates is a major bottleneck in elucidating their physiological roles. Here, we conducted a quantitative phosphoproteomic analysis in data-independent acquisition mode to systematically identify CK1 substrates. We extracted proteins from seedlings overexpressing individual AEL genes (AEL1/2/3/4-OE) or lacking AEL function (all ael single mutants and two triple mutants) to identify the high-confidence phosphopeptides with significantly altered abundance compared to wild-type Col-0. Among these, we selected 3985 phosphopeptides with higher abundance in AEL-OE lines or lower abundance in ael mutants compared with Col-0 as AEL-upregulated phosphopeptides, and defined 1032 phosphoproteins. Eight CK1s substrate motifs were enriched among AEL-upregulated phosphopeptides and verified, which allowed us to predict additional candidate substrates and functions of CK1s. We functionally characterized a newly identified substrate C3H17, a CCCH-type zinc finger transcription factor, through biochemical and genetic analyses, revealing a role for AEL-promoted C3H17 protein stability and transactivation activity in regulating embryogenesis. As CK1s are highly conserved across eukaryotes, we searched the rice, mouse, and human protein databases using newly identified CK1 substrate motifs, yielding many more candidate substrates than currently known, largely expanding our understanding of the common and distinct functions exerted by CK1s in Arabidopsis and humans, facilitating future mechanistic studies of CK1-mediated phosphorylation in different species.
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Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Moyang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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12
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Baoxiang W, Zhiguang S, Yan L, Bo X, Jingfang L, Ming C, Yungao X, Bo Y, Jian L, Jinbo L, Tingmu C, Zhaowei F, Baiguan L, Dayong X, Bello BK. A pervasive phosphorylation cascade modulation of plant transcription factors in response to abiotic stress. PLANTA 2023; 258:73. [PMID: 37668677 DOI: 10.1007/s00425-023-04232-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
MAIN CONCLUSION Transcriptional regulation of stress-responsive genes is a crucial step in establishing the mechanisms behind plant abiotic stress tolerance. A sensitive method of regulating transcription factors activity, stability, protein interaction, and subcellular localization is through phosphorylation. This review highlights a widespread regulation mechanism that involves phosphorylation of plant TFs in response to abiotic stress. Abiotic stress is one of the main components limiting crop yield and sustainability on a global scale. It greatly reduces the land area that is planted and lowers crop production globally. In all living organisms, transcription factors (TFs) play a crucial role in regulating gene expression. They participate in cell signaling, cell cycle, development, and plant stress response. Plant resilience to diverse abiotic stressors is largely influenced by TFs. Transcription factors modulate gene expression by binding to their target gene's cis-elements, which are impacted by genomic characteristics, DNA structure, and TF interconnections. In this review, we focus on the six major TFs implicated in abiotic stress tolerance, namely, DREB, bZIP, WRKY, ABF, MYB, and NAC, and the cruciality of phosphorylation of these transcription factors in abiotic stress signaling, as protein phosphorylation has emerged as one of the key post-translational modifications, playing a critical role in cell signaling, DNA amplification, gene expression and differentiation, and modification of other biological configurations. These TFs have been discovered after extensive study as stress-responsive transcription factors which may be major targets for crop development and important contributors to stress tolerance and crop production.
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Grants
- CARS-01-61 the earmarked funds for China Agricultural Research System
- 2015BAD01B01 National Science and Technology Support Program of China
- BE2016370-3 Science and Technology Support Program of Jiangsu Province, China
- BE2017323 Science and Technology Support Program of Jiangsu Province, China
- BK20201214 Natural Science Foundation of Jiangsu Province of China
- BK20161299 the Natural Science Foundation of Jiangsu Province, China
- QNJJ1704 the Financial Grant Support Program of Lianyungang City, Jiangsu Province, China
- QNJJ2102 the Financial Grant Support Program of Lianyungang City, Jiangsu Province, China
- QNJJ2107 the Financial Grant Support Program of Lianyungang City, Jiangsu Province, China
- QNJJ2211 the Financial Grant Support Program of Lianyungang City, Jiangsu Province, China
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Affiliation(s)
- Wang Baoxiang
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Sun Zhiguang
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Liu Yan
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Xu Bo
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Li Jingfang
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Chi Ming
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Xing Yungao
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Yang Bo
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Li Jian
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Liu Jinbo
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Chen Tingmu
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Fang Zhaowei
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Lu Baiguan
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China
| | - Xu Dayong
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China.
| | - Babatunde Kazeem Bello
- Collaborative Innovation Center for Modern Crop Production, Lianyungang Institute of Agricultural Sciences, Lianyungang, 222006, Jiangsu, China.
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13
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Xin X, Wei D, Lei L, Zheng H, Wallace IS, Li S, Gu Y. CALCIUM-DEPENDENT PROTEIN KINASE32 regulates cellulose biosynthesis through post-translational modification of cellulose synthase. THE NEW PHYTOLOGIST 2023; 239:2212-2224. [PMID: 37431066 DOI: 10.1111/nph.19106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/05/2023] [Indexed: 07/12/2023]
Abstract
Cellulose is an essential component of plant cell walls and an economically important source of food, paper, textiles, and biofuel. Despite its economic and biological significance, the regulation of cellulose biosynthesis is poorly understood. Phosphorylation and dephosphorylation of cellulose synthases (CESAs) were shown to impact the direction and velocity of cellulose synthase complexes (CSCs). However, the protein kinases that phosphorylate CESAs are largely unknown. We conducted research in Arabidopsis thaliana to reveal protein kinases that phosphorylate CESAs. In this study, we used yeast two-hybrid, protein biochemistry, genetics, and live-cell imaging to reveal the role of calcium-dependent protein kinase32 (CPK32) in the regulation of cellulose biosynthesis in A. thaliana. We identified CPK32 using CESA3 as a bait in a yeast two-hybrid assay. We showed that CPK32 phosphorylates CESA3 while it interacts with both CESA1 and CESA3. Overexpressing functionally defective CPK32 variant and phospho-dead mutation of CESA3 led to decreased motility of CSCs and reduced crystalline cellulose content in etiolated seedlings. Deregulation of CPKs impacted the stability of CSCs. We uncovered a new function of CPKs that regulates cellulose biosynthesis and a novel mechanism by which phosphorylation regulates the stability of CSCs.
