1
|
Li D, Cai Y, Guo J, Liu Y, Lu F, Li Q, Liu Y, Li Y. Screening signal peptidase based on split-GFP assembly technology to promote the secretion of alkaline protease AprE in Bacillus amyloliquefaciens. Int J Biol Macromol 2024; 269:132166. [PMID: 38723822 DOI: 10.1016/j.ijbiomac.2024.132166] [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: 02/04/2024] [Revised: 04/04/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Improving the ability of bacteria to secrete protein is essential for large-scale production of food enzymes. However, due to the lack of effective tracking technology for target proteins, the optimization of the secretory system is facing many problems. In this study, we utilized the split-GFP system to achieve self-assembly into mature GFP in Bacillus amyloliquefaciens and successfully tracked the alkaline protease AprE. The split-GFP system was employed to assess the signal peptidases, a crucial component in the secretory system, and signal peptidase sipA was identified as playing a role in the secretion of AprE. Deletion of sipA resulted in a higher accumulation of the precursor protein of AprE compared to other signal peptidase deletion strains. To explore the mechanism of signal peptidase on signal peptide, molecular docking and calculation of free energy were performed. The action strength of the signal peptidase is determined by its binding affinity with the tripeptides at the C-terminal of the signal peptide. The functions of signal peptides YdbK and NucB rely on sipA, and overexpression of sipA by integrating it into genome of B. amyloliquefaciens increased the activity of extracellular AprE by 19.9 %. These findings provide insights into enhancing the secretion efficiency of chassis strains.
Collapse
Affiliation(s)
- Dengke Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yian Cai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiejie Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yexue Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| |
Collapse
|
2
|
Jin S, Youn G, Kim SY, Kang T, Shin HY, Jung JY, Seo PJ, Ahn JH. The CUL3A-LFH1-UBC15 ubiquitin ligase complex mediates SHORT VEGETATIVE PHASE degradation to accelerate flowering at high ambient temperature. PLANT COMMUNICATIONS 2024; 5:100814. [PMID: 38213026 PMCID: PMC11009155 DOI: 10.1016/j.xplc.2024.100814] [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: 03/13/2023] [Revised: 09/15/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Ambient temperature affects flowering time in plants, and the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a crucial role in the response to changes in ambient temperature. SVP protein stability is regulated by the 26S proteasome pathway and decreases at high ambient temperature, but the details of SVP degradation are unclear. Here, we show that SVP degradation at high ambient temperature is mediated by the CULLIN3-RING E3 ubiquitin ligase (CRL3) complex in Arabidopsis thaliana. We identified a previously uncharacterized protein that interacts with SVP at high ambient temperature and contains a BTB/POZ domain. We named this protein LATE FLOWERING AT HIGH TEMPERATURE 1 (LFH1). Single mutants of LFH1 or CULLIN3A (CUL3A) showed late flowering specifically at 27°C. LFH1 protein levels increased at high ambient temperature. We found that LFH1 interacts with CUL3A in the cytoplasm and is important for SVP-CUL3A complex formation. Mutations in CUL3A and/or LFH1 led to increased SVP protein stability at high ambient temperature, suggesting that the CUL3-LFH1 complex functions in SVP degradation. Screening E2 ubiquitin-conjugating enzymes (UBCs) using RING-BOX PROTEIN 1 (RBX1), a component of the CRL3 complex, as bait identified UBC15. ubc15 mutants also showed late flowering at high ambient temperature. In vitro and in vivo ubiquitination assays using recombinant CUL3A, LFH1, RBX1, and UBC15 showed that SVP is highly ubiquitinated in an ATP-dependent manner. Collectively, these results indicate that the degradation of SVP at high ambient temperature is mediated by a CRL3 complex comprising CUL3A, LFH1, and UBC15.
