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Liu L, Liu X, Bai Z, Tanveer M, Zhang Y, Chen W, Shabala S, Huang L. Small but powerful: RALF peptides in plant adaptive and developmental responses. Plant Sci 2024; 343:112085. [PMID: 38588983 DOI: 10.1016/j.plantsci.2024.112085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Plants live in a highly dynamic environment and require to rapidly respond to a plethora of environmental stimuli, so that to maintain their optimal growth and development. A small plant peptide, rapid alkalization factor (RALF), can rapidly increase the pH value of the extracellular matrix in plant cells. RALFs always function with its corresponding receptors. Mechanistically, effective amount of RALF is induced and released at the critical period of plant growth and development or under different external environmental factors. Recent studies also highlighted the role of RALF peptides as important regulators in plant intercellular communications, as well as their operation in signal perception and as ligands for different receptor kinases on the surface of the plasma membrane, to integrate various environmental cues. In this context, understanding the fine-print of above processes may be essential to solve the problems of crop adaptation to various harsh environments under current climate trends scenarios, by genetic means. This paper summarizes the current knowledge about the structure and diversity of RALF peptides and their roles in plant development and response to stresses, highlighting unanswered questions and problems to be solved.
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Affiliation(s)
- Lining Liu
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Xing Liu
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhenkun Bai
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Mohsin Tanveer
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yujing Zhang
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Wenjie Chen
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Sergey Shabala
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China; School of Biological Science, University of Western Australia, Crawley, Perth, Australia.
| | - Liping Huang
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China.
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Priyanka P, Gopalakrishnan AP, Nisar M, Shivamurthy PB, George M, John L, Sanjeev D, Yandigeri T, Thomas SD, Rafi A, Dagamajalu S, Velikkakath AKG, Abhinand CS, Kanekar S, Prasad TSK, Balaya RDA, Raju R. A global phosphosite-correlated network map of Thousand And One Kinase 1 (TAOK1). Int J Biochem Cell Biol 2024; 170:106558. [PMID: 38479581 DOI: 10.1016/j.biocel.2024.106558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
Thousand and one amino acid kinase 1 (TAOK1) is a sterile 20 family Serine/Threonine kinase linked to microtubule dynamics, checkpoint signaling, DNA damage response, and neurological functions. Molecular-level alterations of TAOK1 have been associated with neurodevelopment disorders and cancers. Despite their known involvement in physiological and pathophysiological processes, and as a core member of the hippo signaling pathway, the phosphoregulatory network of TAOK1 has not been visualized. Aimed to explore this network, we first analyzed the predominantly detected and differentially regulated TAOK1 phosphosites in global phosphoproteome datasets across diverse experimental conditions. Based on 709 qualitative and 210 quantitative differential cellular phosphoproteome datasets that were systematically assembled, we identified that phosphorylation at Ser421, Ser9, Ser965, and Ser445 predominantly represented TAOK1 in almost 75% of these datasets. Surprisingly, the functional role of all these phosphosites in TAOK1 remains unexplored. Hence, we employed a robust strategy to extract the phosphosites in proteins that significantly correlated in expression with predominant TAOK1 phosphosites. This led to the first categorization of the phosphosites including those in the currently known and predicted interactors, kinases, and substrates, that positively/negatively correlated with the expression status of each predominant TAOK1 phosphosites. Subsequently, we also analyzed the phosphosites in core proteins of the hippo signaling pathway. Based on the TAOK1 phosphoregulatory network analysis, we inferred the potential role of the predominant TAOK1 phosphosites. Especially, we propose pSer9 as an autophosphorylation and TAOK1 kinase activity-associated phosphosite and pS421, the most frequently detected phosphosite in TAOK1, as a significant regulatory phosphosite involved in the maintenance of genome integrity. Considering that the impact of all phosphosites that predominantly represent each kinase is essential for the efficient interpretation of global phosphoproteome datasets, we believe that the approach undertaken in this study is suitable to be extended to other kinases for accelerated research.
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Affiliation(s)
- Pahal Priyanka
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Athira Perunelly Gopalakrishnan
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | - Mejo George
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Tanuja Yandigeri
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Sonet D Thomas
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Ahmad Rafi
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Anoop Kumar G Velikkakath
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | | | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
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Siddiqui MF, Li J, Wang S, Zhang H, Qin C, Lu Y. FAM20A is a golgi-localized Type II transmembrane protein. Sci Rep 2024; 14:6518. [PMID: 38499693 PMCID: PMC10948845 DOI: 10.1038/s41598-024-57007-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
Family with sequence similarity 20, member A (FAM20A) is a pseudo-kinase in the secretory pathway and is essential for enamel formation in humans. Here we examine if FAM20A is a membrane-associated protein. We show that the full-length FAM20A can be purified from HEK293 cells transfected with a FAM20A-expresing construct. Further, it is only found in the membrane fraction, but not in the soluble fraction, of cell lysate. Consistently, it is not secreted out of the expressing cells. Moreover, it is co-localized with GM130, a cis-Golgi network marker, and membrane topology analysis indicates that it has its C-terminus oriented towards the lumen of the organelle. Our results support that FAM20A is a Type II transmembrane protein within the secretory compartments.
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Affiliation(s)
- Mohammad Faizan Siddiqui
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave, Dallas, TX, 75246, USA
| | - Jiahe Li
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave, Dallas, TX, 75246, USA
| | - Suzhen Wang
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave, Dallas, TX, 75246, USA
| | - Hua Zhang
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave, Dallas, TX, 75246, USA
| | - Chunlin Qin
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave, Dallas, TX, 75246, USA
| | - Yongbo Lu
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave, Dallas, TX, 75246, USA.
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Xu F, Chen J, Li Y, Ouyang S, Yu M, Wang Y, Fang X, He K, Yu F. The soil emergence-related transcription factor PIF3 controls root penetration by interacting with the receptor kinase FER. Dev Cell 2024; 59:434-447.e8. [PMID: 38295794 DOI: 10.1016/j.devcel.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/23/2023] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence-related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) controls root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in Arabidopsis and soybean (Glycine max) mutants resulted in a severe defect in root penetration into agar medium or hard soil. Single-cell RNA sequencing (scRNA-seq) profiling of Arabidopsis roots identified a distinct cell clustering pattern, especially for root cap cells, and identified PIF3 as a FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root penetration into soil. Moreover, FER interacted with and stabilized PIF3 to modulate the expression of mechanosensitive ion channel PIEZO and the sloughing of outer root cap cells.
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Affiliation(s)
- Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Jia Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Yingbin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Shilin Ouyang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Mengting Yu
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yirong Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Xianming Fang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Kai He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China.
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Abel NB, Nørgaard MMM, Hansen SB, Gysel K, Díez IA, Jensen ON, Stougaard J, Andersen KR. Phosphorylation of the alpha-I motif in SYMRK drives root nodule organogenesis. Proc Natl Acad Sci U S A 2024; 121:e2311522121. [PMID: 38363863 PMCID: PMC10895371 DOI: 10.1073/pnas.2311522121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/15/2023] [Indexed: 02/18/2024] Open
Abstract
Symbiosis receptor-like kinase SYMRK is required for root nodule symbiosis between legume plants and nitrogen-fixing bacteria. To understand symbiotic signaling from SYMRK, we determined the crystal structure to 1.95 Å and mapped the phosphorylation sites onto the intracellular domain. We identified four serine residues in a conserved "alpha-I" motif, located on the border between the kinase core domain and the flexible C-terminal tail, that, when phosphorylated, drives organogenesis. Substituting the four serines with alanines abolished symbiotic signaling, while substituting them with phosphorylation-mimicking aspartates induced the formation of spontaneous nodules in the absence of bacteria. These findings show that the signaling pathway controlling root nodule organogenesis is mediated by SYMRK phosphorylation, which may help when engineering this trait into non-legume plants.
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Affiliation(s)
- Nikolaj B. Abel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Malita M. M. Nørgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Simon B. Hansen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Ignacio Arribas Díez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M5230, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M5230, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Kasper R. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
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Liu MCJ, Yeh FLJ, Yvon R, Simpson K, Jordan S, Chambers J, Wu HM, Cheung AY. Extracellular pectin-RALF phase separation mediates FERONIA global signaling function. Cell 2024; 187:312-330.e22. [PMID: 38157854 DOI: 10.1016/j.cell.2023.11.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/01/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
The FERONIA (FER)-LLG1 co-receptor and its peptide ligand RALF regulate myriad processes for plant growth and survival. Focusing on signal-induced cell surface responses, we discovered that intrinsically disordered RALF triggers clustering and endocytosis of its cognate receptors and FER- and LLG1-dependent endocytosis of non-cognate regulators of diverse processes, thus capable of broadly impacting downstream responses. RALF, however, remains extracellular. We demonstrate that RALF binds the cell wall polysaccharide pectin. They phase separate and recruit FER and LLG1 into pectin-RALF-FER-LLG1 condensates to initiate RALF-triggered cell surface responses. We show further that two frequently encountered environmental challenges, elevated salt and temperature, trigger RALF-pectin phase separation, promiscuous receptor clustering and massive endocytosis, and that this process is crucial for recovery from stress-induced growth attenuation. Our results support that RALF-pectin phase separation mediates an exoskeletal mechanism to broadly activate FER-LLG1-dependent cell surface responses to mediate the global role of FER in plant growth and survival.
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Affiliation(s)
- Ming-Che James Liu
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA
| | - Fang-Ling Jessica Yeh
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA; Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Robert Yvon
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA; Molecular and Cell Biology Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kelly Simpson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA; Molecular and Cell Biology Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Samuel Jordan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA
| | - James Chambers
- Light Microscopy Core Facility, Institute of Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Hen-Ming Wu
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA; Molecular and Cell Biology Program, University of Massachusetts, Amherst, MA 01003, USA.