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Affiliation(s)
- Xiaoran Xin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Donghui Wei
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lei Lei
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Shundai Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ying Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
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14
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Hawk TE, Piya S, Zadegan SB, Li P, Rice JH, Hewezi T. The soybean immune receptor GmBIR1 regulates host transcriptome, spliceome, and immunity during cyst nematode infection. THE NEW PHYTOLOGIST 2023; 239:2335-2352. [PMID: 37337845 DOI: 10.1111/nph.19087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
BAK1-INTERACTING RECEPTOR LIKE KINASE1 (BIR1) is a negative regulator of various aspects of disease resistance and immune responses. Here, we investigated the functional role of soybean (Glycine max) BIR1 (GmBIR1) during soybean interaction with soybean cyst nematode (SCN, Heterodera glycines) and the molecular mechanism through which GmBIR1 regulates plant immunity. Overexpression of wild-type variant of GmBIR1 (WT-GmBIR1) using transgenic soybean hairy roots significantly increased soybean susceptibility to SCN, whereas overexpression of kinase-dead variant (KD-GmBIR1) significantly increased plant resistance. Transcriptome analysis revealed that genes oppositely regulated in WT-GmBIR1 and KD-GmBIR1 upon SCN infection were enriched primarily in defense and immunity-related functions. Quantitative phosphoproteomic analysis identified 208 proteins as putative substrates of the GmBIR1 signaling pathway, 114 of which were differentially phosphorylated upon SCN infection. In addition, the phosphoproteomic data pointed to a role of the GmBIR1 signaling pathway in regulating alternative pre-mRNA splicing. Genome-wide analysis of splicing events provided compelling evidence supporting a role of the GmBIR1 signaling pathway in establishing alternative splicing during SCN infection. Our results provide novel mechanistic insights into the function of the GmBIR1 signaling pathway in regulating soybean transcriptome and spliceome via differential phosphorylation of splicing factors and regulation of splicing events of pre-mRNA decay- and spliceosome-related genes.
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Affiliation(s)
- Tracy E Hawk
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sobhan Bahrami Zadegan
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Peitong Li
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - John H Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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15
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Cutolo EA, Caferri R, Guardini Z, Dall'Osto L, Bassi R. Analysis of state 1-state 2 transitions by genome editing and complementation reveals a quenching component independent from the formation of PSI-LHCI-LHCII supercomplex in Arabidopsis thaliana. Biol Direct 2023; 18:49. [PMID: 37612770 PMCID: PMC10463614 DOI: 10.1186/s13062-023-00406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The light-harvesting antennae of photosystem (PS) I and PSII are pigment-protein complexes responsible of the initial steps of sunlight conversion into chemical energy. In natural environments plants are constantly confronted with the variability of the photosynthetically active light spectrum. PSII and PSI operate in series but have different optimal excitation wavelengths. The prompt adjustment of light absorption by photosystems is thus crucial to ensure efficient electron flow needed to sustain downstream carbon fixing reactions. Fast structural rearrangements equilibrate the partition of excitation pressure between PSII and PSI following the enrichment in the red (PSII-favoring) or far-red (PSI-favoring) spectra. Redox imbalances trigger state transitions (ST), a photoacclimation mechanism which involves the reversible phosphorylation/dephosphorylation of light harvesting complex II (LHCII) proteins by the antagonistic activities of the State Transition 7 (STN7) kinase/TAP38 phosphatase enzyme pair. During ST, a mobile PSII antenna pool associates with PSI increasing its absorption cross section. LHCII consists of assorted trimeric assemblies of Lhcb1, Lhcb2 and Lhcb3 protein isoforms (LHCII), several being substrates of STN7. However, the precise roles of Lhcb phosphorylation during ST remain largely elusive. RESULTS We inactivated the complete Lhcb1 and Lhcb2 gene clades in Arabidopsis thaliana and reintroduced either wild type Lhcb1.3 and Lhcb2.1 isoforms, respectively, or versions lacking N-terminal phosphorylatable residues proposed to mediate state transitions. While the substitution of Lhcb2.1 Thr-40 prevented the formation of the PSI-LHCI-LHCII complex, replacement of Lhcb1.3 Thr-38 did not affect the formation of this supercomplex, nor did influence the amplitude or kinetics of PSII fluorescence quenching upon state 1-state 2 transition. CONCLUSIONS Phosphorylation of Lhcb2 Thr-40 by STN7 alone accounts for ≈ 60% of PSII fluorescence quenching during state transitions. Instead, the presence of Thr-38 phosphosite in Lhcb1.3 was not required for the formation of the PSI-LHCI-LHCII supercomplex nor for re-equilibration of the plastoquinone redox state. The Lhcb2 phosphomutant was still capable of ≈ 40% residual fluorescence quenching, implying that a yet uncharacterized, STN7-dependent, component of state transitions, which is unrelated to Lhcb2 Thr-40 phosphorylation and to the formation of the PSI-LHCI-LHCII supercomplex, contributes to the equilibration of the PSI/PSII excitation pressure upon plastoquinone over-reduction.
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Affiliation(s)
- Edoardo Andrea Cutolo
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Roberto Caferri
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Zeno Guardini
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Luca Dall'Osto
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Roberto Bassi
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.
- Accademia Nazionale dei Lincei, Palazzo Corsini, Via Della Lungara, 10, 00165, Rome, Italy.
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16
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Domingo G, Marsoni M, Chiodaroli L, Fortunato S, Bracale M, De Pinto MC, Gehring C, Vannini C. Quantitative phosphoproteomics reveals novel roles of cAMP in plants. Proteomics 2023; 23:e2300165. [PMID: 37264754 DOI: 10.1002/pmic.202300165] [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: 03/27/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
3',5'-cyclic adenosine monophosphate (cAMP) is finally recognized as an essential signaling molecule in plants where cAMP-dependent processes include responses to hormones and environmental stimuli. To better understand the role of 3',5'-cAMP at the systems level, we have undertaken a phosphoproteomic analysis to elucidate the cAMP-dependent response of tobacco BY-2 cells. These cells overexpress a molecular "sponge" that buffers free intracellular cAMP level. The results show that, firstly, in vivo cAMP dampening profoundly affects the plant kinome and notably mitogen-activated protein kinases, receptor-like kinases, and calcium-dependent protein kinases, thereby modulating the cellular responses at the systems level. Secondly, buffering cAMP levels also affects mRNA processing through the modulation of the phosphorylation status of several RNA-binding proteins with roles in splicing, including many serine and arginine-rich proteins. Thirdly, cAMP-dependent phosphorylation targets appear to be conserved among plant species. Taken together, these findings are consistent with an ancient role of cAMP in mRNA processing and cellular programming and suggest that unperturbed cellular cAMP levels are essential for cellular homeostasis and signaling in plant cells.
