1
|
Van Leene J, Eeckhout D, Gadeyne A, Matthijs C, Han C, De Winne N, Persiau G, Van De Slijke E, Persyn F, Mertens T, Smagghe W, Crepin N, Broucke E, Van Damme D, Pleskot R, Rolland F, De Jaeger G. Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins. NATURE PLANTS 2022; 8:1245-1261. [PMID: 36376753 DOI: 10.1038/s41477-022-01269-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
The central metabolic regulator SnRK1 controls plant growth and survival upon activation by energy depletion, but detailed molecular insight into its regulation and downstream targets is limited. Here we used phosphoproteomics to infer the sucrose-dependent processes targeted upon starvation by kinases as SnRK1, corroborating the relation of SnRK1 with metabolic enzymes and transcriptional regulators, while also pointing to SnRK1 control of intracellular trafficking. Next, we integrated affinity purification, proximity labelling and crosslinking mass spectrometry to map the protein interaction landscape, composition and structure of the SnRK1 heterotrimer, providing insight in its plant-specific regulation. At the intersection of this multi-dimensional interactome, we discovered a strong association of SnRK1 with class II T6P synthase (TPS)-like proteins. Biochemical and cellular assays show that TPS-like proteins function as negative regulators of SnRK1. Next to stable interactions with the TPS-like proteins, similar intricate connections were found with known regulators, suggesting that plants utilize an extended kinase complex to fine-tune SnRK1 activity for optimal responses to metabolic stress.
Collapse
Affiliation(s)
- Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Nancy De Winne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Freya Persyn
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Toon Mertens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wouter Smagghe
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nathalie Crepin
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Ellen Broucke
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Daniël Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Roman Pleskot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| |
Collapse
|
2
|
Chen M, Farmer N, Zhong Z, Zheng W, Tang W, Han Y, Lu G, Wang Z, Ebbole DJ. HAG Effector Evolution in Pyricularia Species and Plant Cell Death Suppression by HAG4. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:694-705. [PMID: 35345886 DOI: 10.1094/mpmi-01-22-0010-r] [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: 06/14/2023]
Abstract
Seventy host-adapted gene (HAG) effector family members from Pyricularia species are found in P. oryzae and three closely related species (isolates LS and 18-2 from an unknown Pyricularia sp., P. grisea, and P. pennisetigena) that share at least eight orthologous HAG family members with P. oryzae. The genome sequence of a more distantly related species, P. penniseti, lacks HAG genes, suggesting a time frame for the origin of the gene family in the genus. In P. oryzae, HAG4 is uniquely found in the genetic lineage that contains populations adapted to Setaria and Oryza hosts. We find a nearly identical HAG4 allele in a P. grisea isolate, suggesting transfer of HAG4 from P. grisea to P. oryzae. HAG4 encodes a suppressor of plant cell death. Yeast two-hybrid screens with several HAG genes independently identify common interacting clones from a rice complementary DNA library, suggesting conservation of protein surface motifs between HAG homologs with as little as 40% protein sequence identity. HAG family orthologs have diverged rapidly and HAG15 orthologs display unusually high rates of sequence divergence compared with adjacent genes suggesting gene-specific accelerated divergence. The sequence diversity of the HAG homologs in Pyricularia species provides a resource for examining mechanisms of gene family evolution and the relationship to structural and functional evolution of HAG effector family activity. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Meilian Chen
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
- Key Laboratory of Bio-Pesticide and Chemistry-Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nick Farmer
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
| | - Zhenhui Zhong
- Key Laboratory of Bio-Pesticide and Chemistry-Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zheng
- Key Laboratory of Bio-Pesticide and Chemistry-Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Tang
- Key Laboratory of Bio-Pesticide and Chemistry-Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yijuan Han
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
| | - Guodong Lu
- Key Laboratory of Bio-Pesticide and Chemistry-Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
- Key Laboratory of Bio-Pesticide and Chemistry-Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Daniel J Ebbole
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, U.S.A
| |
Collapse
|
3
|
Jamsheer K M, Kumar M, Srivastava V. SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6042-6065. [PMID: 33693699 DOI: 10.1093/jxb/erab079] [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: 09/04/2020] [Accepted: 02/17/2021] [Indexed: 05/03/2023]
Abstract
The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.
Collapse
Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Manoj Kumar
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| |
Collapse
|
4
|
Song J, Shang L, Wang X, Xing Y, Xu W, Zhang Y, Wang T, Li H, Zhang J, Ye Z. MAPK11 regulates seed germination and ABA signaling in tomato by phosphorylating SnRKs. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1677-1690. [PMID: 33448300 DOI: 10.1093/jxb/eraa564] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Seed germination is a critical stage in the plant life cycle and it plays an important role in the efficiency of agricultural production. However, our knowledge of the mechanisms that regulate seed germination remains limited. In this study, we identified a novel gene, MAPK11, that encodes mitogen-activated protein kinase 11; its expression was significantly higher in seeds of tomato varieties with a low optimum germination temperature than in those with a high optimum germination temperature. In tests at 25 °C, overexpression of MAPK11 in an accession with optimum germination at 25 °C resulted in a decrease in germination, whereas RNAi of MAPK11 in an accession with optimum germination at 15 °C resulted in increased germination. Furthermore, we found that lines overexpressing MAPK11 exhibited hypersensitivity to ABA during germination. These observations were at least partially explained by the fact that MAPK11 up-regulated both NCED1 expression and ABA biosynthesis, and that it also affected ABA signaling and negatively regulated germination by influencing the phosphorylation of SnRK2.2 in vivo. In addition, we found that MAPK11 interacts with and phosphorylates SnRK1 in vivo, thereby potentially inhibiting its activation. SnRK1 interacted with ABI5 and suppressed the transcription of ABI5, thereby affecting ABA signaling and the regulation of germination. Our results demonstrate that ABA signaling in tomato is affected by a mechanism that depends on MAPK11 phosphorylating SnRKs, and this ultimately influences seed germination.