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 N. Pleasant St., Lederle Graduate Tower, Amherst, MA 01003, USA; Molecular and Cell Biology Program, University of Massachusetts, Amherst, MA 01003, USA; Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA.
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7
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Zhu H, Wu Y, Zhuang Z, Xu J, Chen F, Wang Q, Tang Q. Ampelopsis japonica aqueous extract improves ovulatory dysfunction in PCOS by modulating lipid metabolism. Biomed Pharmacother 2024; 170:116093. [PMID: 38159378 DOI: 10.1016/j.biopha.2023.116093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024] Open
Abstract
Polycystic ovary syndrome (PCOS) is a highly prevalent endocrine and metabolic disorder that is closely associated with the proliferation and apoptosis of ovarian granulosa cells (GCs). Ampelopsis japonica (AJ) is the dried tuberous root of Ampelopsis japonica (Thunb.) Makino (A. japonica), with anti-inflammatory, antioxidant, antibacterial, antiviral, wound-healing, and antitumor properties; however, it is unclear whether this herb has a therapeutic effect on PCOS. Therefore, this study aimed to investigate the pharmacological effect of AJ on PCOS and reveal its potential mechanism of action. A PCOS rat model was established using letrozole. After establishing the PCOS model, the rats received oral treatment of AJ and Diane-35 (Positive drug: ethinylestradiol + cyproterone tablets) for 2 weeks. Lipidomics was conducted using liquid-phase mass spectrometry and chromatography. AJ significantly regulated serum hormone levels and attenuated pathological variants in the ovaries of rats with PCOS. Furthermore, AJ significantly reduced the apoptotic rate of ovarian GCs. Lipidomic analysis revealed that AJ modulated glycerolipid and glycerophospholipid metabolic pathways mediated by lipoprotein lipase (Lpl), diacylglycerol choline phosphotransferase (Chpt1), and choline/ethanolamine phosphotransferase (Cept1). Therefore, we established that AJ may reduce ovarian GC apoptosis by modulating lipid metabolism, ultimately improving ovulatory dysfunction in PCOS. Therefore, AJ is a novel candidate for PCOS treatment.
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Affiliation(s)
- Huiqing Zhu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou 510515, China
| | - Yuanyuan Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou 510515, China
| | - Ziming Zhuang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou 510515, China
| | - Jing Xu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou 510515, China
| | - Feilong Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou 510515, China
| | - Qirui Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China.
| | - Qingfa Tang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China; Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou 510515, China.
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Gupta S, Guérin A, Herger A, Hou X, Schaufelberger M, Roulard R, Diet A, Roffler S, Lefebvre V, Wicker T, Pelloux J, Ringli C. Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module. PLoS Genet 2024; 20:e1011087. [PMID: 38190412 PMCID: PMC10824444 DOI: 10.1371/journal.pgen.1011087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/29/2024] [Accepted: 11/29/2023] [Indexed: 01/10/2024] Open
Abstract
Plant cell growth involves coordination of numerous processes and signaling cascades among the different cellular compartments to concomitantly enlarge the protoplast and the surrounding cell wall. The cell wall integrity-sensing process involves the extracellular LRX (LRR-Extensin) proteins that bind RALF (Rapid ALkalinization Factor) peptide hormones and, in vegetative tissues, interact with the transmembrane receptor kinase FERONIA (FER). This LRX/RALF/FER signaling module influences cell wall composition and regulates cell growth. The numerous proteins involved in or influenced by this module are beginning to be characterized. In a genetic screen, mutations in Apyrase 7 (APY7) were identified to suppress growth defects observed in lrx1 and fer mutants. APY7 encodes a Golgi-localized NTP-diphosphohydrolase, but opposed to other apyrases of Arabidopsis, APY7 revealed to be a negative regulator of cell growth. APY7 modulates the growth-inhibiting effect of RALF1, influences the cell wall architecture and -composition, and alters the pH of the extracellular matrix, all of which affect cell growth. Together, this study reveals a function of APY7 in cell wall formation and cell growth that is connected to growth processes influenced by the LRX/RALF/FER signaling module.
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Affiliation(s)
- Shibu Gupta
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Amandine Guérin
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Aline Herger
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Xiaoyu Hou
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Myriam Schaufelberger
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Romain Roulard
- UMR INRAe BioEcoAgro, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, Amiens, France
| | - Anouck Diet
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Stefan Roffler
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Valérie Lefebvre
- UMR INRAe BioEcoAgro, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, Amiens, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Jérôme Pelloux
- UMR INRAe BioEcoAgro, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, Amiens, France
| | - Christoph Ringli
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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VanSchouwen B, Melacini G. Probing ligand selectivity in pathogens. eLife 2023; 12:e94720. [PMID: 38126364 PMCID: PMC10735216 DOI: 10.7554/elife.94720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Why does protein kinase A respond to purine nucleosides in certain pathogens, but not to the cyclic nucleotides that activate this kinase in most other organisms?
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster UniversityHamiltonCanada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, and the Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamiltonCanada
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10
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Wang Z, Tan J, Li M, Gao C, Li W, Xu J, Guo C, Chen Z, Cai R. Clickable Photoreactive ATP-Affinity Probe for Global Profiling of ATP-Binding Proteins. Anal Chem 2023; 95:17533-17540. [PMID: 37993803 DOI: 10.1021/acs.analchem.3c02694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Adenosine triphosphate (ATP) is the major energy carrier in organisms, and there are many cellular proteins that can bind to ATP. Among these proteins, kinases are key regulators in several cell signaling processes, and aberrant kinase signaling contributes to the development of many human diseases, including cancer. Hence, small-molecule kinase inhibitors have been successfully used for the treatment of various diseases. Since the ATP-binding pockets are similar for many kinases, it is very important to evaluate the selectivity of different kinase inhibitors. We report here a clickable ATP photoaffinity probe for the global profiling of ATP-binding proteins. After incubating the protein lysate with the ATP probe followed by ultraviolet (UV) irradiation, ATP-binding proteins were labeled with an alkyne handle for subsequent biotin conjugation through click chemistry. Labeled proteins were enriched with streptavidin beads, digested with trypsin, and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). More than 400 ATP-binding proteins, including approximately 200 kinases, could be identified in a single LC-MS/MS run in the data-dependent acquisition mode. We then applied this method to the analysis of targets of three selected ATP-competitive kinase inhibitors. We were able to successfully identify some of their reported target proteins from label-free quantification results and validated the results using Western blot analyses. Together, we developed a clickable ATP photoaffinity probe for proteome-wide profiling of ATP-binding proteins and demonstrated that this chemoproteomic method is amenable to high-throughput target identification of kinase inhibitors.
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Affiliation(s)
- Zhiming Wang
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Jing Tan
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Mengxuan Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Can Gao
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Wenwen Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Jing Xu
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Changchuan Guo
- Shandong Institute for Food and Drug Control, Jinan 250101, Shandong, China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Rong Cai
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
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11
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Wei Y, Miao Q, Zhang Q, Mao S, Li M, Xu X, Xia X, Wei K, Fan Y, Zheng X, Fang Y, Mei M, Zhang Q, Ding J, Fan Y, Lu M, Hu G. Aerobic glycolysis is the predominant means of glucose metabolism in neuronal somata, which protects against oxidative damage. Nat Neurosci 2023; 26:2081-2089. [PMID: 37996529 DOI: 10.1038/s41593-023-01476-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/29/2023] [Indexed: 11/25/2023]
Abstract
It is generally thought that under basal conditions, neurons produce ATP mainly through mitochondrial oxidative phosphorylation (OXPHOS), and glycolytic activity only predominates when neurons are activated and need to meet higher energy demands. However, it remains unknown whether there are differences in glucose metabolism between neuronal somata and axon terminals. Here, we demonstrated that neuronal somata perform higher levels of aerobic glycolysis and lower levels of OXPHOS than terminals, both during basal and activated states. We found that the glycolytic enzyme pyruvate kinase 2 (PKM2) is localized predominantly in the somata rather than in the terminals. Deletion of Pkm2 in mice results in a switch from aerobic glycolysis to OXPHOS in neuronal somata, leading to oxidative damage and progressive loss of dopaminergic neurons. Our findings update the conventional view that neurons uniformly use OXPHOS under basal conditions and highlight the important role of somatic aerobic glycolysis in maintaining antioxidant capacity.
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Affiliation(s)
- Yao Wei
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - QianQian Miao
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Qian Zhang
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shiyu Mao
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Mengke Li
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xing Xu
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xian Xia
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ke Wei
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Fan
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinlei Zheng
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yinquan Fang
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Meng Mei
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qingyu Zhang
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianhua Ding
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Yi Fan
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Ming Lu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Gang Hu
- Department of Pharmacology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China.
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12
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Mascari CA, Little JL, Kristich CJ. PASTA-kinase-mediated signaling drives accumulation of the peptidoglycan synthesis protein MurAA to promote cephalosporin resistance in Enterococcus faecalis. Mol Microbiol 2023; 120:811-829. [PMID: 37688380 PMCID: PMC10872757 DOI: 10.1111/mmi.15150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/27/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
The bacterial PASTA kinase, IreK, is required for intrinsic cephalosporin resistance in the Gram-positive opportunistic pathogen, Enterococcus faecalis. IreK activity is enhanced in response to cell wall stress, such as cephalosporin exposure. The downstream consequences of IreK activation are not well understood in E. faecalis, but recent work in other low-GC Gram-positive bacteria demonstrated PASTA kinase-dependent regulation of MurAA, an enzyme that performs the first committed step in the peptidoglycan synthesis pathway. Here, we used genetic suppressor selections to identify MurAA as a downstream target of IreK signaling in E. faecalis. Using complementary genetic and biochemical approaches, we demonstrated that MurAA abundance is regulated by IreK signaling in response to physiologically relevant cell wall stress to modulate substrate flux through the peptidoglycan synthesis pathway. Specifically, the IreK substrate, IreB, promotes proteolysis of MurAA through a direct physical interaction in a manner responsive to phosphorylation by IreK. MurAB, a homolog of MurAA, also promotes MurAA proteolysis and interacts directly with IreB. Our results therefore establish a connection between the cell wall stress sensor IreK and one critical physiological output to modulate peptidoglycan synthesis and drive cephalosporin resistance.