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Affiliation(s)
- Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Milena Marsoni
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | | | | | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | | | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
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17
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Sharma N, Madan B, Khan MS, Sandhu KS, Raghuram N. Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1135675. [PMID: 37351205 PMCID: PMC10282765 DOI: 10.3389/fpls.2023.1135675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/10/2023] [Indexed: 06/24/2023]
Abstract
Rice is an important target to improve crop nitrogen (N) use efficiency (NUE), and the identification and shortlisting of the candidate genes are still in progress. We analyzed data from 16 published N-responsive transcriptomes/microarrays to identify, eight datasets that contained the maximum number of 3020 common genes, referred to as N-responsive genes. These include different classes of transcription factors, transporters, miRNA targets, kinases and events of post-translational modifications. A Weighted gene co-expression network analysis (WGCNA) with all the 3020 N-responsive genes revealed 15 co-expression modules and their annotated biological roles. Protein-protein interaction network analysis of the main module revealed the hub genes and their functional annotation revealed their involvement in the ubiquitin process. Further, the occurrences of G-quadruplex sequences were examined, which are known to play important roles in epigenetic regulation but are hitherto unknown in N-response/NUE. Out of the 3020 N-responsive genes studied, 2298 contained G-quadruplex sequences. We compared these N-responsive genes containing G-quadruplex sequences with the 3601 genes we previously identified as NUE-related (for being both N-responsive and yield-associated). This analysis revealed 389 (17%) NUE-related genes containing G-quadruplex sequences. These genes may be involved in the epigenetic regulation of NUE, while the rest of the 83% (1811) genes may regulate NUE through genetic mechanisms and/or other epigenetic means besides G-quadruplexes. A few potentially important genes/processes identified as associated with NUE were experimentally validated in a pair of rice genotypes contrasting for NUE. The results from the WGCNA and G4 sequence analysis of N-responsive genes helped identify and shortlist six genes as candidates to improve NUE. Further, the hitherto unavailable segregation of genetic and epigenetic gene targets could aid in informed interventions through genetic and epigenetic means of crop improvement.
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Affiliation(s)
- Narendra Sharma
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Bhumika Madan
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - M. Suhail Khan
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Kuljeet S. Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) - Mohali, Nagar, Punjab, India
| | - Nandula Raghuram
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
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18
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Singh H, Singh Z, Zhu T, Xu X, Waghmode B, Garg T, Yadav S, Sircar D, De Smet I, Yadav SR. Auxin-Responsive (Phospho)proteome Analysis Reveals Key Biological Processes and Signaling Associated with Shoot-Borne Crown Root Development in Rice. PLANT & CELL PHYSIOLOGY 2023; 63:1968-1979. [PMID: 34679169 DOI: 10.1093/pcp/pcab155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/13/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The rice root system is primarily composed of shoot-borne adventitious/crown roots (ARs/CRs) that develop from the coleoptile base, and therefore, it is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance and protein phosphorylation in response to an auxin stimulus during CR development. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) analyses of developing crown root primordia (CRP) and emerged CRs identified 334 proteins and 12 amino acids, respectively, that were differentially regulated upon auxin treatment. Gene ontology enrichment analysis of global proteome data uncovered the biological processes associated with chromatin conformational change, gene expression and cell cycle that were regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Further, the phosphoproteome analysis identified 8,220 phosphosites, which could be mapped to 1,594 phosphoproteins and of which 66 phosphosites were differentially phosphorylated upon auxin treatment. Importantly, we observed differential phosphorylation of the cyclin-dependent kinase G-2 (OsCDKG;2) and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CR development downstream of the auxin signaling pathway.
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Affiliation(s)
- Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Zeenu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Bhairavnath Waghmode
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Shivani Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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19
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Kathare PK, Xin R, Ganesan AS, June VM, Reddy ASN, Huq E. SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2214565119. [PMID: 36282917 PMCID: PMC9636961 DOI: 10.1073/pnas.2214565119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light-absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length-independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swap1sfps, swap1rrc1, and sfpsrrc1 double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swap1sfps double and swap1sfpsrrc1 triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre-messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors.
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Affiliation(s)
- Praveen Kumar Kathare
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Ruijiao Xin
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Abirama Sundari Ganesan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Viviana M. June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Anireddy S. N. Reddy
- Department of Biology, Program in Cell and Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
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20
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Carper DL, Appidi MR, Mudbhari S, Shrestha HK, Hettich RL, Abraham PE. The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont. Microorganisms 2022; 10:microorganisms10102013. [PMID: 36296289 PMCID: PMC9609723 DOI: 10.3390/microorganisms10102013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Sameer Mudbhari
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence:
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21
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Wang J, Li C, Yao L, Ma Z, Ren P, Si E, Li B, Meng Y, Ma X, Yang K, Shang X, Wang H. Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery. FRONTIERS IN PLANT SCIENCE 2022; 13:917652. [PMID: 36061799 PMCID: PMC9433975 DOI: 10.3389/fpls.2022.917652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein-protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.
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Affiliation(s)
- Juncheng Wang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lirong Yao
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zengke Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Panrong Ren
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
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22
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Song W, Hu L, Ma Z, Yang L, Li J. Importance of Tyrosine Phosphorylation in Hormone-Regulated Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23126603. [PMID: 35743047 PMCID: PMC9224382 DOI: 10.3390/ijms23126603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 02/01/2023] Open
Abstract
Protein phosphorylation is the most frequent post-translational modification (PTM) that plays important regulatory roles in a wide range of biological processes. Phosphorylation mainly occurs on serine (Ser), threonine (Thr), and tyrosine (Tyr) residues, with the phosphorylated Tyr sites accounting for ~1–2% of all phosphorylated residues. Tyr phosphorylation was initially believed to be less common in plants compared to animals; however, recent investigation indicates otherwise. Although they lack typical protein Tyr kinases, plants possess many dual-specificity protein kinases that were implicated in diverse cellular processes by phosphorylating Ser, Thr, and Tyr residues. Analyses of sequenced plant genomes also identified protein Tyr phosphatases and dual-specificity protein phosphatases. Recent studies have revealed important regulatory roles of Tyr phosphorylation in many different aspects of plant growth and development and plant interactions with the environment. This short review summarizes studies that implicated the Tyr phosphorylation in biosynthesis and signaling of plant hormones.
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Affiliation(s)
- Weimeng Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Li Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Zhihui Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Lei Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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23
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G-Protein Phosphorylation: Aspects of Binding Specificity and Function in the Plant Kingdom. Int J Mol Sci 2022; 23:ijms23126544. [PMID: 35742988 PMCID: PMC9224535 DOI: 10.3390/ijms23126544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Plant survival depends on adaptive mechanisms that constantly rely on signal recognition and transduction. The predominant class of signal discriminators is receptor kinases, with a vast member composition in plants. The transduction of signals occurs in part by a simple repertoire of heterotrimeric G proteins, with a core composed of α-, β-, and γ-subunits, together with a 7-transmembrane Regulator G Signaling (RGS) protein. With a small repertoire of G proteins in plants, phosphorylation by receptor kinases is critical in regulating the active state of the G-protein complex. This review describes the in vivo detected phosphosites in plant G proteins and conservation scores, and their in vitro corresponding kinases. Furthermore, recently described outcomes, including novel arrestin-like internalization of RGS and a non-canonical phosphorylation switching mechanism that drives G-protein plasticity, are discussed.