Collapse
Affiliation(s)
- Jianwen Song
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Lele Shang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Xin Wang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Yali Xing
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Wei Xu
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China) Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
5
|
Lei L, Stevens DM, Coaker G. Phosphorylation of the Pseudomonas Effector AvrPtoB by Arabidopsis SnRK2.8 Is Required for Bacterial Virulence. MOLECULAR PLANT 2020; 13:1513-1522. [PMID: 32889173 PMCID: PMC7808569 DOI: 10.1016/j.molp.2020.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 08/20/2020] [Accepted: 08/30/2020] [Indexed: 05/03/2023]
Abstract
A critical component controlling bacterial virulence is the delivery of pathogen effectors into plant cells during infection. Effectors alter host metabolism and immunity for the benefit of pathogens. Multiple effectors are phosphorylated by host kinases, and this posttranslational modification is important for their activity. We sought to identify host kinases involved in effector phosphorylation. Multiple phosphorylated effector residues matched the proposed consensus motif for the plant calcium-dependent protein kinase (CDPK) and Snf1-related kinase (SnRK) superfamily. The conserved Pseudomonas effector AvrPtoB acts as an E3 ubiquitin ligase and promotes bacterial virulence. In this study, we identified a member of the Arabidopsis SnRK family, SnRK2.8, which interacts with AvrPtoB in yeast and in planta. We showed that SnRK2.8 was required for AvrPtoB virulence functions, including facilitating bacterial colonization, suppression of callose deposition, and targeting the plant defense regulator NPR1 and analyses receptor FLS2. Mass spectrometry analysis revealed that AvrPtoB phosphorylation occurs at multiple serine residues in planta, with S258 phosphorylation significantly reduced in the snrk2.8 knockout. AvrPtoB phospho-null mutants exhibited compromised virulence functions and were unable to suppress NPR1 accumulation, FLS2 accumulation, or inhibit FLS2-BAK1 complex formation upon flagellin perception. Taken together, these data identify a conserved plant kinase utilized by a pathogen effector to promote disease.
Collapse
Affiliation(s)
- Lei Lei
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Danielle M Stevens
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA.
| |
Collapse
|
6
|
Han X, Zhang L, Zhao L, Xue P, Qi T, Zhang C, Yuan H, Zhou L, Wang D, Qiu J, Shen QH. SnRK1 Phosphorylates and Destabilizes WRKY3 to Enhance Barley Immunity to Powdery Mildew. PLANT COMMUNICATIONS 2020; 1:100083. [PMID: 33367247 PMCID: PMC7747994 DOI: 10.1016/j.xplc.2020.100083] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 05/19/2023]
Abstract
Plants recognize pathogens and activate immune responses, which usually involve massive transcriptional reprogramming. The evolutionarily conserved kinase, Sucrose non-fermenting-related kinase 1 (SnRK1), functions as a metabolic regulator that is essential for plant growth and stress responses. Here, we identify barley SnRK1 and a WRKY3 transcription factor by screening a cDNA library. SnRK1 interacts with WRKY3 in yeast, as confirmed by pull-down and luciferase complementation assays. Förster resonance energy transfer combined with noninvasive fluorescence lifetime imaging analysis indicates that the interaction occurs in the barley nucleus. Transient expression and virus-induced gene silencing analyses indicate that WRKY3 acts as a repressor of disease resistance to the Bgh fungus. Barley plants overexpressing WRKY3 have enhanced fungal microcolony formation and sporulation. Phosphorylation assays show that SnRK1 phosphorylates WRKY3 mainly at Ser83 and Ser112 to destabilize the repressor, and WRKY3 non-phosphorylation-null mutants at these two sites are more stable than the wild-type protein. SnRK1-overexpressing barley plants display enhanced disease resistance to Bgh. Transient expression of SnRK1 reduces fungal haustorium formation in barley cells, which probably requires SnRK1 nuclear localization and kinase activity. Together, these findings suggest that SnRK1 is directly involved in plant immunity through phosphorylation and destabilization of the WRKY3 repressor, revealing a new regulatory mechanism of immune derepression in plants.
Collapse
Affiliation(s)
- Xinyun Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
| | - Lifang Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengya Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Qi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
| | - Chunlei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixun Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
| | - Jinlong Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author
| |
Collapse
|
7
|
Yeo IC, Devarenne TP. Screening for potential nuclear substrates for the plant cell death suppressor kinase Adi3 using peptide microarrays. PLoS One 2020; 15:e0234011. [PMID: 32484825 PMCID: PMC7266335 DOI: 10.1371/journal.pone.0234011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022] Open
Abstract
The tomato AGC protein kinase Adi3 is a Ser/Thr kinase that functions as a negative regulator of programmed cell death through cell death suppression (CDS) activity in the nucleus. In this study, to understand the mechanism of Adi3 CDS, peptide microarrays containing random Ser- and Thr-peptide phosphorylation substrates were used to screen for downstream phosphorylation substrates. In the microarray phosphorylation assay, Adi3 showed promiscuous kinase activity more toward Ser-peptides compared to Thr-peptides, and a preference for aromatic and cyclic amino acids on both Ser- and Thr-peptides was seen. The 63 highest phosphorylated peptide sequences from the Ser-peptide microarray were selected as queries for a BLAST search against the tomato proteome. As a result, 294 candidate nuclear Adi3 substrates were selected and categorized based on their functions. Many of these proteins were classified as DNA/RNA polymerases or regulators involved in transcription and translation events. The list of potential Adi3 substrates was narrowed to eleven and four candidates were tested for phosphorylation by Adi3. Two of these candidates, RNA polymerase II 2nd largest subunit (RPB2) and the pathogen defense related transcription factor Pti5, were confirmed as Adi3 phosphorylation substrates by in vitro kinase assays. Using a mutational approach two residues, Thr675 and Thr676, were identified as Adi3 phosphorylation sites on RPB2. This study provides the foundation for understanding Adi3 CDS mechanisms in the nucleus as well as other cellular functions.
Collapse
Affiliation(s)
- In-Cheol Yeo
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Timothy P. Devarenne
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| |
Collapse
|
8
|
Lai T, Wang X, Ye B, Jin M, Chen W, Wang Y, Zhou Y, Blanks AM, Gu M, Zhang P, Zhang X, Li C, Wang H, Liu Y, Gallusci P, Tör M, Hong Y. Molecular and functional characterization of the SBP-box transcription factor SPL-CNR in tomato fruit ripening and cell death. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2995-3011. [PMID: 32016417 PMCID: PMC7260717 DOI: 10.1093/jxb/eraa067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/01/2020] [Indexed: 05/19/2023]
Abstract
SlSPL-CNR, an SBP-box transcription factor (TF) gene residing at the epimutant Colourless non-ripening (Cnr) locus, is involved in tomato ripening. This epimutant provides a unique model to investigate the (epi)genetic basis of fruit ripening. Here we report that SlSPL-CNR is a nucleus-localized protein with a distinct monopartite nuclear localization signal (NLS). It consists of four consecutive residues ' 30KRKR33' at the N-terminus of the protein. Mutation of the NLS abolishes SlSPL-CNR's ability to localize in the nucleus. SlSPL-CNR comprises two zinc-finger motifs (ZFMs) within the C-terminal SBP-box domain. Both ZFMs contribute to zinc-binding activity. SlSPL-CNR can induce cell death in tomato and tobacco, dependent on its nuclear localization. However, the two ZFMs have differential impacts on SlSPL-CNR's induction of severe necrosis or mild necrotic ringspot. NLS and ZFM mutants cannot complement Cnr fruits to ripen. SlSPL-CNR interacts with SlSnRK1. Virus-induced SlSnRK1 silencing leads to reduction in expression of ripening-related genes and inhibits ripening in tomato. We conclude that SlSPL-CNR is a multifunctional protein that consists of a distinct monopartite NLS, binds to zinc, and interacts with SlSnRK1 to affect cell death and tomato fruit ripening.