Collapse
Affiliation(s)
- Suhyun Jin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Geummin Youn
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sun Young Kim
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Taewook Kang
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun-Young Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ji-Yul Jung
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
3
|
Hong S, Huh SU. Members of the Capsicum annuum CaTrxh Family Respond to High Temperature and Exhibit Dynamic Hetero/Homo Interactions. Int J Mol Sci 2024; 25:1729. [PMID: 38339006 PMCID: PMC10855718 DOI: 10.3390/ijms25031729] [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: 12/17/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Climate change adversely affects the water and temperature conditions required for plant growth, leading to a decrease in yield. In high temperatures, oxidative stress causes cellular damage in plant cells, which is a negative factor for crop production. Thioredoxin (Trx) is a small redox protein containing a conserved WC(G/P)PC motif that catalyzes the exchange of disulfide bonds. It is known to play an important role in maintaining cellular redox homeostasis. Trx proteins are widely distributed across various subcellular locations, and they play a crucial role in responding to cellular stresses. In this study, seven CaTrxh-type genes present in pepper were identified and the CaTrxh-type family was classified into three subgroups. CaTrxh genes responded to heat stress. Moreover, subcellular locations of the CaTrxh family exhibited dynamic patterns in normal conditions, and we observed relocalizations in heat stress conditions. Each CaTrxh family protein member formed homo-/heteromeric protein complexes in BiFC assay. Unexpectedly, subgroup III CaTrxh9 and CaTrxh10 can recruit subgroup I and II CaTrxh proteins into the plasma membrane. Thus, the function of the CaTrxh-type family is expected to play a protective role in the cell in response to high-temperature stress via protein complex formations. CaTrxh may have potential applications in the development of crops with enhanced tolerance to oxidative stress.
Collapse
Affiliation(s)
| | - Sung Un Huh
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea;
| |
Collapse
|
4
|
Safi A, Smagghe W, Gonçalves A, Wang Q, Xu K, Fernandez AI, Cappe B, Riquet FB, Mylle E, Eeckhout D, De Winne N, Van De Slijke E, Persyn F, Persiau G, Van Damme D, Geelen D, De Jaeger G, Beeckman T, Van Leene J, Vanneste S. Phase separation-based visualization of protein-protein interactions and kinase activities in plants. THE PLANT CELL 2023; 35:3280-3302. [PMID: 37378595 PMCID: PMC10473206 DOI: 10.1093/plcell/koad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
Protein activities depend heavily on protein complex formation and dynamic posttranslational modifications, such as phosphorylation. The dynamic nature of protein complex formation and posttranslational modifications is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to assay protein-protein interactions (PPIs) (separation of phases-based protein interaction reporter) and kinase activities (separation of phases-based activity reporter of kinase) in planta, based on phase separation. This technology enabled easy detection of inducible, binary and ternary PPIs among cytoplasmic and nuclear proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SNF1-related kinase 1 activity, allowing us to visualize tissue-specific, dynamic SnRK1 activity in stable transgenic Arabidopsis (Arabidopsis thaliana) plants. The SYMPL cloning toolbox provides a means to explore PPIs, phosphorylation, and other posttranslational modifications with unprecedented ease and sensitivity.
Collapse
Affiliation(s)
- Alaeddine Safi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Wouter Smagghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- VIB, Bioimaging Core, B-9052 Ghent, Belgium
| | - Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Ibis Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Benjamin Cappe
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Franck B Riquet
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Freya Persyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| |
Collapse
|
5
|
Jin S, Kim SY, Susila H, Nasim Z, Youn G, Ahn JH. FLOWERING LOCUS M isoforms differentially affect the subcellular localization and stability of SHORT VEGETATIVE PHASE to regulate temperature-responsive flowering in Arabidopsis. MOLECULAR PLANT 2022; 15:1696-1709. [PMID: 36016495 DOI: 10.1016/j.molp.2022.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Temperature is an important environmental cue that affects flowering time in plants. The MADS-box transcription factor FLOWERING LOCUS M (FLM) forms a heterodimeric complex with SHORT VEGETATIVE PHASE (SVP) and controls ambient temperature-responsive flowering in Arabidopsis. FLM-β and FLM-δ, two major splice variants produced from the FLM locus, exert opposite effects on flowering, but the molecular mechanism by which the interaction between FLM isoforms and SVP affects temperature-responsive flowering remains poorly understood. Here, we show that FLM-β and FLM-δ play important roles in modulating the temperature-dependent behavior, conformation, and stability of SVP. Nuclear localization of SVP decreases as temperature increases. FLM-β is required for SVP nuclear translocation at low temperature, whereas SVP interacts with FLM-δ mainly in the cytoplasm at high temperature. SVP preferentially binds to FLM-β at low temperature in tobacco leaf cells. SVP shows high binding affinity to FLM-β at low temperature and to FLM-δ at high temperature. SVP undergoes similar structural changes in the interactions with FLM-β and FLM-δ; however, FLM-δ likely causes more pronounced conformational changes in the SVP structure. FLM-δ causes rapid degradation of SVP at high temperature, compared with FLM-β, possibly via ubiquitination. Mutation of lysine 53 or lysine 165 in SVP causes increased abundance of SVP due to reduced ubiquitination of SVP and thus delays flowering at high temperature. Our findings suggest that temperature-dependent differential interactions between SVP and FLM isoforms modulate the temperature-responsive induction of flowering in Arabidopsis.