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24
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Ji Y, Xu M, Liu Z, Yuan H, Lv T, Li H, Xu Y, Si Y, Wang A. NUCLEOCYTOPLASMIC shuttling of ETHYLENE RESPONSE FACTOR 5 mediated by nitric oxide suppresses ethylene biosynthesis in apple fruit. THE NEW PHYTOLOGIST 2022; 234:1714-1734. [PMID: 35254663 PMCID: PMC9313842 DOI: 10.1111/nph.18071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Nitric oxide (NO) is known to modulate the action of several phytohormones. This includes the gaseous hormone ethylene, but the molecular mechanisms underlying the effect of NO on ethylene biosynthesis are unclear. Here, we observed a decrease in endogenous NO abundance during apple (Malus domestica) fruit development and exogenous treatment of apple fruit with a NO donor suppressed ethylene production, suggesting that NO is a ripening suppressor. Expression of the transcription factor MdERF5 was activated by NO donor treatment. NO induced the nucleocytoplasmic shuttling of MdERF5 by modulating its interaction with the protein phosphatase, MdPP2C57. MdPP2C57-induced dephosphorylation of MdERF5 at Ser260 is sufficient to promote nuclear export of MdERF5. As a consequence of this export, MdERF5 proteins in the cytoplasm interacted with and suppressed the activity of MdACO1, an enzyme that converts 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene. The NO-activated MdERF5 was observed to increase in abundance in the nucleus and bind to the promoter of the ACC synthase gene MdACS1 and directly suppress its transcription. Together, these results suggest that NO-activated nucleocytoplasmic MdERF5 suppresses the action of ethylene biosynthetic genes, thereby suppressing ethylene biosynthesis and limiting fruit ripening.
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Affiliation(s)
- Yinglin Ji
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Mingyang Xu
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Zhi Liu
- Liaoning Institute of PomologyXiongyue115009China
| | - Hui Yuan
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Tianxing Lv
- Liaoning Institute of PomologyXiongyue115009China
| | - Hongjian Li
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
- Liaoning Institute of PomologyXiongyue115009China
| | - Yaxiu Xu
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Yajing Si
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Aide Wang
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province)Key Laboratory of Protected Horticulture (Ministry of Education)National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning)College of HorticultureShenyang Agricultural UniversityShenyang110866China
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25
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Wang M, Garneau MG, Poudel AN, Lamm D, Koo AJ, Bates PD, Thelen JJ. Overexpression of pea α-carboxyltransferase in Arabidopsis and camelina increases fatty acid synthesis leading to improved seed oil content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1035-1046. [PMID: 35220631 DOI: 10.1111/tpj.15721] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
SUMMARYHeteromeric acetyl‐CoA carboxylase (htACCase) catalyzes the committed step of de novo fatty acid biosynthesis in most plant plastids. Plant htACCase is comprised of four subunits: α‐ and β‐carboxyltransferase (α‐ and β‐CT), biotin carboxylase, and biotin carboxyl carrier protein. Based on in vivo absolute quantification of htACCase subunits, α‐CT is 3‐ to 10‐fold less abundant than its partner subunit β‐CT in developing Arabidopsis seeds [Wilson and Thelen, J. Proteome Res., 2018, 17 (5)]. To test the hypothesis that low expression of α‐CT limits htACCase activity and flux through fatty acid synthesis in planta, we overexpressed Pisum sativum α‐CT, either with or without its C‐terminal non‐catalytic domain, in both Arabidopsis thaliana and Camelina sativa. First‐generation Arabidopsis seed of 35S::Ps α‐CT (n = 25) and 35S::Ps α‐CTΔ406‐875 (n = 47) were on average 14% higher in oil content (% dry weight) than wild type co‐cultivated in a growth chamber. First‐generation camelina seed showed an average 8% increase compared to co‐cultivated wild type. Biochemical analyses confirmed the accumulation of Ps α‐CT and Ps α‐CTΔ406‐875 protein and higher htACCase activity in overexpression lines during early seed development. Overexpressed Ps α‐CT co‐migrated with native At β‐CT during anion exchange chromatography, indicating co‐association. By successfully increasing seed oil content upon heterologous overexpression of α‐CT, we demonstrate how absolute quantitation of in vivo protein complex stoichiometry can be used to guide rational metabolic engineering.
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Affiliation(s)
- Minmin Wang
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Matthew G Garneau
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, 99164, USA
| | - Arati N Poudel
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Daniel Lamm
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Abraham J Koo
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, 99164, USA
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
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26
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Shedding Light on the Role of Phosphorylation in Plant Autophagy. FEBS Lett 2022; 596:2172-2185. [DOI: 10.1002/1873-3468.14352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022]
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27
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Chong YK, Tartey S, Yoshikawa Y, Imami K, Li S, Yoshinaga M, Hirabayashi A, Liu G, Vandenbon A, Hia F, Uehata T, Mino T, Suzuki Y, Noda T, Ferrandon D, Standley DM, Ishihama Y, Takeuchi O. Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism. Sci Signal 2022; 15:eabm5011. [PMID: 35412849 DOI: 10.1126/scisignal.abm5011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Toll-like receptor (TLR) stimulation induces glycolysis and the production of mitochondrial reactive oxygen species (ROS), both of which are critical for inflammatory responses in macrophages. Here, we demonstrated that cyclin J, a TLR-inducible member of the cyclin family, reduced cytokine production in macrophages by coordinately controlling glycolysis and mitochondrial functions. Cyclin J interacted with cyclin-dependent kinases (CDKs), which increased the phosphorylation of a subset of CDK substrates, including the transcription factor FoxK1 and the GTPase Drp1. Cyclin J-dependent phosphorylation of FoxK1 decreased the transcription of glycolytic genes and Hif-1α activation, whereas hyperactivation of Drp1 by cyclin J-dependent phosphorylation promoted mitochondrial fragmentation and impaired the production of mitochondrial ROS. In mice, cyclin J in macrophages limited the growth of tumor xenografts and protected against LPS-induced shock but increased the susceptibility to bacterial infection. Collectively, our findings indicate that cyclin J-CDK signaling promotes antitumor immunity and the resolution of inflammation by opposing the metabolic changes that drive inflammatory responses in macrophages.
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Affiliation(s)
- Yee Kien Chong
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sarang Tartey
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,IGM Biosciences Inc., Mountain View, CA, USA
| | - Yuki Yoshikawa
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Songling Li
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Guohao Liu
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexis Vandenbon
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | | | - Daron M Standley
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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28
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Wang B, Andargie M, Fang R. The function and biosynthesis of callose in high plants. Heliyon 2022; 8:e09248. [PMID: 35399384 PMCID: PMC8991245 DOI: 10.1016/j.heliyon.2022.e09248] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
The two main glucan polymers cellulose and callose in plant cell wall are synthesized at the plasma membrane by cellulose or callose synthase complexes. Cellulose is the prevalent glucan in cell wall and provides strength to the walls to support directed cell expansion. By contrast, callose is mainly produced in special cell wall and exercises important functions during development and stress responses. However, the structure and precise regulatory mechanism of callose synthase complex is not very clear. This review therefore compares and analyzes the regulation of callose and cellulose synthesis, and further emphasize the future research direction of callose synthesis.