Collapse
Affiliation(s)
- Tongfei Lai
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaohong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bishun Ye
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mingfei Jin
- School of Life Sciences, East China Normal University, Shanghai, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ying Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yingying Zhou
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Andrew M Blanks
- Cell and Developmental Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Mei Gu
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Chunyang Li
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRA, Bordeaux Science Agro, Villenave d’Ornon, France
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Correspondence: , or
| |
Collapse
|
9
|
Perochon A, Váry Z, Malla KB, Halford NG, Paul MJ, Doohan FM. The wheat SnRK1α family and its contribution to Fusarium toxin tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110217. [PMID: 31521211 DOI: 10.1016/j.plantsci.2019.110217] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 05/09/2023]
Abstract
Deoxynivalenol (DON) is a mycotoxin produced by phytopathogenic Fusarium fungi in cereal grain and plays a role as a disease virulence factor. TaFROG (Triticum aestivum Fusarium Resistance Orphan Gene) enhances wheat resistance to DON and it interacts with a sucrose non-fermenting-1 (SNF1)-related protein kinase 1 catalytic subunit α (SnRK1α). This protein kinase family is central integrator of stress and energy signalling, regulating plant metabolism and growth. Little is known regarding the role of SnRK1α in the biotic stress response, especially in wheat. In this study, 15 wheat (Triticum aestivum) SnRK1α genes (TaSnRK1αs) belonging to four homoeologous groups were identified in the wheat genome. TaSnRK1αs are expressed ubiquitously in all organs and developmental stages apart from two members predominantly detected in grain. While DON treatment had either no effect or downregulated the transcription of TaSnRK1αs, it increased both the kinase activity associated with SnRK1α and the level of active (phosphorylated) SnRK1α. Down-regulation of two TaSnRK1αs homoeolog groups using virus induced gene silencing (VIGS) increased the DON-induced damage of wheat spikelets. Thus, we demonstrate that TaSnRK1αs contribute positively to wheat tolerance of DON and conclude that this gene family may provide useful tools for the improvement of crop biotic stress resistance.
Collapse
Affiliation(s)
- Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Zsolt Váry
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Keshav B Malla
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Nigel G Halford
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom.
| | - Matthew J Paul
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom.
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland.
| |
Collapse
|
10
|
Rodriguez M, Parola R, Andreola S, Pereyra C, Martínez-Noël G. TOR and SnRK1 signaling pathways in plant response to abiotic stresses: Do they always act according to the "yin-yang" model? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110220. [PMID: 31521220 DOI: 10.1016/j.plantsci.2019.110220] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
Plants are sessile photo-autotrophic organisms continuously exposed to a variety of environmental stresses. Monitoring the sugar level and energy status is essential, since this knowledge allows the integration of external and internal cues required for plant physiological and developmental plasticity. Most abiotic stresses induce severe metabolic alterations and entail a great energy cost, restricting plant growth and producing important crop losses. Therefore, balancing energy requirements with supplies is a major challenge for plants under unfavorable conditions. The conserved kinases target of rapamycin (TOR) and sucrose-non-fermenting-related protein kinase-1 (SnRK1) play central roles during plant growth and development, and in response to environmental stresses; these kinases affect cellular processes and metabolic reprogramming, which has physiological and phenotypic consequences. The "yin-yang" model postulates that TOR and SnRK1 act in opposite ways in the regulation of metabolic-driven processes. In this review, we describe and discuss the current knowledge about the complex and intricate regulation of TOR and SnRK1 under abiotic stresses. We especially focus on the physiological perspective that, under certain circumstances during the plant stress response, the TOR and SnRK1 kinases could be modulated differently from what is postulated by the "yin-yang" concept.
Collapse
Affiliation(s)
- Marianela Rodriguez
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Rodrigo Parola
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Sofia Andreola
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Cintia Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), y Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
| | - Giselle Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), y Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
| |
Collapse
|
11
|
Margalha L, Confraria A, Baena-González E. SnRK1 and TOR: modulating growth-defense trade-offs in plant stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2261-2274. [PMID: 30793201 DOI: 10.1093/jxb/erz066] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/07/2019] [Indexed: 05/11/2023]
Abstract
The evolutionarily conserved protein kinase complexes SnRK1 and TOR are central metabolic regulators essential for plant growth, development, and stress responses. They are activated by opposite signals, and the outcome of their activation is, in global terms, antagonistic. Similarly to their yeast and animal counterparts, SnRK1 is activated by the energy deficit often associated with stress to restore homeostasis, while TOR is activated in nutrient-rich conditions to promote growth. Recent evidence suggests that SnRK1 represses TOR in plants, revealing evolutionary conservation also in their crosstalk. Given their importance for integrating environmental information into growth and developmental programs, these signaling pathways hold great promise for reducing the growth penalties caused by stress. Here we review the literature connecting SnRK1 and TOR to plant stress responses. Although SnRK1 and TOR emerge mostly as positive regulators of defense and growth, respectively, the outcome of their activities in plant growth and performance is not always straightforward. Manipulation of both pathways under similar experimental setups, as well as further biochemical and genetic analyses of their molecular and functional interaction, is essential to fully understand the mechanisms through which these two metabolic pathways contribute to stress responses, growth, and development.
Collapse
Affiliation(s)
- Leonor Margalha
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,Oeiras, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,Oeiras, Portugal
| | | |
Collapse
|
12
|
Song Y, Zhang H, You H, Liu Y, Chen C, Feng X, Yu X, Wu S, Wang L, Zhong S, Li Q, Zhu Y, Ding X. Identification of novel interactors and potential phosphorylation substrates of GsSnRK1 from wild soybean (Glycine soja). PLANT, CELL & ENVIRONMENT 2019; 42:145-157. [PMID: 29664126 DOI: 10.1111/pce.13217] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
The plant sucrose nonfermenting kinase 1 (SnRK1) kinases play the central roles in the processes of energy balance, hormone perception, stress resistance, metabolism, growth, and development. However, the functions of these kinases are still elusive. In this study, we used GsSnRK1 of wild soybean as bait to perform library-scale screens by the means of yeast two-hybrid to identify its interacting proteins. The putative interactions were verified by yeast retransformation and β-galactosidase assays, and the selected interactions were further confirmed in planta by bimolecular fluorescence complementation and biochemical Co-IP assays. Protein phosphorylation analyses were carried out by phos-tag assay and anti-phospho-(Ser/Thr) substrate antibodies. Finally, we obtained 24 GsSnRK1 interactors and several putative substrates that can be categorized into SnRK1 regulatory β subunit, protein modification, biotic and abiotic stress-related, hormone perception and signalling, gene expression regulation, water and nitrogen transport, metabolism, and unknown proteins. Intriguingly, we first discovered that GsSnRK1 interacted with and phosphorylated the components of soybean nodulation and symbiotic nitrogen fixation. The interactions and potential functions of GsSnRK1 and its associated proteins were extensively discussed and analysed. This work provides plausible clues to elucidate the novel functions of SnRK1 in response to variable environmental, metabolic, and physiological requirements.