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Affiliation(s)
- Carly A. Mascari
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226
| | - Jaime L. Little
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226
| | - Christopher J. Kristich
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226
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13
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Xia L, Li P, Bi W, Yang R, Zhang Y. CDK5R1 promotes Schwann cell proliferation, migration, and production of neurotrophic factors via CDK5/BDNF/TrkB after sciatic nerve injury. Neurosci Lett 2023; 817:137514. [PMID: 37848102 DOI: 10.1016/j.neulet.2023.137514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/25/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
Cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1) is necessary for central nervous system development and neuronal migration. At present, there are few reports about the role of CDK5R1 in peripheral nerve injury, and these need to be further explored. The CCK-8 and EdU assay was performed to examine cell proliferation. The migration ability of Schwann cells was tested by the cell scratch test. The apoptosis of Schwann cells was detected by flow cytometry. Sciatic nerve injury model in rats was established by crush injury. The sciatic function index (SFI) and the paw withdrawal mechanical threshold (PWMT) were measured at different time points. The results revealed that overexpression of CDK5R1 promoted the proliferation and migration of Schwann cells, and inhibited the apoptosis. Further studies found that pcDNA3.1-CDK5R1 significantly upregulated the expression of CDK5, BDNF and TrkB. More importantly, CDK5R1 promoted the recovery of nerve injury in rats. In addition, the CDK5 mediated BDNF/TrkB pathway was involved in the molecular mechanism of CDK5R1 on Schwann cells. It is suggested that the mechanism by which CDK5R1 promotes functional recovery after sciatic nerve injury is by CDK5 mediated activation of BDNF/TrkB signaling pathways.
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Affiliation(s)
- Lei Xia
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Department of Hand Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China
| | - Peng Li
- Department of Hand Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China
| | - Wenchao Bi
- Department of Hand Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China
| | - Ruize Yang
- Department of Hand Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China
| | - Yuelin Zhang
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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14
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Willet AH, Turner LA, Park JS, Ren L, Snider CE, Gould KL. Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis. J Cell Sci 2023; 136:jcs261415. [PMID: 37815455 PMCID: PMC10629694 DOI: 10.1242/jcs.261415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
Phosphatidylinositol (PI)-4-phosphate (PI4P) is a lipid found at the plasma membrane (PM) and Golgi in cells from yeast to humans. PI4P is generated from PI by PI4-kinases and can be converted into PI-4,5-bisphosphate [PI(4,5)P2]. Schizosaccharomyces pombe have two essential PI4-kinases - Stt4 and Pik1. Stt4 localizes to the PM, and its loss from the PM results in a decrease of PM PI4P and PI(4,5)P2. As a result, cells divide non-medially due to disrupted cytokinetic ring-PM anchoring. However, the localization and function of S. pombe Pik1 has not been thoroughly examined. Here, we found that Pik1 localizes exclusively to the trans-Golgi and is required for Golgi PI4P production. We determined that Ncs1 regulates Pik1, but unlike in other organisms, it is not required for Pik1 Golgi localization. When Pik1 function was disrupted, PM PI4P but not PI(4,5)P2 levels were reduced, a major difference compared with Stt4. We conclude that Stt4 is the chief enzyme responsible for producing the PI4P that generates PI(4,5)P2. Also, that cells with disrupted Pik1 do not divide asymmetrically highlights the specific importance of PM PI(4,5)P2 for cytokinetic ring-PM anchoring.
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Affiliation(s)
- Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lesley A. Turner
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Joshua S. Park
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chloe E. Snider
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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15
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Pratap Reddy Gajulapalli V. Development of Kinase-Centric Drugs: A Computational Perspective. ChemMedChem 2023; 18:e202200693. [PMID: 37442809 DOI: 10.1002/cmdc.202200693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023]
Abstract
Kinases are prominent drug targets in the pharmaceutical and research community due to their involvement in signal transduction, physiological responses, and upon dysregulation, in diseases such as cancer, neurological and autoimmune disorders. Several FDA-approved small-molecule drugs have been developed to combat human diseases since Gleevec was approved for the treatment of chronic myelogenous leukemia. Kinases were considered "undruggable" in the beginning. Several FDA-approved small-molecule drugs have become available in recent years. Most of these drugs target ATP-binding sites, but a few target allosteric sites. Among kinases that belong to the same family, the catalytic domain shows high structural and sequence conservation. Inhibitors of ATP-binding sites can cause off-target binding. Because members of the same family have similar sequences and structural patterns, often complex relationships between kinases and inhibitors are observed. To design and develop drugs with desired selectivity, it is essential to understand the target selectivity for kinase inhibitors. To create new inhibitors with the desired selectivity, several experimental methods have been designed to profile the kinase selectivity of small molecules. Experimental approaches are often expensive, laborious, time-consuming, and limited by the available kinases. Researchers have used computational methodologies to address these limitations in the design and development of effective therapeutics. Many computational methods have been developed over the last few decades, either to complement experimental findings or to forecast kinase inhibitor activity and selectivity. The purpose of this review is to provide insight into recent advances in theoretical/computational approaches for the design of new kinase inhibitors with the desired selectivity and optimization of existing inhibitors.
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16
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El-Araby AM, Jiménez-Faraco E, Feltzer R, Martin-Garcia JM, Karri BR, Ramachandran B, Kim C, Fisher JF, Hermoso JA, Mobashery S. Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa. J Biol Chem 2023; 299:105198. [PMID: 37660917 PMCID: PMC10570956 DOI: 10.1016/j.jbc.2023.105198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023] Open
Abstract
The bacterial cell envelope is the structure with which the bacterium engages with, and is protected from, its environment. Within this envelop is a conserved peptidoglycan polymer which confers shape and strength to the cell envelop. The enzymatic processes that build, remodel, and recycle the chemical components of this cross-linked polymer are preeminent targets of antibiotics and exploratory targets for emerging antibiotic structures. We report a comprehensive kinetic and structural analysis for one such enzyme, the Pseudomonas aeruginosa anhydro-N-acetylmuramic acid (anhNAM) kinase (AnmK). AnmK is an enzyme in the peptidoglycan-recycling pathway of this pathogen. It catalyzes the pairing of hydrolytic ring opening of anhNAM with concomitant ATP-dependent phosphoryl transfer. AnmK follows a random-sequential kinetic mechanism with respect to its anhNAM and ATP substrates. Crystallographic analyses of four distinct structures (apo AnmK, AnmK:AMPPNP, AnmK:AMPPNP:anhNAM, and AnmK:ATP:anhNAM) demonstrate that both substrates enter the active site independently in an ungated conformation of the substrate subsites, with protein loops acting as gates for anhNAM binding. Catalysis occurs within a closed conformational state for the enzyme. We observe this state crystallographically using ATP-mimetic molecules. A remarkable X-ray structure for dimeric AnmK sheds light on the precatalytic and postcatalytic ternary complexes. Computational simulations in conjunction with the high-resolution X-ray structures reveal the full catalytic cycle. We further report that a P. aeruginosa strain with disrupted anmK gene is more susceptible to the β-lactam imipenem compared to the WT strain. These observations position AnmK for understanding the nexus among peptidoglycan recycling, susceptibility to antibiotics, and bacterial virulence.
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Affiliation(s)
- Amr M El-Araby
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Eva Jiménez-Faraco
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jose M Martin-Garcia
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Bhaskara Rao Karri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Balajee Ramachandran
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
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17
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Zanetti ME. FER meets the Nod factor pathway. Nat Plants 2023; 9:1581-1582. [PMID: 37749241 DOI: 10.1038/s41477-023-01531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Affiliation(s)
- María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.
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18
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Stasiak AC, Gogler K, Borisova M, Fink P, Mayer C, Stehle T, Zocher G. N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia. J Biol Chem 2023; 299:105076. [PMID: 37481208 PMCID: PMC10465942 DOI: 10.1016/j.jbc.2023.105076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023] Open
Abstract
The bacterial cell wall consists of a three-dimensional peptidoglycan layer, composed of peptides linked to the sugars N-acetylmuramic acid (MurNAc) and GlcNAc. Unlike other bacteria, the pathogenic Tannerella forsythia, a member of the red complex group of bacteria associated with the late stages of periodontitis, lacks biosynthetic pathways for MurNAc production and therefore obtains MurNAc from the environment. Sugar kinases play a crucial role in the MurNAc recycling process, activating the sugar molecules by phosphorylation. In this study, we present the first crystal structures of a MurNAc kinase, called murein sugar kinase (MurK), in its unbound state as well as in complexes with the ATP analog β-γ-methylene adenosine triphosphate (AMP-PCP) and with MurNAc. We also determined the crystal structures of K1058, a paralogous MurNAc kinase of T. forsythia, in its unbound state and in complex with MurNAc. We identified the active site and residues crucial for MurNAc specificity as the less bulky side chains of S133, P134, and L135, which enlarge the binding cavity for the lactyl ether group, unlike the glutamate or histidine residues present in structural homologs. In establishing the apparent kinetic parameters for both enzymes, we showed a comparable affinity for MurNAc (Km 180 μM and 30 μM for MurK and K1058, respectively), with MurK being over two hundred times faster than K1058 (Vmax 80 and 0.34 μmol min-1 mg-1, respectively). These data might support a structure-guided approach to development of inhibitory MurNAc analogs for pathogen MurK enzymes.