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29
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Figueroa CM, Asencion Diez MD, Ballicora MA, Iglesias AA. Structure, function, and evolution of plant ADP-glucose pyrophosphorylase. PLANT MOLECULAR BIOLOGY 2022; 108:307-323. [PMID: 35006475 DOI: 10.1007/s11103-021-01235-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023]
Abstract
This review outlines research performed in the last two decades on the structural, kinetic, regulatory and evolutionary aspects of ADP-glucose pyrophosphorylase, the regulatory enzyme for starch biosynthesis. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the pathway of glycogen and starch synthesis in bacteria and plants, respectively. Plant ADP-Glc PPase is a heterotetramer allosterically regulated by metabolites and post-translational modifications. In this review, we focus on the three-dimensional structure of the plant enzyme, the amino acids that bind the regulatory molecules, and the regions involved in transmitting the allosteric signal to the catalytic site. We provide a model for the evolution of the small and large subunits, which produce heterotetramers with distinct catalytic and regulatory properties. Additionally, we review the various post-translational modifications observed in ADP-Glc PPases from different species and tissues. Finally, we discuss the subcellular localization of the enzyme found in grain endosperm from grasses, such as maize and rice. Overall, this work brings together research performed in the last two decades to better understand the multiple mechanisms involved in the regulation of ADP-Glc PPase. The rational modification of this enzyme could improve the yield and resilience of economically important crops, which is particularly important in the current scenario of climate change and food shortage.
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Affiliation(s)
- Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA.
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina.
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Matiolli CC, Soares RC, Alves HLS, Abreu IA. Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism. FRONTIERS IN PLANT SCIENCE 2022; 12:781508. [PMID: 35087551 PMCID: PMC8787203 DOI: 10.3389/fpls.2021.781508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.
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Pascual J, Kangasjärvi S. Targeted Mass Spectrometry Analysis of Protein Phosphorylation by Selected Ion Monitoring Coupled to Parallel Reaction Monitoring (tSIM/PRM). Methods Mol Biol 2022; 2526:227-240. [PMID: 35657524 DOI: 10.1007/978-1-0716-2469-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent developments in targeted mass spectrometry-based proteomics have provided new methodological solutions for accurate and quantitative analysis of proteins and their posttranslational control, which has significantly advanced our understanding of stress responses in different plant species. Instrumentation allowing high-resolution, accurate-mass (HR/AM) analysis has provided new acquisition strategies for targeted quantitative proteomic analysis by targeted selected ion monitoring (tSIM) and parallel reaction monitoring (PRM). Here we report a sensitive and accurate method for targeted analysis of protein phosphorylation by tSIM coupled to PRM (tSIM/PRM). The tSIM/PRM method takes advantage of HR/AM mass spectrometers and benefits from the combination of highly sensitive precursor ion quantification by tSIM and highly confident peptide identification by spectral library matching in PRM. The detailed protocol describes tSIM/PRM analysis of Arabidopsis thaliana foliar proteins, from the building of a spectral library to sample preparation, mass spectrometry, and data analysis, and provides a methodological approach for specifying the molecular mechanisms of interest.
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Affiliation(s)
- Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FIN-00014 University of Helsinki, Helsinki, Finland.
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, FIN-00014 University of Helsinki, Helsinki, Finland.
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Xavier LR, Almeida FA, Pinto VB, Passamani LZ, Santa-Catarina C, de Souza Filho GA, Mooney BP, Thelen JJ, Silveira V. Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153587. [PMID: 34906795 DOI: 10.1016/j.jplph.2021.153587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/14/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Plant embryogenic cell culture allows mass propagation and genetic manipulation, but the mechanisms that determine the fate of these totipotent cells in somatic embryos have not yet been elucidated. Here, we performed label-free quantitative proteomics and phosphoproteomics analyses to determine signaling events related to sugarcane somatic embryo differentiation, especially those related to protein phosphorylation. Embryogenic calli were compared at multiplication (EC0, dedifferentiated cells) and after 14 days of maturation (EC14, onset of embryo differentiation). Metabolic pathway analysis showed enriched lysine degradation and starch/sucrose metabolism proteins during multiplication, whereas the differentiation of somatic embryos was found to involve the enrichment of energy metabolism, including the TCA cycle and oxidative phosphorylation. Multiplication-related phosphoproteins were associated with transcriptional regulation, including SNF1 kinase homolog 10 (KIN10), SEUSS (SEU), and LEUNIG_HOMOLOG (LUH). The regulation of multiple light harvesting complex photosystem II proteins and phytochrome interacting factor 3-LIKE 5 were predicted to promote bioenergetic metabolism and carbon fixation during the maturation stage. A motif analysis revealed 15 phosphorylation motifs. The [D-pS/T-x-D] motif was overrepresented during somatic embryo differentiation. A protein-protein network analysis predicted interactions among SNF1-related protein kinase 2 (SnRK2), abscisic acid-responsive element-binding factor 2 (ABF2), and KIN10, which indicated the role of these proteins in embryogenic competence. The predicted interactions between TOPLESS (TPL) and histone deacetylase 19 (HD19) may be involved in posttranslational protein regulation during somatic embryo differentiation. These results reveal the protein regulation dynamics of somatic embryogenesis and new players in somatic embryo differentiation, including their predicted phosphorylation motifs and phosphosites.
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Affiliation(s)
- Lucas R Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Felipe A Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Vitor B Pinto
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | - Lucas Z Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | | | - Gonçalo A de Souza Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Brian P Mooney
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211, Columbia, MO, USA
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211, Columbia, MO, USA
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
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Zhang Z, Zheng Y, Zhang J, Wang N, Wang Y, Liu W, Bai S, Xie W. High-Altitude Genetic Selection and Genome-Wide Association Analysis of Yield-Related Traits in Elymus sibiricus L. Using SLAF Sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:874409. [PMID: 35800604 PMCID: PMC9253694 DOI: 10.3389/fpls.2022.874409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/26/2022] [Indexed: 05/04/2023]
Abstract
The genetic adaptations to harsh climatic conditions in high altitudes and genetic basis of important agronomic traits are poorly understood in Elymus sibiricus L. In this study, an association population of 210 genotypes was used for population structure, selective sweep analysis, and genome-wide association study (GWAS) based on 88,506 single nucleotide polymorphisms (SNPs). We found 965 alleles under the natural selection of high altitude, which included 7 hub genes involved in the response to UV, and flavonoid and anthocyanin biosynthetic process based on the protein-protein interaction (PPI) analysis. Using a mixed linear model (MLM), the GWAS test identified a total of 1,825 significant loci associated with 12 agronomic traits. Based on the gene expression data of two wheat cultivars and the PPI analysis, we finally identified 12 hub genes. Especially, in plant height traits, the top hub gene (TOPLESS protein) encoding auxins and jasmonic acid signaling pathway, shoot apical meristem specification, and xylem and phloem pattern formation was highly overexpressed. These genes might play essential roles in controlling the growth and development of E. sibiricus. Therefore, this study provides fundamental insights relevant to hub genes and will benefit molecular breeding and improvement in E. sibiricus and other Elymus species.