Collapse
Affiliation(s)
- Yu Song
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Hang Zhang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Hongguang You
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Yuanming Liu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chao Chen
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Xu Feng
- College of Life Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Xingyu Yu
- College of Life Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Shengyang Wu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Libo Wang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Shihua Zhong
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Qiang Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
- College of Life Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Yanming Zhu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Xiaodong Ding
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
- College of Life Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| |
Collapse
|
13
|
Su D, Devarenne TP. In vitro activity characterization of the tomato SnRK1 complex proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:857-864. [PMID: 29777861 DOI: 10.1016/j.bbapap.2018.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/28/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Plant Sucrose non-Fermenting 1-Related Protein Kinase1 (SnRK1) complexes are members of the Snf1/AMPK/SnRK protein kinase family and play important roles in many aspects of metabolism. In tomato (Solanum lycopersicum, Sl), only one α-subunit of the SnRK1 complex, SlSnRK1.1, has been characterized to date. In this study, the phylogenetic placement and in vitro kinase activity of a second tomato SnRK1 α-subunit, SlSnRK1.2, were characterized. Interestingly, in the phylogenetic analysis of SnRK1 sequences from monocots and dicots SlSnRK1.2 clusters only with other Solanaceae SnRK1.2 sequences, suggesting possible functional divergence of these kinases from other SnRK1 kinases. For analysis of kinase activity, SlSnRK1.2 was able to autophosphorylate, phosphorylate the complex β-subunits, and phosphorylate the SnRK1 AMARA peptide substrate, all with drastically lower overall kinase activity compared to SlSnRK1.1. Activation by the upstream kinase SlSnAK was able to increase the kinase activity of both SlSnRK1.1 and SlSnRK1.2, although the increase is less dramatic for SlSnRK1.2. The highest kinase activity on the AMARA peptide for SlSnRK1.2 was seen when reconstituting the complex in vitro with SlSip1 as the β-subunit. In comparison, SlSnRK1.1 showed the lowest kinase activity on the AMARA peptide when SlSip1 was used. These studies suggest the SlSnRK1.2 phylogenetic divergence and lower SlSnRK1.2 kinase activity compared to SlSnRK1.1 may be indicative of different in vivo roles for each kinase.
Collapse
Affiliation(s)
- Dongyin Su
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Timothy P Devarenne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
14
|
Maya-Bernal JL, Ávila A, Ruiz-Gayosso A, Trejo-Fregoso R, Pulido N, Sosa-Peinado A, Zúñiga-Sánchez E, Martínez-Barajas E, Rodríguez-Sotres R, Coello P. Expression of recombinant SnRK1 in E. coli. Characterization of adenine nucleotide binding to the SnRK1.1/AKINβγ-β3 complex. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:116-125. [PMID: 28818366 DOI: 10.1016/j.plantsci.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
The SnRK1 complexes in plants belong to the family of AMPK/SNF1 kinases, which have been associated with the control of energy balance, in addition to being involved in the regulation of other aspects of plant growth and development. Analysis of complex formation indicates that increased activity is achieved when the catalytic subunit is phosphorylated and bound to regulatory subunits. SnRK1.1 subunit activity is higher than that of SnRK1.2, which also exhibits reduced activation due to the regulatory subunits. The catalytic phosphomimetic subunits (T175/176D) do not exhibit high activity levels, which indicate that the amino acid change does not produce the same effect as phosphorylation. Based on the mammalian AMPK X-ray structure, the plant SnRK1.1/AKINβγ-β3 was modeled by homology modeling and Molecular Dynamics simulations (MD). The model predicted an intimate and extensive contact between a hydrophobic region of AKINβγ and the β3 subunit. While the AKINβγ prediction retains the 4 CBS domain organization of the mammalian enzyme, significant differences are found in the putative nucleotide binding pockets. Docking and MD studies identified two sites between CBS 3 and 4 which may bind adenine nucleotides, but only one appears to be functional, as judging from the predicted binding energies. The recombinant AKINβγ-βs complexes were found to bind adenine nucleotides with dissociation constant (Kd) in the range of the AMP low affinity site in AMPK. The saturation binding data was consistent with a one-site model, in agreement with the in silico calculations. As has been suggested previously, the effect of AMP was found to slow down dephosphorylation but did not influence activity.
Collapse
Affiliation(s)
- José Luis Maya-Bernal
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Alejandra Ávila
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Ana Ruiz-Gayosso
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Ricardo Trejo-Fregoso
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Nancy Pulido
- Centro de Investigaciones Químicas, UAEM, Morelos, 62210, Mexico
| | | | - Esther Zúñiga-Sánchez
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | | | | | - Patricia Coello
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico.
| |
Collapse
|
15
|
Salhi A, Negrão S, Essack M, Morton MJL, Bougouffa S, Razali R, Radovanovic A, Marchand B, Kulmanov M, Hoehndorf R, Tester M, Bajic VB. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. Sci Rep 2017; 7:5968. [PMID: 28729549 PMCID: PMC5519719 DOI: 10.1038/s41598-017-05448-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/25/2017] [Indexed: 12/29/2022] Open
Abstract
Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.