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Affiliation(s)
| | - Karolin Gogler
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, University of Tuebingen, Tuebingen, Germany
| | - Phillipp Fink
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, University of Tuebingen, Tuebingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany.
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19
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Qiao W, Richards CM, Jabs S. LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway. Autophagy 2023; 19:2143-2145. [PMID: 36633450 PMCID: PMC10283412 DOI: 10.1080/15548627.2023.2167376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Degradation of macromolecules delivered to lysosomes by processes such as autophagy or endocytosis is crucial for cellular function. Lysosomes require more than 60 soluble hydrolases in order to catabolize such macromolecules. These soluble hydrolases are tagged with mannose6-phosphate (M6P) moieties in sequential reactions by the Golgi-resident GlcNAc-1-phosphotransferase complex and NAGPA/UCE/uncovering enzyme (N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase), which allows their delivery to endosomal/lysosomal compartments through trafficking mediated by cation-dependent and -independent mannose 6-phosphate receptors (MPRs). We and others recently identified TMEM251 as a novel regulator of the M6P pathway via independent genome-wide genetic screening strategies. We renamed TMEM251 to LYSET (lysosomal enzyme trafficking factor) to establish nomenclature reflective to this gene's function. LYSET is a Golgi-localized transmembrane protein important for the retention of the GlcNAc-1-phosphotransferase complex in the Golgi-apparatus. The current understanding of LYSET's importance regarding human biology is 3-fold: 1) highly pathogenic viruses that depend on lysosomal hydrolase activity require LYSET for infection. 2) The presence of LYSET is critical for cancer cell proliferation in nutrient-deprived environments in which extracellular proteins must be catabolized. 3) Inherited pathogenic alleles of LYSET can cause a severe inherited disease which resembles GlcNAc-1-phosphotransferase deficiency (i.e., mucolipidosis type II).Abbreviations: GlcNAc-1-PT: GlcNAc-1-phosphotransferase; KO: knockout; LSD: lysosomal storage disorder; LYSET: lysosomal enzyme trafficking factor; M6P: mannose 6-phosphate; MPRs: mannose-6-phosphate receptors, cation-dependent or -independent; MBTPS1/site-1 protease: membrane bound transcription factor peptidase, site 1; MLII: mucolipidosis type II; WT: wild-type.
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Affiliation(s)
- Wenjie Qiao
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher M. Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Schleswig-Holstein, Germany
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20
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Basanta CDLAC, Bazzi M, Hijazi M, Bessant C, Cutillas PR. Community detection in empirical kinase networks identifies new potential members of signalling pathways. PLoS Comput Biol 2023; 19:e1010459. [PMID: 37352361 PMCID: PMC10325051 DOI: 10.1371/journal.pcbi.1010459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 07/06/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Phosphoproteomics allows one to measure the activity of kinases that drive the fluxes of signal transduction pathways involved in biological processes such as immune function, senescence and cell growth. However, deriving knowledge of signalling network circuitry from these data is challenging due to a scarcity of phosphorylation sites that define kinase-kinase relationships. To address this issue, we previously identified around 6,000 phosphorylation sites as markers of kinase-kinase relationships (that may be conceptualised as network edges), from which empirical cell-model-specific weighted kinase networks may be reconstructed. Here, we assess whether the application of community detection algorithms to such networks can identify new components linked to canonical signalling pathways. Phosphoproteomics data from acute myeloid leukaemia (AML) cells treated separately with PI3K, AKT, MEK and ERK inhibitors were used to reconstruct individual kinase networks. We used modularity maximisation to detect communities in each network, and selected the community containing the main target of the inhibitor used to treat cells. These analyses returned communities that contained known canonical signalling components. Interestingly, in addition to canonical PI3K/AKT/mTOR members, the community assignments returned TTK (also known as MPS1) as a likely component of PI3K/AKT/mTOR signalling. We drew similar insights from an external phosphoproteomics dataset from breast cancer cells treated with rapamycin and oestrogen. We confirmed this observation with wet-lab laboratory experiments showing that TTK phosphorylation was decreased in AML cells treated with AKT and MTOR inhibitors. This study illustrates the application of community detection algorithms to the analysis of empirical kinase networks to uncover new members linked to canonical signalling pathways.
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Affiliation(s)
- Celia De Los Angeles Colomina Basanta
- Cell signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Marya Bazzi
- Warwick Mathematics Institute, University of Warwick, Coventry, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Maruan Hijazi
- Cell signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Conrad Bessant
- The Alan Turing Institute, London, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Pedro R. Cutillas
- Cell signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- The Alan Turing Institute, London, United Kingdom
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21
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Xiong T, Ye F, Chen J, Chen Y, Zhang Z. Peptide signaling in anther development and pollen-stigma interactions. Gene 2023; 865:147328. [PMID: 36870426 DOI: 10.1016/j.gene.2023.147328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/25/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Polypeptides play irreplaceable roles in cell-cell communication by binding to receptor-like kinases. Various types of peptide-receptor-like kinase-mediated signaling have been identified in anther development and male-female interactions in flowering plants. Here, we provide a comprehensive summary of the biological functions and signaling pathways of peptides and receptors involved in anther development, self-incompatibility, pollen tube growth and pollen tube guidance.
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Affiliation(s)
- Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, China
| | - Fan Ye
- College of International Education, Xinyang Normal University, Xinyang, China
| | - Jiahui Chen
- College of International Education, Xinyang Normal University, Xinyang, China
| | - Yurui Chen
- College of International Education, Xinyang Normal University, Xinyang, China
| | - Zaibao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, China.
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22
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Wang L, Zhou M. Structure of a eukaryotic cholinephosphotransferase-1 reveals mechanisms of substrate recognition and catalysis. Nat Commun 2023; 14:2753. [PMID: 37179328 PMCID: PMC10182977 DOI: 10.1038/s41467-023-38003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic cell membranes. In eukaryotes, two highly homologous enzymes, cholinephosphotransferase-1 (CHPT1) and choline/ethanolamine phosphotransferase-1 (CEPT1) catalyze the final step of de novo PC synthesis. CHPT1/CEPT1 joins two substrates, cytidine diphosphate-choline (CDP-choline) and diacylglycerol (DAG), to produce PC, and Mg2+ is required for the reaction. However, mechanisms of substrate recognition and catalysis remain unresolved. Here we report structures of a CHPT1 from Xenopus laevis (xlCHPT1) determined by cryo-electron microscopy to an overall resolution of ~3.2 Å. xlCHPT1 forms a homodimer, and each protomer has 10 transmembrane helices (TMs). The first 6 TMs carve out a cone-shaped enclosure in the membrane in which the catalysis occurs. The enclosure opens to the cytosolic side, where a CDP-choline and two Mg2+ are coordinated. The structures identify a catalytic site unique to eukaryotic CHPT1/CEPT1 and suggest an entryway for DAG. The structures also reveal an internal pseudo two-fold symmetry between TM3-6 and TM7-10, and suggest that CHPT1/CEPT1 may have evolved from their distant prokaryotic ancestors through gene duplication.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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23
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Liu X, Li L, Jiang J, Ge W, Huang Y, Jin Z, Liu X, Kong Y, Zhanmu O, Zeng X, Li F, Li M, Chen H. Role of Type I Cannabinoid Receptor in Sensory Neurons in Psoriasiform Skin Inflammation and Pruritus. J Invest Dermatol 2023; 143:812-821.e3. [PMID: 36410425 DOI: 10.1016/j.jid.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/23/2022]
Abstract
Type I cannabinoid receptor (CB1R) has been reported to exhibit favorable anti-inflammation and antipruritus effects against inflammation-based skin diseases, but the specific mechanism remains to be explored. In this study, we found that the activation of CB1R significantly relieved the scratching behavior and skin inflammation in a psoriatic mouse model, whereas CB1R antagonist aggravated these symptoms. Because the expression of CB1R was abundant in dorsal root ganglia, we constructed mice with conditional CB1R knockout in primary sensory neurons and found that imiquimod-induced psoriasiform inflammation and itch were both worsened in CB1R-conditional knockout mice. Next, we observed that the CB1R was mostly located in peptidergic neurons, and deletion of CB1R in primary sensory neurons promoted the production and release of substance P to the skin tissue. Furthermore, the elevated substance P in the skin affected the activation of extracellular signal‒regulated kinase in keratinocytes and induced the accumulation of mast cells in the dermis. Finally, we showed that blocking the substance P signal significantly alleviated the exacerbation of psoriasiform inflammation and itch caused by imiquimod in CB1R-conditional knockout mice. Together, our work reveals that CB1R in sensory neurons plays a key role in psoriasiform skin inflammation and pruritus by regulating substance P expression.
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Affiliation(s)
- Xin Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Li
- Department of Dermatology, School of Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jian Jiang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenqiang Ge
- Department of Neurobiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqiong Huang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilin Jin
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - XinXin Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Kong
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ouyang Zhanmu
- Department of Neurobiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Zeng
- Department of Dermatology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Fei Li
- Department of Dermatology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Man Li
- Department of Neurobiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongxiang Chen
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Dermatology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China.
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24
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Smokvarska M, Bayle V, Maneta-Peyret L, Fouillen L, Poitout A, Dongois A, Fiche JB, Gronnier J, Garcia J, Höfte H, Nolmann M, Zipfel C, Maurel C, Moreau P, Jaillais Y, Martiniere A. The receptor kinase FERONIA regulates phosphatidylserine localization at the cell surface to modulate ROP signaling. Sci Adv 2023; 9:eadd4791. [PMID: 37027473 PMCID: PMC10081841 DOI: 10.1126/sciadv.add4791] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Cells maintain a constant dialog between the extracellular matrix and their plasma membrane to fine tune signal transduction processes. We found that the receptor kinase FERONIA (FER), which is a proposed cell wall sensor, modulates phosphatidylserine plasma membrane accumulation and nano-organization, a key regulator of Rho GTPase signaling in Arabidopsis. We demonstrate that FER is required for both Rho-of-Plant 6 (ROP6) nano-partitioning at the membrane and downstream production of reactive oxygen species upon hyperosmotic stimulus. Genetic and pharmacological rescue experiments indicate that phosphatidylserine is required for a subset of, but not all, FER functions. Furthermore, application of FER ligand shows that its signaling controls both phosphatidylserine membrane localization and nanodomains formation, which, in turn, tunes ROP6 signaling. Together, we propose that a cell wall-sensing pathway controls via the regulation of membrane phospholipid content, the nano-organization of the plasma membrane, which is an essential cell acclimation to environmental perturbations.