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Affiliation(s)
- Zongyu Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuying Zheng
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Junchao Zhang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Na Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Wengang Xie,
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Duan G, Ma X, Shi Z, Yang Y, Chen H, Huang Q, Yang J. MoSDT1 triggers defense response through modulating phosphorylated proteins in rice. PLANT MOLECULAR BIOLOGY 2022; 108:15-30. [PMID: 34622380 DOI: 10.1007/s11103-021-01201-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
MoSDT1, a rice blast fungus transcription factor, is as an inducer to activate defense response through mainly mediating phosphorylated proteins in rice. Pathogen effector proteins play a dual role in infecting the host or triggering a defense response. Our previous research found a Magnaporthe oryzae effector, MoSDT1, which could activate the rice defense response when it was overexpressed in rice. However, we still know little about the mechanisms on how MoSDT1 in vivo or in vitro influences the resistance ability of rice. Our results showed that decreased ROS and increased lignin contents appeared along with significant upregulation of defense-related genes, raffinose synthesis gene, and phenylalanine ammonialyase gene. Moreover, we revealed that the contents of lignin were increased, which was in accordance with the upregulation of its precursor phenylalanine gene despite the fact that the glutamate-/thiamine-responsive genes were inhibited in MoSDT1 transgenic rice, and these indicated that MoSDT1 triggered the defense system of rice in vivo. Interestingly, in vitro studies, we further found that MoSDT1 induced the defense system by ROS synthesis, callose deposition, PR gene expression and SA/JA synthesis/signal genes using the purified prokaryotic expression system in rice plants. In addition, this defense response was confirmed to be activated by the zinc finger domain of MoSDT1 via prokaryotic expression of MoSDT1 truncated mutants in rice plants. To elucidate the regulative effects of MoSDT1 on protein phosphorylation in rice, phosphoproteome analysis was performed in both MoSDT1-transgenic and wild type rice. We found that MoSDT1 specifically up-regulated the expression levels of a few phosphorylated proteins, which were involved in multiple functions, such as biotic/abiotic stress and growth. In addition, the motifs in these specific proteins ranked the top among the top-five conserved motifs in the MoSDT1-transgenic rice. MoSDT1 played a crucial role in enhancing rice resistance by modulating several genes and signaling pathways.
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Affiliation(s)
- Guihua Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Xiaoqing Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Zhufeng Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Yaqiong Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Qiong Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China.
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China.
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China.
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China.
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35
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Subba P, Prasad TSK. Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:750-769. [PMID: 34882020 DOI: 10.1089/omi.2021.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant systems science research depends on the dynamic functional maps of the biological substrates of plant phenotypes and host/environment interactions in diverse ecologies. In this context, high-resolution mass spectrometry platforms offer comprehensive insights into the molecular pathways regulated by protein phosphorylation. Reversible protein phosphorylation is a ubiquitous reaction in signal transduction mechanisms in biological systems. In contrast to human and animal biology research, a plethora of experimental options for functional mapping and regulation of plant biology are, however, not currently available. Plant phosphoproteomics is an emerging field of research that aims at addressing this gap in systems science and plant omics, and thus has a large scope to empower fundamental discoveries. To date, large-scale data-intensive identification of phosphorylation events in plants remained technically challenging. In this expert review, we present a critical analysis and overview of phosphoproteomic studies performed in the model plant Arabidopsis thaliana. We discuss the technical strategies used for the enrichment of phosphopeptides and methods used for their quantitative assessment. Various types of mass spectrometry data acquisition and fragmentation methods are also discussed. The insights gathered here can allow plant biology and systems science researchers to design high-throughput function-oriented experimental workflows that elucidate the regulatory signaling mechanisms impacting plant physiology and plant diseases.
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Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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36
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Akaki K, Ogata K, Yamauchi Y, Iwai N, Tse KM, Hia F, Mochizuki A, Ishihama Y, Mino T, Takeuchi O. IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay. eLife 2021; 10:71966. [PMID: 34636324 PMCID: PMC8553338 DOI: 10.7554/elife.71966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/08/2021] [Indexed: 01/14/2023] Open
Abstract
Regnase-1 is an endoribonuclease crucial for controlling inflammation by degrading mRNAs encoding cytokines and inflammatory mediators in mammals. However, it is unclear how Regnase-1-mediated mRNA decay is controlled in interleukin (IL)-1β- or Toll-like receptor (TLR) ligand-stimulated cells. Here, by analyzing the Regnase-1 interactome, we found that IL-1β or TLR stimulus dynamically induced the formation of Regnase-1-β-transducin repeat-containing protein (βTRCP) complex. Importantly, we also uncovered a novel interaction between Regnase-1 and 14-3-3 in both mouse and human cells. In IL-1R/TLR-stimulated cells, the Regnase-1-14-3-3 interaction is mediated by IRAK1 through a previously uncharacterized C-terminal structural domain. Phosphorylation of Regnase-1 at S494 and S513 is critical for Regnase-1-14-3-3 interaction, while a different set of phosphorylation sites of Regnase-1 is known to be required for the recognition by βTRCP and proteasome-mediated degradation. We found that Regnase-1-14-3-3 and Regnase-1-βTRCP interactions are not sequential events. Rather, 14-3-3 protects Regnase-1 from βTRCP-mediated degradation. On the other hand, 14-3-3 abolishes Regnase-1-mediated mRNA decay by inhibiting Regnase-1-mRNA association. In addition, nuclear-cytoplasmic shuttling of Regnase-1 is abrogated by 14-3-3 interaction. Taken together, the results suggest that a novel inflammation-induced interaction of 14-3-3 with Regnase-1 stabilizes inflammatory mRNAs by sequestering Regnase-1 in the cytoplasm to prevent mRNA recognition.
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Affiliation(s)
- Kotaro Akaki
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yuhei Yamauchi
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ka Man Tse
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Clark NM, Nolan TM, Wang P, Song G, Montes C, Valentine CT, Guo H, Sozzani R, Yin Y, Walley JW. Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nat Commun 2021; 12:5858. [PMID: 34615886 PMCID: PMC8494934 DOI: 10.1038/s41467-021-26165-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/22/2021] [Indexed: 11/14/2022] Open
Abstract
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Trevor M Nolan
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Ping Wang
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Conner T Valentine
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Hongqing Guo
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yanhai Yin
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
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38
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Kathare PK, Huq E. Light-regulated pre-mRNA splicing in plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102037. [PMID: 33823333 PMCID: PMC8487434 DOI: 10.1016/j.pbi.2021.102037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/26/2021] [Indexed: 05/11/2023]
Abstract
Light signal perceived by the red/far-red absorbing phytochrome (phy) family of photoreceptors regulates plant growth and development throughout the life cycle. Phytochromes regulate the light-triggered physiological responses by controlling gene expression both at the transcriptional and post-transcriptional levels. Recent large-scale RNA-seq studies have demonstrated the roles of phys in altering the global transcript diversity by modulating the pre-mRNA splicing in response to light. Moreover, several phy-interacting splicing factors/regulators from different species have been identified using forward genetics and protein-protein interaction studies, which modulate the light-regulated pre-mRNA splicing. In this article, we summarize our current understanding of the role of phys in the light-mediated pre-mRNA splicing and how that contributes to the regulation of gene expression to promote photomorphogenesis.