Collapse
Affiliation(s)
- Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Sónia Negrão
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Mitchell J L Morton
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Salim Bougouffa
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Rozaimi Razali
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Aleksandar Radovanovic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | | | - Maxat Kulmanov
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
16
|
Holappa LD, Ronald PC, Kramer EM. Evolutionary Analysis of Snf1-Related Protein Kinase2 (SnRK2) and Calcium Sensor (SCS) Gene Lineages, and Dimerization of Rice Homologs, Suggest Deep Biochemical Conservation across Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:395. [PMID: 28424709 PMCID: PMC5381359 DOI: 10.3389/fpls.2017.00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/08/2017] [Indexed: 05/14/2023]
Abstract
Members of the sucrose non-fermenting related kinase Group2 (SnRK2) subclasses are implicated in both direct and indirect abscisic acid (ABA) response pathways. We have used phylogenetic, biochemical, and transient in vivo approaches to examine interactions between Triticum tauschii protein kinase 1 (TtPK1) and an interacting protein, Oryza sativa SnRK2-calcium sensor (OsSCS1). Given that TtPK1 has 100% identity with its rice ortholog, osmotic stress/ABA-activated protein kinase (OsSAPK2), we hypothesized that the SCS and TtPK1 interactions are present in both wheat and rice. Here, we show that SnRK2s are clearly divided into four pan-angiosperm clades with those in the traditionally defined Subclass II encompassing two distinct clades (OsSAPK1/2 and OsSAPK3), although OsSAPK3 lacks an Arabidopsis ortholog. We also show that SCSs are distinct from a second lineage, that we term SCSsister, and while both clades pre-date land plants, the SCSsister clade lacks Poales representatives. Our Y2H assays revealed that the removal of the OsSCS1 C-terminal region along with its N-terminal EF-hand abolished its interaction with the kinase. Using transient in planta bimolecular fluorescence complementation experiments, we demonstrate that TtPK1/OsSCS1 dimerization co-localizes with DAPI-stained nuclei and with FM4-64-stained membranes. Finally, OsSCS1- and OsSAPK2-hybridizing transcripts co-accumulate in shoots/coleoptile of drying seedlings, consistent with up-regulated kinase transcripts of PKABA1 and TtPK1. Our studies suggest that interactions between homologs of the SnRK2 and SCS lineages are broadly conserved across angiosperms and offer new directions for investigations of related proteins.
Collapse
Affiliation(s)
- Lynn D. Holappa
- Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA
- Plant Pathology and the Genome Center, University of California DavisDavis, CA, USA
- *Correspondence: Lynn D. Holappa
| | - Pamela C. Ronald
- Plant Pathology and the Genome Center, University of California DavisDavis, CA, USA
| | - Elena M. Kramer
- Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA
| |
Collapse
|
17
|
Broeckx T, Hulsmans S, Rolland F. The plant energy sensor: evolutionary conservation and divergence of SnRK1 structure, regulation, and function. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6215-6252. [PMID: 27856705 DOI: 10.1093/jxb/erw416] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The SnRK1 (SNF1-related kinase 1) kinases are the plant cellular fuel gauges, activated in response to energy-depleting stress conditions to maintain energy homeostasis while also gatekeeping important developmental transitions for optimal growth and survival. Similar to their opisthokont counterparts (animal AMP-activated kinase, AMPK, and yeast Sucrose Non-Fermenting 1, SNF), they function as heterotrimeric complexes with a catalytic (kinase) α subunit and regulatory β and γ subunits. Although the overall configuration of the kinase complexes is well conserved, plant-specific structural modifications (including a unique hybrid βγ subunit) and associated differences in regulation reflect evolutionary divergence in response to fundamentally different lifestyles. While AMP is the key metabolic signal activating AMPK in animals, the plant kinases appear to be allosterically inhibited by sugar-phosphates. Their function is further fine-tuned by differential subunit expression, localization, and diverse post-translational modifications. The SnRK1 kinases act by direct phosphorylation of key metabolic enzymes and regulatory proteins, extensive transcriptional regulation (e.g. through bZIP transcription factors), and down-regulation of TOR (target of rapamycin) kinase signaling. Significant progress has been made in recent years. New tools and more directed approaches will help answer important fundamental questions regarding their structure, regulation, and function, as well as explore their potential as targets for selection and modification for improved plant performance in a changing environment.
Collapse
Affiliation(s)
- Tom Broeckx
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Sander Hulsmans
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| |
Collapse
|
18
|
Hulsmans S, Rodriguez M, De Coninck B, Rolland F. The SnRK1 Energy Sensor in Plant Biotic Interactions. TRENDS IN PLANT SCIENCE 2016; 21:648-661. [PMID: 27156455 DOI: 10.1016/j.tplants.2016.04.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/24/2016] [Accepted: 04/07/2016] [Indexed: 05/20/2023]
Abstract
Our understanding of plant biotic interactions has grown significantly in recent years with the identification of the mechanisms involved in innate immunity, hormone signaling, and secondary metabolism. The impact of such interactions on primary metabolism and the role of metabolic signals in the response of the plants, however, remain far less explored. The SnRK1 (SNF1-related kinase 1) kinases act as metabolic sensors, integrating very diverse stress conditions, and are key in maintaining energy homeostasis for growth and survival. Consistently, an important role is emerging for these kinases as regulators of biotic stress responses triggered by viral, bacterial, fungal, and oomycete infections as well as by herbivory. While this identifies SnRK1 as a promising target for directed modification or selection for more quantitative and sustainable resistance, its central function also increases the chances of unwanted side effects on growth and fitness, stressing the need for identification and in-depth characterization of the mechanisms and target processes involved. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- Sander Hulsmans
- Laboratory of Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Marianela Rodriguez
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 cuadras km 5.5 X5020ICA, Córdoba, Argentina
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, Microbial and Molecular Systems Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee-Leuven, Belgium; Vlaams Instituut voor Biotechnologie (VIB), Department of Plant Systems Biology, Technologiepark 927, 9052 Gent, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium.
| |
Collapse
|
19
|
Cho HY, Wen TN, Wang YT, Shih MC. Quantitative phosphoproteomics of protein kinase SnRK1 regulated protein phosphorylation in Arabidopsis under submergence. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2745-60. [PMID: 27029354 PMCID: PMC4861021 DOI: 10.1093/jxb/erw107] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed to be a central integrator of the plant stress and energy starvation signalling pathways. We observed that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1 (K48M) ) had lower tolerance to submergence than the wild type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in signalling pathways triggered by submergence. We conducted quantitative phosphoproteomics and found that the phosphorylation levels of 57 proteins increased and the levels of 27 proteins decreased in Col-0 within 0.5-3h of submergence. Among the 57 proteins with increased phosphorylation in Col-0, 38 did not show increased phosphorylation levels in SnRK1.1 (K48M) under submergence. These proteins are involved mainly in sugar and protein synthesis. In particular, the phosphorylation of MPK6, which is involved in regulating ROS responses under abiotic stresses, was disrupted in the SnRK1.1 (K48M) mutant. In addition, PTP1, a negative regulator of MPK6 activity that directly dephosphorylates MPK6, was also regulated by SnRK1.1. We also showed that energy conservation was disrupted in SnRK1.1 (K48M) , mpk6, and PTP1 (S7AS8A) under submergence. These results reveal insights into the function of SnRK1 and the downstream signalling factors related to submergence.