Collapse
Affiliation(s)
- Suhyun Jin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sun Young Kim
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Geummin Youn
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
6
|
Jin H, Han X, Wang Z, Xie Y, Zhang K, Zhao X, Wang L, Yang J, Liu H, Ji X, Dong L, Zheng H, Hu W, Liu Y, Wang X, Zhou X, Zhang Y, Qian W, Zheng W, Shen Q, Gou M, Wang D. Barley GRIK1-SnRK1 kinases subvert a viral virulence protein to upregulate antiviral RNAi and inhibit infection. EMBO J 2022; 41:e110521. [PMID: 35929182 PMCID: PMC9475517 DOI: 10.15252/embj.2021110521] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/25/2022] [Accepted: 06/03/2022] [Indexed: 12/21/2022] Open
Abstract
Viruses often usurp host machineries for their amplification, but it remains unclear if hosts may subvert virus proteins to regulate viral proliferation. Here, we show that the 17K protein, an important virulence factor conserved in barley yellow dwarf viruses (BYDVs) and related poleroviruses, is phosphorylated by host GRIK1‐SnRK1 kinases, with the phosphorylated 17K (P17K) capable of enhancing the abundance of virus‐derived small interfering RNAs (vsiRNAs) and thus antiviral RNAi. Furthermore, P17K interacts with barley small RNA‐degrading nuclease 1 (HvSDN1) and impedes HvSDN1‐catalyzed vsiRNA degradation. Additionally, P17K weakens the HvSDN1‐HvAGO1 interaction, thus hindering HvSDN1 from accessing and degrading HvAGO1‐carried vsiRNAs. Importantly, transgenic expression of 17K phosphomimetics (17K5D), or genome editing of SDN1, generates stable resistance to BYDV through elevating vsiRNA abundance. These data validate a novel mechanism that enhances antiviral RNAi through host subversion of a viral virulence protein to inhibit SDN1‐catalyzed vsiRNA degradation and suggest new ways for engineering BYDV‐resistant crops.
Collapse
Affiliation(s)
- Huaibing Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China.,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xinyun Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhaohui Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Kunpu Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Xiaoge Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lina Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Jin Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Huiyun Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Xiang Ji
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongyuan Zheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Weijuan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xifeng Wang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Wenming Zheng
- National Biological Experimental Teaching Demonstration Center, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qianhua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China.,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,National Biological Experimental Teaching Demonstration Center, College of Life Sciences, Henan Agricultural University, Zhengzhou, China.,The Shennong Laboratory, Zhengzhou, China
| |
Collapse
|
7
|
Winkler J, Mylle E, De Meyer A, Pavie B, Merchie J, Grones P, Van Damme D. Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization. THE PLANT CELL 2021; 33:1101-1117. [PMID: 33793859 PMCID: PMC7612334 DOI: 10.1093/plcell/koab004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/15/2020] [Indexed: 05/19/2023]
Abstract
Identifying protein-protein interactions (PPIs) is crucial for understanding biological processes. Many PPI tools are available, yet only some function within the context of a plant cell. Narrowing down even further, only a few tools allow complex multi-protein interactions to be visualized. Here, we present a conditional in vivo PPI tool for plant research that meets these criteria. Knocksideways in plants (KSP) is based on the ability of rapamycin to alter the localization of a bait protein and its interactors via the heterodimerization of FKBP and FRB domains. KSP is inherently free from many limitations of other PPI systems. This in vivo tool does not require spatial proximity of the bait and prey fluorophores and it is compatible with a broad range of fluorophores. KSP is also a conditional tool and therefore the visualization of the proteins in the absence of rapamycin acts as an internal control. We used KSP to confirm previously identified interactions in Nicotiana benthamiana leaf epidermal cells. Furthermore, the scripts that we generated allow the interactions to be quantified at high throughput. Finally, we demonstrate that KSP can easily be used to visualize complex multi-protein interactions. KSP is therefore a versatile tool with unique characteristics and applications that complements other plant PPI methods.