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Affiliation(s)
- Praveen Kumar Kathare
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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Activation loop phosphorylaton of a non-RD receptor kinase initiates plant innate immune signaling. Proc Natl Acad Sci U S A 2021; 118:2108242118. [PMID: 34531323 PMCID: PMC8463890 DOI: 10.1073/pnas.2108242118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 01/01/2023] Open
Abstract
Receptor kinases (RKs) are fundamental for extracellular sensing and regulate development and stress responses across kingdoms. In plants, leucine-rich repeat receptor kinases (LRR-RKs) are primarily peptide receptors that regulate responses to myriad internal and external stimuli. Phosphorylation of LRR-RK cytoplasmic domains is among the earliest responses following ligand perception, and reciprocal transphosphorylation between a receptor and its coreceptor is thought to activate the receptor complex. Originally proposed based on characterization of the brassinosteroid receptor, the prevalence of complex activation via reciprocal transphosphorylation across the plant RK family has not been tested. Using the LRR-RK ELONGATION FACTOR TU RECEPTOR (EFR) as a model, we set out to understand the steps critical for activating RK complexes. While the EFR cytoplasmic domain is an active protein kinase in vitro and is phosphorylated in a ligand-dependent manner in vivo, catalytically deficient EFR variants are functional in antibacterial immunity. These results reveal a noncatalytic role for EFR in triggering immune signaling and indicate that reciprocal transphoshorylation is not a ubiquitous requirement for LRR-RK complex activation. Rather, our analysis of EFR along with a detailed survey of the literature suggests a distinction between LRR-RKs with RD- versus non-RD protein kinase domains. Based on newly identified phosphorylation sites that regulate the activation state of the EFR complex in vivo, we propose that LRR-RK complexes containing a non-RD protein kinase may be regulated by phosphorylation-dependent conformational changes of the ligand-binding receptor, which could initiate signaling either allosterically or through driving the dissociation of negative regulators of the complex.
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Duminil P, Davanture M, Oury C, Boex-Fontvieille E, Tcherkez G, Zivy M, Hodges M, Glab N. Arabidopsis thaliana 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2 activity requires serine 82 phosphorylation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1478-1489. [PMID: 34174129 DOI: 10.1111/tpj.15395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Phosphoglycerate mutases (PGAMs) catalyse the reversible isomerisation of 3-phosphoglycerate and 2-phosphoglycerate, a step of glycolysis. PGAMs can be sub-divided into 2,3-bisphosphoglycerate-dependent (dPGAM) and -independent (iPGAM) enzymes. In plants, phosphoglycerate isomerisation is carried out by cytosolic iPGAM. Despite its crucial role in catabolism, little is known about post-translational modifications of plant iPGAM. In Arabidopsis thaliana, phosphoproteomics analyses have previously identified an iPGAM phosphopeptide where serine 82 is phosphorylated. Here, we show that this phosphopeptide is less abundant in dark-adapted compared to illuminated Arabidopsis leaves. In silico comparison of iPGAM protein sequences and 3D structural modelling of AtiPGAM2 based on non-plant iPGAM enzymes suggest a role for phosphorylated serine in the catalytic reaction mechanism. This is confirmed by the activity (or the lack thereof) of mutated recombinant Arabidopsis iPGAM2 forms, affected in different steps of the reaction mechanism. We thus propose that the occurrence of the S82-phosphopeptide reflects iPGAM2 steady-state catalysis. Based on this assumption, the metabolic consequences of a higher iPGAM activity in illuminated versus darkened leaves are discussed.
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Affiliation(s)
- Pauline Duminil
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Marlène Davanture
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, PAPPSO, GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Céline Oury
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Edouard Boex-Fontvieille
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, Canberra, ACT, 2601, Australia
- Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAe, 42 rue Georges Morel, Beaucouzé, 49070, France
| | - Michel Zivy
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, PAPPSO, GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Nathalie Glab
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
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López-Marqués RL. Lipid flippases as key players in plant adaptation to their environment. NATURE PLANTS 2021; 7:1188-1199. [PMID: 34531559 DOI: 10.1038/s41477-021-00993-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Lipid flippases (P4 ATPases) are active transporters that catalyse the translocation of lipids between the two sides of the biological membranes in the secretory pathway. This activity modulates biological membrane properties, contributes to vesicle formation, and is the trigger for lipid signalling events, which makes P4 ATPases essential for eukaryotic cell survival. Plant P4 ATPases (also known as aminophospholipid ATPases (ALAs)) are crucial for plant fertility and proper development, and are involved in key adaptive responses to biotic and abiotic stress, including chilling tolerance, heat adaptation, nutrient deficiency responses and pathogen defence. While ALAs present many analogies to mammalian and yeast P4 ATPases, they also show characteristic features as the result of their independent evolution. In this Review, the main properties, roles, regulation and mechanisms of action of ALA proteins are discussed.
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Affiliation(s)
- Rosa L López-Marqués
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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Abstract
Crassulacean acid metabolism (CAM) has evolved from a C3 ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C3 genes and their regulators to enable the trait. The circadian pattern of CO2 fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C3 plants. The metabolic CAM cycle relies on enzymes and transporters that exist in C3 plants and requires tight regulatory control to avoid futile cycles between carboxylation and decarboxylation. Ecological observations and modeling point to mesophyll conductance as a major factor during CAM evolution. The present state of knowledge enables suggestions for genes for a minimal CAM cycle for proof-of-concept engineering, assuming altered regulation of starch synthesis and degradation are not critical elements of CAM photosynthesis and sufficient malic acid export from the vacuole is possible.
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Affiliation(s)
- Katharina Schiller
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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Juarez-Escobar J, Elizalde-Contreras JM, Loyola-Vargas VM, Ruiz-May E. A Phosphoproteomic Analysis Pipeline for Peels of Tropical Fruits. Methods Mol Biol 2021; 2139:179-196. [PMID: 32462587 DOI: 10.1007/978-1-0716-0528-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phosphorylation is a posttranslational reversible modification related to signaling and regulatory mechanisms. Protein phosphorylation is linked to structural changes that modulate protein activity, interaction, or localization and therefore the cell signaling pathways. The use of techniques for phosphoprotein enrichment along with mass spectrometry has become a powerful tool for the characterization of signal transduction in model organisms. However, limited efforts have focused on the establishment of protocols for the analysis of the phosphoproteome in nonmodel organisms such as tropical fruits. This chapter describes a potential pipeline for sample preparation and enrichment of phosphorylated proteins/peptides before MS analysis of peels of some species of tropical fruits.