Collapse
Affiliation(s)
- Hsing-Yi Cho
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Academia Sinica, Taiwan Agricultural Biotechnology Research Center, Academia Sinica, Taiwan Graduate Institute of Biotechnology, National Chung-Hsing University, Taiwan
| | - Tuan-Nan Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taiwan
| | - Ying-Tsui Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Academia Sinica, Taiwan Agricultural Biotechnology Research Center, Academia Sinica, Taiwan Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
| |
Collapse
|
20
|
Emanuelle S, Doblin MS, Stapleton DI, Bacic A, Gooley PR. Molecular Insights into the Enigmatic Metabolic Regulator, SnRK1. TRENDS IN PLANT SCIENCE 2016; 21:341-353. [PMID: 26642889 DOI: 10.1016/j.tplants.2015.11.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/13/2015] [Accepted: 11/03/2015] [Indexed: 05/20/2023]
Abstract
Sucrose non-fermenting-1 (SNF1)-related kinase 1 (SnRK1) lies at the heart of metabolic homeostasis in plants and is crucial for normal development and response to stress. Evolutionarily related to SNF1 in yeast and AMP-activated kinase (AMPK) in mammals, SnRK1 acts protectively to maintain homeostasis in the face of fluctuations in energy status. Despite a conserved function, the structure and regulation of the plant kinase differ considerably from its relatively well-understood opisthokont orthologues. In this review, we highlight the known plant-specific modes of regulation involving SnRK1 together with new insights based on a 3D molecular model of the kinase. We also summarise how these differences from other orthologues may be specific adaptations to plant metabolism, and offer insights into possible avenues of future inquiry into this enigmatic enzyme.
Collapse
Affiliation(s)
- Shane Emanuelle
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - David I Stapleton
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Paul R Gooley
- Department of Biochemistry & Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
21
|
Plant SnRK1 Kinases: Structure, Regulation, and Function. EXPERIENTIA SUPPLEMENTUM 2016; 107:403-438. [DOI: 10.1007/978-3-319-43589-3_17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
22
|
Williams SP, Gillaspy GE, Perera IY. Biosynthesis and possible functions of inositol pyrophosphates in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:67. [PMID: 25729385 PMCID: PMC4325660 DOI: 10.3389/fpls.2015.00067] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/26/2015] [Indexed: 05/24/2023]
Abstract
Inositol phosphates (InsPs) are intricately tied to lipid signaling, as at least one portion of the inositol phosphate signaling pool is derived from hydrolysis of the lipid precursor, phosphatidyl inositol (4,5) bisphosphate. The focus of this review is on the inositol pyrophosphates, which are a novel group of InsP signaling molecules containing diphosphate or triphosphate chains (i.e., PPx) attached to the inositol ring. These PPx-InsPs are emerging as critical players in the integration of cellular metabolism and stress signaling in non-plant eukaryotes. Most eukaryotes synthesize the precursor molecule, myo-inositol (1,2,3,4,5,6)-hexakisphosphate (InsP6), which can serve as a signaling molecule or as storage compound of inositol, phosphorus, and minerals (referred to as phytic acid). Even though plants produce huge amounts of precursor InsP6 in seeds, almost no attention has been paid to whether PPx-InsPs exist in plants, and if so, what roles these molecules play. Recent work has delineated that Arabidopsis has two genes capable of PP-InsP5 synthesis, and PPx-InsPs have been detected across the plant kingdom. This review will detail the known roles of PPx-InsPs in yeast and animal systems, and provide a description of recent data on the synthesis and accumulation of these novel molecules in plants, and potential roles in signaling.
Collapse
Affiliation(s)
- Sarah P. Williams
- Biochemistry, Virginia Polytechnic and State UniversityBlacksburg, VA, USA
| | - Glenda E. Gillaspy
- Biochemistry, Virginia Polytechnic and State UniversityBlacksburg, VA, USA
| | - Imara Y. Perera
- Plant and Microbial Biology, North Carolina State UniversityRaleigh, NC, USA
| |
Collapse
|
23
|
Zhang T, Zhu M, Song WY, Harmon AC, Chen S. Oxidation and phosphorylation of MAP kinase 4 cause protein aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:156-65. [PMID: 25433264 DOI: 10.1016/j.bbapap.2014.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/12/2014] [Accepted: 11/19/2014] [Indexed: 01/22/2023]
Abstract
Mitogen-activated protein kinase (MPK) cascades are highly conserved signaling pathways that respond to environmental cues. Arabidopsis MPK4 has been identified as a stress-responsive protein kinase. Here we demonstrate that Brassica napus MPK4 (BnMPK4) is activated by hydrogen peroxide (H2O2) and phytohormone abscisic acid (ABA). Transient expression of a constitutively active BnMPK4 causes H2O2 production and cell death in Nicotiana benthamiana leaves. However, little is known about how H2O2 contributes to the regulation of MPK4 kinase function. Biochemical analysis revealed that recombinant BnMPK4 autophosphorylates on both threonine and tyrosine residues in the activation loop. In the presence of H2O2, phosphorylation of BnMPK4 caused protein aggregation in vitro. The aggregation of BnMPK4 could be reversed to the monomeric form by reducing reagents. Point-mutation of cysteine codons indicated that cysteine 232 is involved in protein aggregation. Our results suggest that BnMPK4 is involved in reactive oxygen species (ROS) signaling and metabolism, and its aggregation may be modulated by redox.
Collapse
Affiliation(s)
- Tong Zhang
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mengmeng Zhu
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Wen-yuan Song
- Department of Plant Pathology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Alice C Harmon
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
| |
Collapse
|
24
|
Sheen J. Master Regulators in Plant Glucose Signaling Networks. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2014; 57:67-79. [PMID: 25530701 PMCID: PMC4270195 DOI: 10.1007/s12374-014-0902-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The daily life of photosynthetic plants revolves around sugar production, transport, storage and utilization, and the complex sugar metabolic and signaling networks integrate internal regulators and environmental cues to govern and sustain plant growth and survival. Although diverse sugar signals have emerged as pivotal regulators from embryogenesis to senescence, glucose is the most ancient and conserved regulatory signal that controls gene and protein expression, cell-cycle progression, central and secondary metabolism, as well as growth and developmental programs. Glucose signals are perceived and transduced by two principal mechanisms: direct sensing through glucose sensors and indirect sensing via a variety of energy and metabolite sensors. This review focuses on the comparative and functional analyses of three glucose-modulated master regulators in Arabidopsis thaliana, the hexokinase1 (HXK1) glucose sensor, the energy sensor kinases KIN10/KIN11 inactivated by glucose, and the glucose-activated target of rapamycin (TOR) kinase. These regulators are evolutionarily conserved, but have evolved universal and unique regulatory wiring and functions in plants and animals. They form protein complexes with multiple partners as regulators or effectors to serve distinct functions in different subcellular locales and organs, and play integrative and complementary roles from cellular signaling and metabolism to development in the plant glucose signaling networks.