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Affiliation(s)
- Marija Smokvarska
- IPSiM Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Lilly Maneta-Peyret
- UMR 5200 Membrane Biogenesis Laboratory, CNRS and University of Bordeaux, INRAE Bordeaux, Villenave d'Ornon, France
| | - Laetitia Fouillen
- UMR 5200 Membrane Biogenesis Laboratory, CNRS and University of Bordeaux, INRAE Bordeaux, Villenave d'Ornon, France
- MetaboHub-Bordeaux, Metabolome platform, INRAE, Villenave d’Ornon, France
| | - Arthur Poitout
- IPSiM Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Armelle Dongois
- IPSiM Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Institut National de la Santé et de la Recherche Médicale U1054, Université de Montpellier, 34090 Montpellier, France
| | - Julien Gronnier
- Institute of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
- University of Tübingen, Center for Plant Molecular Biology (ZMBP), 72076 Tübingen, Germany
| | - José Garcia
- IPSiM Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Marcelo Nolmann
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Institut National de la Santé et de la Recherche Médicale U1054, Université de Montpellier, 34090 Montpellier, France
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, UK
| | - Christophe Maurel
- IPSiM Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Patrick Moreau
- UMR 5200 Membrane Biogenesis Laboratory, CNRS and University of Bordeaux, INRAE Bordeaux, Villenave d'Ornon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
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25
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Pacheco JM, Song L, Kuběnová L, Ovečka M, Berdion Gabarain V, Peralta JM, Lehuedé TU, Ibeas MA, Ricardi MM, Zhu S, Shen Y, Schepetilnikov M, Ryabova LA, Alvarez JM, Gutierrez RA, Grossmann G, Šamaj J, Yu F, Estevez JM. Cell surface receptor kinase FERONIA linked to nutrient sensor TORC signaling controls root hair growth at low temperature linked to low nitrate in Arabidopsis thaliana. New Phytol 2023; 238:169-185. [PMID: 36716782 DOI: 10.1111/nph.18723] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Root hairs (RH) are excellent model systems for studying cell size and polarity since they elongate several hundred-fold their original size. Their tip growth is determined both by intrinsic and environmental signals. Although nutrient availability and temperature are key factors for a sustained plant growth, the molecular mechanisms underlying their sensing and downstream signaling pathways remain unclear. We use genetics to address the roles of the cell surface receptor kinase FERONIA (FER) and the nutrient sensing TOR Complex 1 (TORC) in RH growth. We identified that low temperature (10°C) triggers a strong RH elongation response in Arabidopsis thaliana involving FER and TORC. We found that FER is required to perceive limited nutrient availability caused by low temperature. FERONIA interacts with and activates TORC-downstream components to trigger RH growth. In addition, the small GTPase Rho of plants 2 (ROP2) is also involved in this RH growth response linking FER and TOR. We also found that limited nitrogen nutrient availability can mimic the RH growth response at 10°C in a NRT1.1-dependent manner. These results uncover a molecular mechanism by which a central hub composed by FER-ROP2-TORC is involved in the control of RH elongation under low temperature and nitrogen deficiency.
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Affiliation(s)
- Javier Martínez Pacheco
- Fundación Instituto Leloir and IIBBA-CONICET, Av Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - Limei Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
- Laborarory of Species Interaction and Biological Invasion, School of Life Science, Hebei University, Baoding, 071002, China
| | - Lenka Kuběnová
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Victoria Berdion Gabarain
- Fundación Instituto Leloir and IIBBA-CONICET, Av Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - Juan Manuel Peralta
- Fundación Instituto Leloir and IIBBA-CONICET, Av Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - Tomás Urzúa Lehuedé
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186, Santiago, Chile
- ANID - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), 8331150, Santiago, Chile
| | - Miguel Angel Ibeas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186, Santiago, Chile
- ANID - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), 8331150, Santiago, Chile
| | - Martiniano M Ricardi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Yanan Shen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, CNRS, UPR 2357, Université de Strasbourg, 67084, Strasbourg, France
| | - Lyubov A Ryabova
- Institut de Biologie Moléculaire des Plantes, CNRS, UPR 2357, Université de Strasbourg, 67084, Strasbourg, France
| | - José M Alvarez
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186, Santiago, Chile
- ANID - Millennium Institute for Integrative Biology (iBio), 7500000, Santiago, Chile
| | - Rodrigo A Gutierrez
- ANID - Millennium Institute for Integrative Biology (iBio), 7500000, Santiago, Chile
- Millennium Institute Center for Genome Regulation, 6904411, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Av Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186, Santiago, Chile
- ANID - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), 8331150, Santiago, Chile
- ANID - Millennium Institute for Integrative Biology (iBio), 7500000, Santiago, Chile
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26
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Li R, Duan J, Zhou Y, Wang J. Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin. Appl Environ Microbiol 2023; 89:e0006623. [PMID: 36840592 PMCID: PMC10056949 DOI: 10.1128/aem.00066-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 01/27/2023] [Indexed: 02/24/2023] Open
Abstract
Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for pediocin-like (class IIa) bacteriocins. The cognate immunity protein of bacteriocins, which protects the producer cell from its own bacteriocin, recognizes and binds to the bacteriocin-man-PTS complex, consequently blocking membrane leakage. We previously deciphered the mode of action and immunity of class IIa bacteriocins. Here, we determined the structure of the ternary complex of LcnA, LciA (i.e., the immunity protein), and its receptor, i.e., the man-PTS of Lactococcus lactis (ll-man-PTS). An external loop on the membrane-located component IIC of ll-man-PTS was found to prevent specific binding of the N-terminal region of LcnA to the site recognized by pediocin-like bacteriocins. Thus, the N-terminal β-sheet region of LcnA recognized an adjacent site on the extracellular side of ll-man-PTS, with the LcnA C-terminal hydrophobic helix penetrating into the membrane. The cytoplasmic cleft formed within the man-PTS Core and Vmotif domains induced by embedded LcnA from the periplasmic side is adopted by the appropriate angle between helices H3 and H4 of the N terminus of LciA. The flexible C terminus of LciA then blocks membrane leakage. To summarize, our findings reveal the molecular mechanisms of action and immunity of LcnA and LciA, laying a foundation for further design of class IId bacteriocins. IMPORTANCE Class IId (lactococcin-like) bacteriocins and class IIa (pediocin-like) bacteriocins share a few similarities: (i) both induce membrane leakage and cell death by specifically binding the mannose phosphotransferase system (man-PTS) on their target cells, and (ii) cognate immunity proteins recognize and bind to the bacteriocin-man-PTS complex to block membrane leakage. However, class IId bacteriocins lack the "pediocin box" motif, which is typical of class IIa bacteriocins, and basically target only lactococcal cells; in contrast, class IIa bacteriocins target diverse bacterial cells, but not lactococcal cells. We previously solved the structure of class IIa bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. Here, we determined the structure of the ternary complex of class IId bacteriocin LcnA, its cognate immunity protein LciA, and its receptor, the man-PTS of Lactococcus lactis. By comparing the interactions between man-PTS and class IIa and class IId bacteriocins, this study affords some clues to better understand the specificity of bacteriocins targeting the mannose phosphotransferase system.
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Affiliation(s)
- Ruilian Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Yicheng Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
- Independent Researcher, Urbana, Illinois, USA
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
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27
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Chen W, Zhou H, Xu F, Yu M, Coego A, Rodriguez L, Lu Y, Xie Q, Fu Q, Chen J, Xu G, Wu D, Li X, Li X, Jaillais Y, Rodriguez PL, Zhu S, Yu F. CAR modulates plasma membrane nano-organization and immune signaling downstream of RALF1-FERONIA signaling pathway. New Phytol 2023; 237:2148-2162. [PMID: 36527240 DOI: 10.1111/nph.18687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In Arabidopsis, the receptor-like kinase (RLK) FERONIA (FER) senses peptide ligands in the plasma membrane (PM), modulates plant growth and development, and integrates biotic and abiotic stress signaling for downstream adaptive responses. However, the molecular interplay of these diverse processes is largely unknown. Here, we show that FER, the receptor of Rapid Alkalinization Factor 1 (RALF1), physically interacts with C2 domain ABA-related (CAR) proteins to control the nano-organization of the PM. During this process, the RALF1-FER pathway upregulates CAR protein translation, and then more CAR proteins are recruited to the PM. This acts as a rapid feedforward loop that stabilizes the PM liquid-ordered phase. FER interacts with and phosphorylates CARs, thereby reducing their lipid-binding ability and breaking the feedback regulation at later time points. The formation of the flg22-induced FLS2-BAK1 immune complex, which depends on the integrity of FER-containing nanodomains, is impaired in fer and pentuple car14569 mutant. Together, we propose that the FER-CAR module controls the formation of PM nano-organization during RALF signaling through a self-contained amplifying loop including both positive and negative feedback.