Collapse
Affiliation(s)
- Joanna Winkler
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Evelien Mylle
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Andreas De Meyer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | | | - Julie Merchie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Peter Grones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniёl Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| |
Collapse
|
8
|
Li M, Wang F, Li S, Yu G, Wang L, Li Q, Zhu X, Li Z, Yuan L, Liu P. Importers Drive Leaf-to-Leaf Jasmonic Acid Transmission in Wound-Induced Systemic Immunity. MOLECULAR PLANT 2020; 13:1485-1498. [PMID: 32889174 DOI: 10.1016/j.molp.2020.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/06/2020] [Accepted: 08/29/2020] [Indexed: 05/22/2023]
Abstract
The transmission of mobile wound signals along the phloem pathway is essential to the activation of wound-induced systemic response/resistance, which requires an upsurge of jasmonic acid (JA) in the distal undamaged leaves. Among these mobile signals, the electrical signal mediated by the glutamate-dependent activation of several clade three GLUTAMATE RECEPTOR-LIKE (GLR3) proteins is involved in the stimulation of JA production in distal leaves. However, whether JA acts as a mobile wound signal and, if so, how it is transmitted and interacts with the electrical signal remain unclear. Here, we show that JA was translocated from the local to distal leaves in Arabidopsis, and this process was predominantly regulated by two phloem-expressed and plasma membrane-localized jasmonate transporters, AtJAT3 and AtJAT4. In addition to the cooperation between AtJAT3/4 and GLR3.3 in the regulation of long-distance JA translocation, our findings indicate that importer-mediated cell-cell JA transport is important for driving the loading and translocation of JA in the phloem pathway in a self-propagating manner.
Collapse
Affiliation(s)
- Mengya Li
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Feifei Wang
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Shuangzhang Li
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Guanghui Yu
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Lijian Wang
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Qingqing Li
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Xiangyu Zhu
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Lixing Yuan
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Pei Liu
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, P. R. China.
| |
Collapse
|
9
|
Dominant mutants of the calcineurin catalytic subunit (CNA-1) showed developmental defects, increased sensitivity to stress conditions, and CNA-1 interacts with CaM and CRZ-1 in Neurospora crassa. Arch Microbiol 2019; 202:921-934. [DOI: 10.1007/s00203-019-01768-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/12/2019] [Accepted: 10/31/2019] [Indexed: 12/20/2022]
|
10
|
Li P, Wang L, Di LJ. Applications of Protein Fragment Complementation Assays for Analyzing Biomolecular Interactions and Biochemical Networks in Living Cells. J Proteome Res 2019; 18:2987-2998. [PMID: 31274323 DOI: 10.1021/acs.jproteome.9b00154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-protein interactions (PPIs) are indispensable for the dynamic assembly of multiprotein complexes that are central players of nearly all of the intracellular biological processes, such as signaling pathways, metabolic pathways, formation of intracellular organelles, establishment of cytoplasmic skeletons, etc. Numerous approaches have been invented to study PPIs both in vivo and in vitro, including the protein-fragment complementation assay (PCA), which is a widely applied technology to study PPIs and biomolecular interactions. PCA is a technology based on the expression of the bait and prey proteins in fusion with two complementary reporter protein fragments, respectively, that will reassemble when in close proximity. The reporter protein can be the enzymes or fluorescent proteins. Recovery of the enzymatic activity or fluorescent signal can be the indicator of PPI between the bait and prey proteins. Significant effort has been invested in developing many derivatives of PCA, along with various applications, in order to address specific questions. Therefore, a prompt review of these applications is important. In this review, we will categorize these applications according to the scenarios that the PCAs were applied and expect to provide a reference guideline for the future selection of PCA methods in solving a specific problem.
Collapse
Affiliation(s)
- Peipei Li
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| | - Li Wang
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China.,Metabolomics Core, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| |
Collapse
|
11
|
Bally J, Jung H, Mortimer C, Naim F, Philips JG, Hellens R, Bombarely A, Goodin MM, Waterhouse PM. The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:405-426. [PMID: 30149789 DOI: 10.1146/annurev-phyto-080417-050141] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A decade ago, the value of Nicotiana benthamiana as a tool for plant molecular biologists was beginning to be appreciated. Scientists were using it to study plant-microbe and protein-protein interactions, and it was the species of choice with which to activate plasmid-encoded viruses, screen for gene functions with virus-induced gene silencing (VIGS), and transiently express genes by leaf agroinfiltration. However, little information about the species' origin, diversity, genetics, and genomics was available, and biologists were asking the question of whether N. benthamiana is a second fiddle or virtuoso. In this review, we look at the increased knowledge about the species and its applications over the past decade. Although N. benthamiana may still be the sidekick to Arabidopsis, it shines ever more brightly with realized and yet-to-be-exploited potential.