Collapse
Affiliation(s)
- Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| |
Collapse
|
25
|
Crozet P, Margalha L, Confraria A, Rodrigues A, Martinho C, Adamo M, Elias CA, Baena-González E. Mechanisms of regulation of SNF1/AMPK/SnRK1 protein kinases. FRONTIERS IN PLANT SCIENCE 2014; 5:190. [PMID: 24904600 PMCID: PMC4033248 DOI: 10.3389/fpls.2014.00190] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/22/2014] [Indexed: 05/17/2023]
Abstract
The SNF1 (sucrose non-fermenting 1)-related protein kinases 1 (SnRKs1) are the plant orthologs of the budding yeast SNF1 and mammalian AMPK (AMP-activated protein kinase). These evolutionarily conserved kinases are metabolic sensors that undergo activation in response to declining energy levels. Upon activation, SNF1/AMPK/SnRK1 kinases trigger a vast transcriptional and metabolic reprograming that restores energy homeostasis and promotes tolerance to adverse conditions, partly through an induction of catabolic processes and a general repression of anabolism. These kinases typically function as a heterotrimeric complex composed of two regulatory subunits, β and γ, and an α-catalytic subunit, which requires phosphorylation of a conserved activation loop residue for activity. Additionally, SNF1/AMPK/SnRK1 kinases are controlled by multiple mechanisms that have an impact on kinase activity, stability, and/or subcellular localization. Here we will review current knowledge on the regulation of SNF1/AMPK/SnRK1 by upstream components, post-translational modifications, various metabolites, hormones, and others, in an attempt to highlight both the commonalities of these essential eukaryotic kinases and the divergences that have evolved to cope with the particularities of each one of these systems.
Collapse
Affiliation(s)
| | | | | | - Américo Rodrigues
- Instituto Gulbenkian de CiênciaOeiras, Portugal
- Escola Superior de Turismo e Tecnologia do Mar de Peniche, Instituto Politécnico de LeiriaPeniche, Portugal
| | | | | | | | - Elena Baena-González
- Instituto Gulbenkian de CiênciaOeiras, Portugal
- *Correspondence: Elena Baena-González, Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal e-mail:
| |
Collapse
|
26
|
Gray JW, Nelson Dittrich AC, Chen S, Avila J, Giavalisco P, Devarenne TP. Two Pdk1 phosphorylation sites on the plant cell death suppressor Adi3 contribute to substrate phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1099-106. [PMID: 23507047 PMCID: PMC4301410 DOI: 10.1016/j.bbapap.2013.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 12/26/2022]
Abstract
The tomato AGC kinase Adi3 is phosphorylated by Pdk1 for activation of its cell death suppression activity. The Pdk1 phosphorylation site for activation of Adi3 is at Ser539. However, there is at least one additional Pdk1 phosphorylation site on Adi3 that has an unknown function. Here we identify an Arabidopsis thaliana sequence homologue of Adi3 termed AGC1-3. Two Pdk1 phosphorylation sites were identified on AGC1-3, activation site Ser596 and Ser269, and by homology Ser212 on Adi3 was identified as a second Pdk1 phosphorylation site. While Ser212 is not required for Adi3 autophosphorylation, Ser212 was shown to be required for full phosphorylation of the Adi3 substrate Gal83.
Collapse
Affiliation(s)
- Joel W. Gray
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843
| | | | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - Julian Avila
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, 14476 Glom-Potsdam, Germany
| | - Timothy P. Devarenne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843
| |
Collapse
|
27
|
Schuck S, Baldwin IT, Bonaventure G. HSPRO acts via SnRK1-mediated signaling in the regulation of Nicotiana attenuata seedling growth promoted by Piriformospora indica. PLANT SIGNALING & BEHAVIOR 2013; 8:e23537. [PMID: 23333980 PMCID: PMC3829923 DOI: 10.4161/psb.23537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 05/25/2023]
Abstract
Nicotiana attenuata HSPRO (NaHSPRO) is a negative regulator of seedling growth promoted by the fungus Piriformospora indica. Homologs of NaHSPRO in Arabidopsis thaliana (i.e., AtHSPRO1 and AtHSPRO2) are known to physically interact with the AKINβγ subunit of the SnRK1 complex. To investigate whether NaHSPRO is associated with SnRK1 function during the stimulation of seedling growth by P. indica, we studied N. attenuata plants silenced in the expression of NaGAL83 (as-gal83 plants)--a gene that encodes for the regulatory β-subunit of SnRK1--and plants silenced in the expression of both NaHSPRO and NaGAL83 (ir-hspro/as-gal83 plants). The results showed that P. indica differentially stimulated the growth of both as-gal83 and ir-hspro/as-gal83 seedlings compared with control seedlings, with a magnitude similar to that observed in ir-hspro seedlings. Thus, we showed that, similar to NaHSPRO, NaGAL83 is a negative regulator of seedling growth stimulated by P. indica. We propose that the effect of NaHSPRO on seedling growth is associated with SnRK1 signaling.
Collapse
Affiliation(s)
- Stefan Schuck
- Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany
| | - Gustavo Bonaventure
- Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany
| |
Collapse
|
28
|
Li ZY, Xu ZS, Chen Y, He GY, Yang GX, Chen M, Li LC, Ma YZ. A novel role for Arabidopsis CBL1 in affecting plant responses to glucose and gibberellin during germination and seedling development. PLoS One 2013; 8:e56412. [PMID: 23437128 PMCID: PMC3577912 DOI: 10.1371/journal.pone.0056412] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 01/09/2013] [Indexed: 01/28/2023] Open
Abstract
Glucose and phytohormones such as abscisic acid (ABA), ethylene, and gibberellin (GA) coordinately regulate germination and seedling development. However, there is still inadequate evidence to link their molecular roles in affecting plant responses. Calcium acts as a second messenger in a diverse range of signal transduction pathways. As calcium sensors unique to plants, calcineurin B-like (CBL) proteins are well known to modulate abiotic stress responses. In this study, it was found that CBL1 was induced by glucose in Arabidopsis. Loss-of-function mutant cbl1 exhibited hypersensitivity to glucose and paclobutrazol, a GA biosynthetic inhibitor. Several sugar-responsive and GA biosynthetic gene expressions were altered in the cbl1 mutant. CBL1 protein physically interacted with AKINβ1, the regulatory β subunit of the SnRK1 complex which has a central role in sugar signaling. Our results indicate a novel role for CBL1 in modulating responses to glucose and GA signals.