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Affiliation(s)
- Janet Juarez-Escobar
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán (CICY), Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico.
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Uhrig RG, Echevarría‐Zomeño S, Schlapfer P, Grossmann J, Roschitzki B, Koerber N, Fiorani F, Gruissem W. Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome. PLANT, CELL & ENVIRONMENT 2021; 44:821-841. [PMID: 33278033 PMCID: PMC7986931 DOI: 10.1111/pce.13969] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 05/11/2023]
Abstract
Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin-dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.
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Affiliation(s)
- R. Glen Uhrig
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Pascal Schlapfer
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
| | - Jonas Grossmann
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Bernd Roschitzki
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Niklas Koerber
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Fabio Fiorani
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Wilhelm Gruissem
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
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47
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Dvořák P, Krasylenko Y, Zeiner A, Šamaj J, Takáč T. Signaling Toward Reactive Oxygen Species-Scavenging Enzymes in Plants. FRONTIERS IN PLANT SCIENCE 2021; 11:618835. [PMID: 33597960 PMCID: PMC7882706 DOI: 10.3389/fpls.2020.618835] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
Reactive oxygen species (ROS) are signaling molecules essential for plant responses to abiotic and biotic stimuli as well as for multiple developmental processes. They are produced as byproducts of aerobic metabolism and are affected by adverse environmental conditions. The ROS content is controlled on the side of their production but also by scavenging machinery. Antioxidant enzymes represent a major ROS-scavenging force and are crucial for stress tolerance in plants. Enzymatic antioxidant defense occurs as a series of redox reactions for ROS elimination. Therefore, the deregulation of the antioxidant machinery may lead to the overaccumulation of ROS in plants, with negative consequences both in terms of plant development and resistance to environmental challenges. The transcriptional activation of antioxidant enzymes accompanies the long-term exposure of plants to unfavorable environmental conditions. Fast ROS production requires the immediate mobilization of the antioxidant defense system, which may occur via retrograde signaling, redox-based modifications, and the phosphorylation of ROS detoxifying enzymes. This review aimed to summarize the current knowledge on signaling processes regulating the enzymatic antioxidant capacity of plants.
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Wang M, Tian Y, Han C, Zhou C, Bai MY, Fan M. Phospho-Mutant Activity Assays Provide Evidence for the Negative Regulation of Transcriptional Regulator PRE1 by Phosphorylation. Int J Mol Sci 2020; 21:ijms21239183. [PMID: 33276448 PMCID: PMC7729563 DOI: 10.3390/ijms21239183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 11/17/2022] Open
Abstract
The PACLOBUTRAZOL-RESISTANCE (PRE) gene family encodes a group of atypical helix-loop-helix (HLH) proteins that act as the major hub integrating a wide range of environmental and hormonal signals to regulate plant growth and development. PRE1, as a positive regulator of cell elongation, activates HBI1 DNA binding by sequestering its inhibitor IBH1. Furthermore, PRE1 can be phosphorylated at Ser-46 and Ser-67, but how this phosphorylation regulates the functions of PRE1 remains unclear. Here, we used a phospho-mutant activity assay to reveal that the phosphorylation at Ser-67 negatively regulates the functions of PRE1 on cell elongation. Both of mutations of serine 46, either to phospho-dead alanine or phospho-mimicking glutamic acid, had no significant effects on the functions of PRE1. However, the mutation of serine 67 to glutamic acid (PRE1S67E-Ox), but not alanine (PRE1S67A-Ox), significantly reduced the promoting effects of PRE1 on cell elongation. The mutation of Ser-67 to Glu-67 impaired the interaction of PRE1 with IBH1 and resulted in PRE1 failing to inhibit the interaction between IBH1 and HBI1, losing the ability to induce the expression of the subsequent cell elongation-related genes. Furthermore, we showed that PRE1-Ox and PRE1S67A-Ox both suppressed but PRE1S67E-Ox had no strong effects on the dwarf phenotypes of IBH1-Ox. Our study demonstrated that the PRE1 activity is negatively regulated by the phosphorylation at Ser-67.
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Mi R, Rabbi MH, Sun Y, Li X, Ma S, Wen Z, Meng N, Li Y, Du X, Li S. Enhanced protein phosphorylation in Apostichopus japonicus intestine triggered by tussah immunoreactive substances might be involved in the regulation of immune-related signaling pathways. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100757. [PMID: 33197859 DOI: 10.1016/j.cbd.2020.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 11/28/2022]
Abstract
The sea cucumber Apostichopus japonicus is an economically important species owing to its high nutritive and medicinal value. In order to avoid the pollution resulting from the overuse of antibiotics in A. japonicus aquaculture, various immunostimulants have been used as an alternative to improve the efficiency of A. japonicus farming. Our previous proteomic investigation has shown that several proteins participating in the immune-related physiology of A. japonicus were differentially expressed in the intestinal tissue in response to tussah immunoreactive substances (TIS). This study further explored the immunostimulation mechanism of TIS in A. japonicus. Phosphoproteomics technology was used to investigate the effect of TIS on protein phosphorylation in the intestine of A. japonicus following feeding with a TIS-supplemented diet. A total of 213 unique phosphoproteins were detected from 225 unique phosphopeptides. KEGG pathway analysis showed that majority of the phosphoproteins are involved in endocytosis, carbon metabolism and spliceosome functional group. Sixteen of the phosphoproteins exhibited differential phosphorylation in response to TIS and 12 of these were found to associate with biological functions. Of these 12 phosphoproteins, eight exhibited enhanced phosphorylation while four displayed reduced phosphorylation. These 12 proteins were further analyzed and all were found to play a role in regulating some aspects of the immune system and the growth of sea cucumbers, especially in phagocytosis, energy metabolism and disease resistance. The findings of this study could therefore shed new light on the immune pathways of sea cucumber that are affected by TIS. This could help us to better understand the underlying mechanism linked to the immunoenhancement of A. japonicus in response to TIS, one that is associated with the change in protein phosphorylation.
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Affiliation(s)
- Rui Mi
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Md Hasim Rabbi
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116024, PR China
| | - Yongxin Sun
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China.
| | - Xuejun Li
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Shuhui Ma
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Zhixin Wen
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Nan Meng
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Yajie Li
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Xingfan Du
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
| | - Shuying Li
- Liaoning Ocean and Fisheries Science Research Institute, Liaoning Academy of Agricultural Sciences, Dalian 116024, PR China
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50
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Kamal MM, Ishikawa S, Takahashi F, Suzuki K, Kamo M, Umezawa T, Shinozaki K, Kawamura Y, Uemura M. Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. Int J Mol Sci 2020; 21:E8631. [PMID: 33207747 PMCID: PMC7696906 DOI: 10.3390/ijms21228631] [Citation(s) in RCA: 12] [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: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022] Open
Abstract
Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
| | - Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Ko Suzuki
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Masaharu Kamo
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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