Collapse
Affiliation(s)
- Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Cara Mortimer
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Joshua G Philips
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Roger Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002, USA
| | - Michael M Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546, USA;
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| |
Collapse
|
12
|
Wiens MD, Campbell RE. Surveying the landscape of optogenetic methods for detection of protein-protein interactions. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1415. [PMID: 29334187 PMCID: PMC5902417 DOI: 10.1002/wsbm.1415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 01/08/2023]
Abstract
Mapping the protein-protein interaction (PPi) landscape is of critical importance to furthering our understanding how cells and organisms function. Optogenetic methods, that is, approaches that utilize genetically encoded fluorophores or fluorogenic enzyme reactions, uniquely enable the visualization of biochemical phenomena in live cells with high spatial and temporal accuracy. Applying optogenetic methods to the detection of PPis requires the engineering of protein-based systems in which an optical signal undergoes a substantial change when the two proteins of interest interact. In recent years, researchers have developed a number of creative and effective optogenetic methods that achieve this goal, and used them to further elaborate our map of the PPi landscape. In this review, we provide an introduction to the general principles of optogenetic PPi detection, and then provide a number of representative examples of how these principles have been applied. We have organized this review by categorizing methods based on whether the signal generated is reversible or irreversible in nature, and whether the signal is localized or nonlocalized at the subcellular site of the PPi. We discuss these techniques giving both their benefits and drawbacks to enable rational choices about their potential use. This article is categorized under: Laboratory Methods and Technologies > Imaging Laboratory Methods and Technologies > Macromolecular Interactions, Methods Analytical and Computational Methods > Analytical Methods.
Collapse
Affiliation(s)
- Matthew D. Wiens
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 Canada
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 Canada
| |
Collapse
|
13
|
Chiasson DM, Haage K, Sollweck K, Brachmann A, Dietrich P, Parniske M. A quantitative hypermorphic CNGC allele confers ectopic calcium flux and impairs cellular development. eLife 2017; 6:25012. [PMID: 28933692 PMCID: PMC5716663 DOI: 10.7554/elife.25012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
The coordinated control of Ca2+ signaling is essential for development in eukaryotes. Cyclic nucleotide-gated channel (CNGC) family members mediate Ca2+ influx from cellular stores in plants (Charpentier et al., 2016; Gao et al., 2016; Frietsch et al., 2007; Urquhart et al., 2007). Here, we report the unusual genetic behavior of a quantitative gain-of-function CNGC mutation (brush) in Lotus japonicus resulting in a leaky tetrameric channel. brush resides in a cluster of redundant CNGCs encoding subunits which resemble metazoan voltage-gated potassium (Kv1-Kv4) channels in assembly and gating properties. The recessive mongenic brush mutation impaired root development and infection by nitrogen-fixing rhizobia. The brush allele exhibited quantitative behavior since overexpression of the cluster subunits was required to suppress the brush phenotype. The results reveal a mechanism by which quantitative competition between channel subunits for tetramer assembly can impact the phenotype of the mutation carrier.
Collapse
Affiliation(s)
- David M Chiasson
- Faculty of Biology, Institute of Genetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Kristina Haage
- Faculty of Biology, Institute of Genetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Katharina Sollweck
- Faculty of Biology, Institute of Genetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Andreas Brachmann
- Faculty of Biology, Institute of Genetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Petra Dietrich
- Molecular Plant Physiology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Parniske
- Faculty of Biology, Institute of Genetics, Ludwig Maximilian University of Munich, Munich, Germany
| |
Collapse
|
14
|
Close Encounters - Probing Proximal Proteins in Live or Fixed Cells. Trends Biochem Sci 2017; 42:504-515. [PMID: 28566215 DOI: 10.1016/j.tibs.2017.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 12/30/2022]
Abstract
The well-oiled machinery of the cellular proteome operates via variable expression, modifications, and interactions of proteins, relaying genomic and transcriptomic information to coordinate cellular functions. In recent years, a number of techniques have emerged that serve to identify sets of proteins acting in close proximity in the course of orchestrating cellular activities. These proximity-dependent assays, including BiFC, BioID, APEX, FRET, and isPLA, have opened up new avenues to examine protein interactions in live or fixed cells. We review herein the current status of proximity-dependent in situ techniques. We compare the advantages and limitations of the methods, underlining recent progress and the growing importance of these techniques in basic research, and we discuss their potential as tools for drug development and diagnostics.
Collapse
|