Collapse
Affiliation(s)
- Zhi-Yong Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
- * E-mail: (Z-SX); (Y-ZM); (YC)
| | - Yang Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
- * E-mail: (Z-SX); (Y-ZM); (YC)
| | - Guang-Yuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Guang-Xiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Lian-Cheng Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
- * E-mail: (Z-SX); (Y-ZM); (YC)
| |
Collapse
|
29
|
Bifurcation of Arabidopsis NLR immune signaling via Ca²⁺-dependent protein kinases. PLoS Pathog 2013; 9:e1003127. [PMID: 23382673 PMCID: PMC3561149 DOI: 10.1371/journal.ppat.1003127] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 11/28/2012] [Indexed: 11/30/2022] Open
Abstract
Nucleotide-binding domain leucine-rich repeat (NLR) protein complexes sense infections and trigger robust immune responses in plants and humans. Activation of plant NLR resistance (R) proteins by pathogen effectors launches convergent immune responses, including programmed cell death (PCD), reactive oxygen species (ROS) production and transcriptional reprogramming with elusive mechanisms. Functional genomic and biochemical genetic screens identified six closely related Arabidopsis Ca2+-dependent protein kinases (CPKs) in mediating bifurcate immune responses activated by NLR proteins, RPS2 and RPM1. The dynamics of differential CPK1/2 activation by pathogen effectors controls the onset of cell death. Sustained CPK4/5/6/11 activation directly phosphorylates a specific subgroup of WRKY transcription factors, WRKY8/28/48, to synergistically regulate transcriptional reprogramming crucial for NLR-dependent restriction of pathogen growth, whereas CPK1/2/4/11 phosphorylate plasma membrane-resident NADPH oxidases for ROS production. Our studies delineate bifurcation of complex signaling mechanisms downstream of NLR immune sensors mediated by the myriad action of CPKs with distinct substrate specificity and subcellular dynamics. Distinguishing self from non-self is the fundamental principle of immunity. Nucleotide-binding leucine-rich repeat (NLR) proteins were first identified in plants as disease resistance proteins and were recently found to play essential roles in mammalian innate immunity and inflammation. NLR protein complexes sense intracellular pathogenic effectors in plants and microbial patterns and danger signals in humans, but the signaling mechanisms upon NLR activation remain elusive. Using the Arabidopsis-Pseudomonas interaction as a model system, we discovered the molecular link between NLR immune sensors and the convergent immune responses triggered by distinct pathogen effectors. Integrated functional genomic and biochemical genetic screens identified six closely related Ca2+-dependent protein kinases (CPKs) that orchestrate bifurcate NLR immune signaling via distinct substrate specificity and subcellular dynamics. The CPK1/2 regulate the onset of programmed cell death; CPK4/5/6/11 phosphorylate specific WRKY transcription factors to regulate immune gene expression crucial for NLR-dependent restriction of pathogen growth, whereas CPK1/2/4/11 phosphorylate NADPH oxidases for the production of reactive oxygen species. Our studies decode the complex signaling mechanisms via the myriad action of CPKs downstream of NLR immune sensors.
Collapse
|
30
|
Liu YH, Offler CE, Ruan YL. Regulation of fruit and seed response to heat and drought by sugars as nutrients and signals. FRONTIERS IN PLANT SCIENCE 2013; 4:282. [PMID: 23914195 PMCID: PMC3729977 DOI: 10.3389/fpls.2013.00282] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/10/2013] [Indexed: 05/21/2023]
Abstract
A large body of evidence shows that sugars function both as nutrients and signals to regulate fruit and seed set under normal and stress conditions including heat and drought. Inadequate sucrose import to, and its degradation within, reproductive organs cause fruit and seed abortion under heat and drought. As nutrients, sucrose-derived hexoses provide carbon skeletons and energy for growth and development of fruits and seeds. Sugar metabolism can also alleviate the impact of stress on fruit and seed through facilitating biosynthesis of heat shock proteins (Hsps) and non-enzymic antioxidants (e.g., glutathione, ascorbic acid), which collectively maintain the integrity of membranes and prevent programmed cell death (PCD) through protecting proteins and scavenging reactive oxygen species (ROS). In parallel, sugars (sucrose, glucose, and fructose), also exert signaling roles through cross-talk with hormone and ROS signaling pathways and by mediating cell division and PCD. At the same time, emerging data indicate that sugar-derived signaling systems, including trehalose-6 phosphate (T6P), sucrose non-fermenting related kinase-1 (SnRK), and the target of rapamycin (TOR) kinase complex also play important roles in regulating plant development through modulating nutrient and energy signaling and metabolic processes, especially under abiotic stresses where sugar availability is low. This review aims to evaluate recent progress of research on abiotic stress responses of reproductive organs focusing on roles of sugar metabolism and signaling and addressing the possible biochemical and molecular mechanism by which sugars regulate fruit and seed set under heat and drought.
Collapse
Affiliation(s)
- Yong-Hua Liu
- Department of Biology, School of Environmental and Life Sciences, The University of NewcastleNewcastle, NSW, Australia
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Christina E. Offler
- Department of Biology, School of Environmental and Life Sciences, The University of NewcastleNewcastle, NSW, Australia
| | - Yong-Ling Ruan
- Department of Biology, School of Environmental and Life Sciences, The University of NewcastleNewcastle, NSW, Australia
- *Correspondence: Yong-Ling Ruan, Department of Biology, School of Environmental and Life Sciences, The University of Newcastle, Newcastle, NSW, Australia e-mail:
| |
Collapse
|
31
|
Ubiquitination of the tomato cell death suppressor Adi3 by the RING E3 ubiquitin ligase AdBiL. Biochem Biophys Res Commun 2012. [PMID: 23178567 DOI: 10.1016/j.bbrc.2012.11.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Programmed cell death (PCD) is an organized process by which organisms selectively remove cells according to developmental needs or in response to biotic or abiotic stress. Despite recent efforts to understand mechanisms by which cell death takes place in plants, several gaps remain in our understanding of the molecular elements involved. The tomato PCD suppressor Adi3 is an AGC kinase that shares functional homology with the mammalian inhibitor of apoptosis PKB. Regulation of PKB stability, cell localization, and activation state is achieved through post-translational modifications such as ubiquitination. In an effort to understand the regulation of Adi3 function, we studied its interaction with the E3 ubiquitin ligase AdBiL. Using in vitro ubiquitination assays we show that AdBiL is an active E3 ubiquitin ligase using the E2 ubiquitin ligase UBC8 to ubiquitinate Adi3. Adi3 is also degraded in a proteasome-dependent manner. Our data draws additional parallels between Adi3 and PKB to support the functional relationship between these two PCD regulators.
Collapse
|