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Affiliation(s)
- Weijun Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Huina Zhou
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022, Valencia, Spain
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022, Valencia, Spain
| | - Yuqing Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Qijun Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Qiong Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Jia Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Guoyun Xu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Dousheng Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiushan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022, Valencia, Spain
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
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28
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Huang J, Yang L, Yang L, Wu X, Cui X, Zhang L, Hui J, Zhao Y, Yang H, Liu S, Xu Q, Pang M, Guo X, Cao Y, Chen Y, Ren X, Lv J, Yu J, Ding J, Xu G, Wang N, Wei X, Lin Q, Yuan Y, Zhang X, Ma C, Dai C, Wang P, Wang Y, Cheng F, Zeng W, Palanivelu R, Wu HM, Zhang X, Cheung AY, Duan Q. Stigma receptors control intraspecies and interspecies barriers in Brassicaceae. Nature 2023; 614:303-308. [PMID: 36697825 PMCID: PMC9908550 DOI: 10.1038/s41586-022-05640-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/09/2022] [Indexed: 01/26/2023]
Abstract
Flowering plants have evolved numerous intraspecific and interspecific prezygotic reproductive barriers to prevent production of unfavourable offspring1. Within a species, self-incompatibility (SI) is a widely utilized mechanism that rejects self-pollen2,3 to avoid inbreeding depression. Interspecific barriers restrain breeding between species and often follow the SI × self-compatible (SC) rule, that is, interspecific pollen is unilaterally incompatible (UI) on SI pistils but unilaterally compatible (UC) on SC pistils1,4-6. The molecular mechanisms underlying SI, UI, SC and UC and their interconnections in the Brassicaceae remain unclear. Here we demonstrate that the SI pollen determinant S-locus cysteine-rich protein/S-locus protein 11 (SCR/SP11)2,3 or a signal from UI pollen binds to the SI female determinant S-locus receptor kinase (SRK)2,3, recruits FERONIA (FER)7-9 and activates FER-mediated reactive oxygen species production in SI stigmas10,11 to reject incompatible pollen. For compatible responses, diverged pollen coat protein B-class12-14 from SC and UC pollen differentially trigger nitric oxide, nitrosate FER to suppress reactive oxygen species in SC stigmas to facilitate pollen growth in an intraspecies-preferential manner, maintaining species integrity. Our results show that SRK and FER integrate mechanisms underlying intraspecific and interspecific barriers and offer paths to achieve distant breeding in Brassicaceae crops.
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Affiliation(s)
- Jiabao Huang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Lin Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Liu Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaoyu Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaoshuang Cui
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Lili Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Jiyun Hui
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yumei Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Hongmin Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Shangjia Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Quanling Xu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Maoxuan Pang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xinping Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yunyun Cao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yu Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xinru Ren
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Jinzhi Lv
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Jianqiang Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Junyi Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Gang Xu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Nian Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qinghui Lin
- Computer Network Information Centre, Chinese Academy of Sciences, Beijing, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengwei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongchao Wang
- Shandong Yiyi Agricultural Science and Technology Co., Ltd, Tai'an, China
| | - Fei Cheng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Weiqing Zeng
- International Flavors & Fragrances, Wilmington, DE, USA
| | | | - Hen-Ming Wu
- Department of Biochemistry and Molecular Biology, Molecular Cell Biology and Plant Biology Programs, University of Massachusetts, Amherst, MA, USA
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, Molecular Cell Biology and Plant Biology Programs, University of Massachusetts, Amherst, MA, USA.
| | - Qiaohong Duan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
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Chen X, Ji Y, Zhao W, Niu H, Yang X, Jiang X, Zhang Y, Lei J, Yang H, Chen R, Gu C, Xu H, Dong H, Duan E, Teng X, Wang Y, Zhang Y, Zhang W, Wang Y, Wan J. Fructose-6-phosphate-2-kinase/fructose-2,6-bisphosphatase regulates energy metabolism and synthesis of storage products in developing rice endosperm. Plant Sci 2023; 326:111503. [PMID: 36270512 DOI: 10.1016/j.plantsci.2022.111503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Starch accounts for about 80-85 % of the dry weight of grains and determines yield by impact on grain weight. And, the content and composition of starch also determine appearance, eating, cooking and nutritional quality of rice. By coordinating crucial reactions of the primary carbohydrate metabolism in all eukaryotes, fructose-2,6-bisphosphate (Fru-2,6-P2) is a traffic signal in metabolism. However, the metabolic regulation of starch in plant sink tissues by Fru-2,6-P2 remains unclear. Here we isolated rice mutant floury endosperm23 (flo23) which has opaque endosperm and anomalous compound starch grains (SGs). flo23 mutant grains had reduced contents of starch, lipids and proteins. Map-based cloning and genetic complementation experiments showed that FLO23 encodes a cytoplasmic Fructose-6-phosphate-2-kinase/Fructose-2,6-bisphosphatase (F2KP). Mutation of OsF2KP2 decreased Fru-2,6-P2 content in endosperm cells, leading to drastically reduced phosphoenolpyruvate (PEP) and pyruvate contents and disordered glycolysis and energy metabolism. The results imply that OsF2KP2 participates in the glycolytic pathway by providing precursors and energy for synthesis of grain storage compounds.
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Affiliation(s)
- Xiaoli Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yi Ji
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Weiying Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huanying Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xue Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaokang Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yipeng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hang Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rongbo Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chuanwei Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hongyi Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hui Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Erchao Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xuan Teng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yunlong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuanyan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wenwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yihua Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, PR China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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30
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Madison I, Amin F, Song K, Sozzani R, Van den Broeck L. A Data-Driven Signaling Network Inference Approach for Phosphoproteomics. Methods Mol Biol 2023; 2690:335-354. [PMID: 37450158 DOI: 10.1007/978-1-0716-3327-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Proteins are rapidly and dynamically post-transcriptionally modified as cells respond to changes in their environment. For example, protein phosphorylation is mediated by kinases while dephosphorylation is mediated by phosphatases. Quantifying and predicting interactions between kinases, phosphatases, and target proteins over time will aid the study of signaling cascades under a variety of environmental conditions. Here, we describe methods to statistically analyze label-free phosphoproteomic data and infer posttranscriptional regulatory networks over time. We provide an R-based method that can be used to normalize and analyze label-free phosphoproteomic data using variance stabilizing normalization and a linear mixed model across multiple time points and conditions. We also provide a method to infer regulator-target interactions over time using a discretization scheme followed by dynamic Bayesian modeling computations to validate our conclusions. Overall, this pipeline is designed to perform functional analyses and predictions of phosphoproteomic signaling cascades.
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Affiliation(s)
- Imani Madison
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA
| | - Fin Amin
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Kuncheng Song
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA.
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA.
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31
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Dias RVR, Ferreira CTA, Jennings PA, Whitford PC, Oliveira LCD. Csk αC Helix: A Computational Analysis of an Essential Region for Conformational Transitions. J Phys Chem B 2022; 126:10587-10596. [PMID: 36512419 DOI: 10.1021/acs.jpcb.2c05408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Conformational changes are an essential feature for the function of some dynamic proteins. Understanding the mechanism of such motions may allow us to identify important properties, which may be directly related to the regulatory function of a protein. Also, this knowledge may be employed for a rational design of drugs that can shift the balance between active and inactive conformations, as well as affect the kinetics of the activation process. Here, the conformational changes in carboxyl-terminal Src kinase, the major catalytic repressor to the Src family of kinases, was investigated, and it was proposed as a functionally related hypothesis. A Cα Structure-Based Model (Cα-SBM) was applied to provide a description of the overall conformational landscape and further analysis complemented by detailed molecular dynamics simulations. As a first approach to Cα-SBM simulations, reversible transitions between active (closed) and inactive (open) forms were modeled as fluctuations between these two energetic basins. It was found that, in addition to the interdomain Carboxyl-terminal SRC Kinase (Csk) correlated motions, a conformational change in the αC helix is required for a complete conformational transition. The result reveals this as an important region of transition control and domain coordination. Restrictions in the αC helix region of the Csk protein were performed, and the analyses showed a direct correlation with the global conformational changes, with this location being propitious for future studies of ligands. Also, the Src Homology 3 (SH3) and SH3 plus Src Homology 2 (SH2) domains were excluded for a direct comparison with experimental results previously published. Simulations where the SH3 was deleted presented a reduction of the transitions during the simulations, while the SH3-SH2 deletion vanishes the Csk transitions, corroborating the experimental results mentioned and linking the conformational changes with the catalytic functionality of Csk. The study was complemented by the introduction of a known kinase inhibitor close to the Csk αC helix region where its consequences for the kinetic behavior and domain displacement of Csk were verified through detailed molecular dynamics. The findings describe the mechanisms involving the Csk αC helix for the transitions and also support the dynamic correlation between SH3 and SH2 domains against the Csk lobes and how local energetic restrictions or interactions in the Csk αC helix can play an important role for long-range motions. The results also allow speculation if the Csk activity is restricted to one specific conformation or a consequence of a state transition, this point being a target for future studies. However, the αC helix is revealed as a potential region for rational drug design.
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Affiliation(s)
- Raphael Vinicius Rodrigues Dias
- São Paulo State University (Unesp), Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo15054-000, Brazil
| | - Carolina Tatiani Alves Ferreira
- São Paulo State University (Unesp), Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo15054-000, Brazil
| | - Patricia Ann Jennings
- University of California, San Diego, 9500 Gilman Drive, Natural Science Building #3110, La Jolla, California92093, United States
| | - Paul Charles Whitford
- Northeastern University, Department of Physics and Center for Theoretical Biological Physics, 360 Huntington Avenue, Boston, Massachusetts02115, United States
| | - Leandro Cristante de Oliveira
- São Paulo State University (Unesp), Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo15054-000, Brazil
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32
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Duan Z, Liu W, Li K, Duan W, Zhu S, Xing J, Chen T, Luo X. Regulation of immune complex formation and signalling by FERONIA, a busy goddess in plant-microbe interactions. Mol Plant Pathol 2022; 23:1695-1700. [PMID: 35951729 PMCID: PMC9562586 DOI: 10.1111/mpp.13256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Being sessile in soil, plant cells rely on cell-surface receptors to sense and transduce environmental stimulus signals into intracellular responses. FERONIA (FER), a Catharanthus roseus receptor-like kinase 1-like protein, has emerged as a versatile regulator of plant growth, development, and stress responses. In recent years, accumulating studies have witnessed rapid advances in dissecting the mechanisms underlying the interaction between FER and its partners in response to pathogen invasion, particularly regulation of immune complex formation and signalling. Moreover, hormonal signalling, rhizosphere microbiota and other constituents are also extensively involved in these processes.
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Affiliation(s)
- Zhikun Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Wei Liu
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kaiwen Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Wenwen Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Shengwei Zhu
- Key Laboratory of Plant PhysiologyInstitute of Botany, Chinese Academy of SciencesBeijingChina
| | - Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Tong Chen
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaomin Luo
- Key Laboratory of Plant PhysiologyInstitute of Botany, Chinese Academy of SciencesBeijingChina
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33
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Zhang M, Wu N, Fan Y, Xu C, Luo J, Wang Y, Yu K, Wang M. Proteomic Profiling and Stress Response in Pediococcus acidilactici under Acetic Acid. J Agric Food Chem 2022; 70:12708-12721. [PMID: 36125361 DOI: 10.1021/acs.jafc.2c04160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lactic acid bacteria are indispensable functional microorganisms for cereal vinegar brewing, but cell activities are inhibited by the dominant acetic acid stress. Herein, an acetic-acid-tolerant strain isolated previously was identified as Pediococcus acidilactici, which also exhibited good resistance to other stresses during vinegar brewing. Proteomics analysis evidenced that differentially expressed proteins involved in the glycolysis and gluconeogenesis pathway, pyruvate metabolism, and sugar phosphotransferase system were all downregulated. Meanwhile, saturation of fatty acids and antioxidant enzymes was strengthened. The effects of several proteins on the resistance of P. acidilactici and Lactobacillus lactis relied on the types of strain and stress. AccA and AcpP participating in fatty acid metabolism and biosynthesis and Mnc related to stress response were found to protect cells by modifying fatty acid compositions and reinforcing the antioxidant defense system. Our works deepen the mechanisms of P. acidilactici under acetic acid and offer targets for engineering cell tolerance.
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Affiliation(s)
- Menghan Zhang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Nan Wu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yaqi Fan
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Chaoye Xu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - JianMei Luo
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yuxuan Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Kaihui Yu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
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34
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Yamazaki A, Battenberg K, Shimoda Y, Hayashi M. NDR1/HIN1-Like Protein 13 Interacts with Symbiotic Receptor Kinases and Regulates Nodulation in Lotus japonicus. Mol Plant Microbe Interact 2022; 35:845-856. [PMID: 36107197 DOI: 10.1094/mpmi-11-21-0263-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lysin-motif receptor-like kinases (LysM-RLKs) are involved in the recognition of microbe-associated molecular patterns to initiate pattern-triggered immunity (PTI). LysM-RLKs are also required for recognition of microbe-derived symbiotic signal molecules upon establishing mutualistic interactions between plants and microsymbionts. A LysM-RLK CHITIN ELICITOR RECEPTOR KINASE1 (CERK1) plays central roles both in chitin-mediated PTI and in arbuscular mycorrhizal symbiosis, suggesting the overlap between immunity and symbiosis, at least in the signal perception and the activation of downstream signal cascades. In this study, we screened for the interacting proteins of Nod factor Receptor1 (NFR1), a CERK1 homolog in the model legume Lotus japonicus, and obtained a protein orthologous to NONRACE-SPECIFIC DISEASE RESISTANCE1/HARPIN-INDUCED1-LIKE13 (NHL13), a protein involved in the activation of innate immunity in Arabidopsis thaliana, which we named LjNHL13a. LjNHL13a interacted with NFR1 and with the symbiosis receptor kinase SymRK. LjNHL13a also displayed positive effects in nodulation. Our results suggest that NHL13 plays a role both in plant immunity and symbiosis, possibly where they overlap. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Akihiro Yamazaki
- Center for Sustainable Resource Science, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kai Battenberg
- Center for Sustainable Resource Science, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization 3-1-3 Kan-nondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization 3-1-3 Kan-nondai, Tsukuba, Ibaraki 305-8604, Japan
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35
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Yoon SH, Tang CC, Wein MN. Salt inducible kinases and PTH1R action. Vitam Horm 2022; 120:23-45. [PMID: 35953111 DOI: 10.1016/bs.vh.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Parathyroid hormone is a central regulator of calcium homeostasis. PTH protects the organism from hypocalcemia through its actions in bone and kidney. Recent physiologic studies have revealed key target genes for PTH receptor (PTH1R) signaling in these target organs. However, the complete signal transduction cascade used by PTH1R to accomplish these physiologic actions has remained poorly defined. Here we will review recent studies that have defined an important role for salt inducible kinases downstream of PTH1R in bone, cartilage, and kidney. PTH1R signaling inhibits the activity of salt inducible kinases. Therefore, direct SIK inhibitors represent a promising novel strategy to mimic PTH actions using small molecules. Moreover, a detailed understanding of the molecular circuitry used by PTH1R to exert its biologic effects will afford powerful new models to better understand the diverse actions of this important G protein coupled receptor in health and disease.
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Affiliation(s)
- Sung-Hee Yoon
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Cheng-Chia Tang
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Marc N Wein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.
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Wang P, Clark NM, Nolan TM, Song G, Bartz PM, Liao CY, Montes-Serey C, Katz E, Polko JK, Kieber JJ, Kliebenstein DJ, Bassham DC, Walley JW, Yin Y, Guo H. Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana. Plant Cell 2022; 34:2594-2614. [PMID: 35435236 PMCID: PMC9252503 DOI: 10.1093/plcell/koac111] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 04/09/2022] [Indexed: 05/20/2023]
Abstract
The receptor kinase FERONIA (FER) is a versatile regulator of plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new FER functions, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of Arabidopsis (Arabidopsis thaliana) wild-type and fer-4 loss-of-function mutant plants. Gene ontology terms for phytohormone signaling, abiotic stress, and biotic stress were significantly enriched among differentially expressed transcripts, differentially abundant proteins, and/or misphosphorylated proteins, in agreement with the known roles for FER in these processes. Analysis of multiomics data and subsequent experimental evidence revealed previously unknown functions for FER in endoplasmic reticulum (ER) body formation and glucosinolate biosynthesis. FER functions through the transcription factor NAI1 to mediate ER body formation. FER also negatively regulates indole glucosinolate biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors is hypophosphorylated in the fer-4 mutant and demonstrated that FER acts through the transcription factor ABA INSENSITIVE5 (ABI5) to negatively regulate the ABA response during cotyledon greening. Our integrated omics study, therefore, reveals novel functions for FER and provides new insights into the underlying mechanisms of FER function.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Parker M Bartz
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Christian Montes-Serey
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Ella Katz
- Department of Plant Science, University of California, Davis, California 95616, USA
| | - Joanna K Polko
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011, USA
| | - Yanhai Yin
- Author for correspondence: (H.G.); (Y.Y)
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Xing J, Ji D, Duan Z, Chen T, Luo X. Spatiotemporal dynamics of FERONIA reveal alternative endocytic pathways in response to flg22 elicitor stimuli. New Phytol 2022; 235:518-532. [PMID: 35358335 DOI: 10.1111/nph.18127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The plant receptor-like kinase FERONIA (FER) functions in the response to multiple extracellular signals, thereby regulating diverse cellular processes, such as polarized cell growth, hormone signaling and responses to pathogens. Here, we reported that in Arabidopsis thaliana, flagellin peptide flg22 stimulus significantly promoted the lateral mobility and dissociation of FER from the plasma membrane by inducing the association of FER with membrane microdomain components. FER underwent constitutive endocytosis and recycling in a brefeldin A (BFA)-sensitive manner via a clathrin-mediated pathway. Following flg22 elicitation, FER localized to bona fide endosomes via two distinct endocytic routes, showing differential sensitivity to BFA. These results at the single-particle level confirm that FER acts as an essential regulator during flg22 perception and immune activation, thus broadening our understanding of location-specific protein dynamics and membrane trafficking in receptor/receptor kinase signaling.
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Affiliation(s)
- Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Dongchao Ji
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhikun Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaomin Luo
- Key Laboratory of Plant Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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38
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Li G, Yao Y. TorR/TorS Two-Component system resists extreme acid environment by regulating the key response factor RpoS in Escherichia coli. Gene 2022; 821:146295. [PMID: 35181503 DOI: 10.1016/j.gene.2022.146295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/26/2021] [Accepted: 02/04/2022] [Indexed: 01/23/2023]
Abstract
Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle. Acid resistance is an indispensable mechanism that allows neutralophilic bacteria, such as E. coli, to survive in the gastrointestinal tract. Escherichia coli acid tolerance has been extensively studied over the past decades, and most studies have focused on mechanisms of gene regulation. Bacterial two-component signal transduction systems sense and respond to external environmental changes through regulating genes expression. However, there has been little research on the mechanism of the TorR/TorS system in acid resistance, and how TorR/TorS regulate the expression ofacid-resistantgenes is still unclear. We found that TorR/TorS deletion in E. coli cells led to a growth defect in extreme acid conditions,andthis defectmightdepend on the nutritional conditionsand growth phase.TorS/TorR sensed an extremely acidic environment, and this TorR phosphorylation process might not be entirely dependent on TorS.RNA-seqand RT-qPCR results suggested that TorR regulated expressions of gadB, gadC, hdeA, gadE, mdtE, mdtF, gadX, and slp acid-resistant genes. Compared with wild-type cells, the stress response factor RpoSlevels and itsexpressions were significantly decreased in Δ torR cellsstimulated by extreme acid. And under these circumstances, the expression of iraM was significantly reduced to 0.6-fold inΔ torR cells. Electrophoreticmobility shift assay showed that TorR-His6 could interact with the rpoS promoter sequence in vitro. β-galactosidase activity assayresultsapprovedthat TorR might bind the rpoS promoter region in vivo. After the mutation of the TorR-box in the rpoS promoter region, these interactions were no longer observed. Taken together, we propose thatTorS and potential Hanks model Ser/Thr kinase received an external acid stress signal and then phosphorylated TorR, which guided the expressions of a variety of acid resistance genes. Moreover,TorRcoped with extreme acid environmentsthroughRpoS, levels of which might be maintained byIraM. Finally,TorR may confer E. coli with the abilityto resist gastric acid, allowing the bacterium to reach the surface of the terminal ileum and large intestine mucosal epithelial cells through the gastric acid barrier, andestablishcolonization and pathogenicity.
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Affiliation(s)
- Guotao Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Yuan Yao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China.
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Walpole GFW, Pacheco J, Chauhan N, Clark J, Anderson KE, Abbas YM, Brabant-Kirwan D, Montaño-Rendón F, Liu Z, Zhu H, Brumell JH, Deiters A, Stephens LR, Hawkins PT, Hammond GRV, Grinstein S, Fairn GD. Kinase-independent synthesis of 3-phosphorylated phosphoinositides by a phosphotransferase. Nat Cell Biol 2022; 24:708-722. [PMID: 35484249 PMCID: PMC9107517 DOI: 10.1038/s41556-022-00895-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 03/08/2022] [Indexed: 01/10/2023]
Abstract
Despite their low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and their survival in host organisms. We demonstrate that PtdIns(3,4)P2 is a major product generated in host cells by the effectors of the enteropathogenic bacteria Salmonella and Shigella. Pharmacological, gene silencing and heterologous expression experiments revealed that, remarkably, the biosynthesis of PtdIns(3,4)P2 occurs independently of phosphoinositide 3-kinases. Instead, we found that the Salmonella effector SopB, heretofore believed to be a phosphatase, generates PtdIns(3,4)P2 de novo via a phosphotransferase/phosphoisomerase mechanism. Recombinant SopB is capable of generating PtdIns(3,4,5)P3 and PtdIns(3,4)P2 from PtdIns(4,5)P2 in a cell-free system. Through a remarkable instance of convergent evolution, bacterial effectors acquired the ability to synthesize 3-phosphorylated phosphoinositides by an ATP- and kinase-independent mechanism, thereby subverting host signalling to gain entry and even provoke oncogenic transformation.
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Affiliation(s)
- Glenn F W Walpole
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Neha Chauhan
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | | | | | - Yazan M Abbas
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Fernando Montaño-Rendón
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Zetao Liu
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hongxian Zhu
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sergio Grinstein
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.
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40
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Gong Z, Qi J, Hu M, Bi G, Zhou JM, Han GZ. The origin and evolution of a plant resistosome. Plant Cell 2022; 34:1600-1620. [PMID: 35166827 PMCID: PMC9048963 DOI: 10.1093/plcell/koac053] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/08/2022] [Indexed: 05/25/2023]
Abstract
The nucleotide-binding, leucine-rich receptor (NLR) protein HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), an immune receptor, interacts with HOPZ-ETI-DEFICIENT 1 (ZED1)-related kinases (ZRKs) and AVRPPHB SUSCEPTIBLE 1-like proteins to form a pentameric resistosome, triggering immune responses. Here, we show that ZAR1 emerged through gene duplication and that ZRKs were derived from the cell surface immune receptors wall-associated protein kinases (WAKs) through the loss of the extracellular domain before the split of eudicots and monocots during the Jurassic period. Many angiosperm ZAR1 orthologs, but not ZAR1 paralogs, are capable of oligomerization in the presence of AtZRKs and triggering cell death, suggesting that the functional ZAR1 resistosome might have originated during the early evolution of angiosperms. Surprisingly, inter-specific pairing of ZAR1 and AtZRKs sometimes results in the formation of a resistosome in the absence of pathogen stimulation, suggesting within-species compatibility between ZAR1 and ZRKs as a result of co-evolution. Numerous concerted losses of ZAR1 and ZRKs occurred in angiosperms, further supporting the ancient co-evolution between ZAR1 and ZRKs. Our findings provide insights into the origin of new plant immune surveillance networks.
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Affiliation(s)
| | | | - Meijuan Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guozhi Bi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | | | - Guan-Zhu Han
- Author for correspondence: (J.M.Z.) and (G.Z.H.)
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41
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Li H, Lee WS, Feng X, Bai L, Jennings BC, Liu L, Doray B, Canfield WM, Kornfeld S, Li H. Structure of the human GlcNAc-1-phosphotransferase αβ subunits reveals regulatory mechanism for lysosomal enzyme glycan phosphorylation. Nat Struct Mol Biol 2022; 29:348-356. [PMID: 35332324 PMCID: PMC9018626 DOI: 10.1038/s41594-022-00748-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/16/2022] [Indexed: 02/07/2023]
Abstract
Vertebrates use the mannose 6-phosphate (M6P)-recognition system to deliver lysosomal hydrolases to lysosomes. Key to this pathway is N-acetylglucosamine (GlcNAc)-1-phosphotransferase (PTase) that selectively adds GlcNAc-phosphate (P) to mannose residues of hydrolases. Human PTase is an α2β2γ2 heterohexamer with a catalytic core and several peripheral domains that recognize and bind substrates. Here we report a cryo-EM structure of the catalytic core of human PTase and the identification of a hockey stick-like motif that controls activation of the enzyme. Movement of this motif out of the catalytic pocket is associated with a rearrangement of part of the peripheral domains that unblocks hydrolase glycan access to the catalytic site, thereby activating PTase. We propose that PTase fluctuates between inactive and active states in solution, and selective substrate binding of a lysosomal hydrolase through its protein-binding determinant to PTase locks the enzyme in the active state to permit glycan phosphorylation. This mechanism would help ensure that only N-linked glycans of lysosomal enzymes are phosphorylated.
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Affiliation(s)
- Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Wang-Sik Lee
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Lin Bai
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Benjamin C Jennings
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lin Liu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- M6P Therapeutics, St. Louis, MO, USA
| | - Balraj Doray
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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42
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Xie Y, Sun P, Li Z, Zhang F, You C, Zhang Z. FERONIA Receptor Kinase Integrates with Hormone Signaling to Regulate Plant Growth, Development, and Responses to Environmental Stimuli. Int J Mol Sci 2022; 23:ijms23073730. [PMID: 35409090 PMCID: PMC8998941 DOI: 10.3390/ijms23073730] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Plant hormones are critical chemicals that participate in almost all aspects of plant life by triggering cellular response cascades. FERONIA is one of the most well studied members in the subfamily of Catharanthus roseus receptor-like kinase1-like (CrRLK1Ls) hormones. It has been proved to be involved in many different processes with the discovery of its ligands, interacting partners, and downstream signaling components. A growing body of evidence shows that FERONIA serves as a hub to integrate inter- and intracellular signals in response to internal and external cues. Here, we summarize the recent advances of FERONIA in regulating plant growth, development, and immunity through interactions with multiple plant hormone signaling pathways.
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Affiliation(s)
- Yinhuan Xie
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (Y.X.); (P.S.); (Z.L.); (F.Z.)
| | - Ping Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (Y.X.); (P.S.); (Z.L.); (F.Z.)
| | - Zhaoyang Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (Y.X.); (P.S.); (Z.L.); (F.Z.)
| | - Fujun Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (Y.X.); (P.S.); (Z.L.); (F.Z.)
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
| | - Chunxiang You
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (Y.X.); (P.S.); (Z.L.); (F.Z.)
- Correspondence: (C.Y.); (Z.Z.)
| | - Zhenlu Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (Y.X.); (P.S.); (Z.L.); (F.Z.)
- Correspondence: (C.Y.); (Z.Z.)
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43
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Agius MP, Ko K, Johnson TK, Phadke S, Soellner MB. Conformation-tunable ATP-competitive kinase inhibitors. Chem Commun (Camb) 2022; 58:3541-3544. [PMID: 35195624 DOI: 10.1039/d1cc06893h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule kinase inhibitors have shown immense clinical utility for diverse indications. While >60 kinase inhibitors have been approved (and many more in clinical trials), it remains unclear whether the clinical efficacy of a kinase inhibitor is solely dependent on enzymatic inhibition, or whether non-catalytic functions play a role in the efficacy of some kinase inhibitors. Here, we designed and synthesized a series of pyrazolopyrimidine kinase inhibitors that modulate the global kinase conformation of c-Src kinase. Expanding upon our findings from the pyrazolopyrimidine inhibitor series, we designed, synthesized, and evaluated three pair of conformation-selective kinase inhibitors, each with a unique hinge-binding scaffold. We profiled each pair of kinase inhibitors across 468 kinases and identified 38 kinases that could be studied using these pair of conformation-selective inhibitors. We also explore the binding of conformation-selective kinase inhibitors to mutant kinases of EGFR, FLT3, and KIT. Together, these studies yield important insight into the design of conformation-tunable kinase inhibitors and provide a toolset of compounds to study the role of protein conformation on kinase signaling.
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Affiliation(s)
- Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Kristin Ko
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
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Das L, Deb S, Arakawa E, Yamasaki S, Das SK. Pufferfish (Tetraodon cutcutia) Sampled from a Freshwater River Serves as an Intermediate Reservoir of a Sucrose Nonfermenting Variant of Vibrio cholerae PS-4. Microbiol Spectr 2022; 10:e0122121. [PMID: 35171023 PMCID: PMC8849079 DOI: 10.1128/spectrum.01221-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/18/2022] [Indexed: 11/20/2022] Open
Abstract
We describe the genomic characteristics of Vibrio cholerae strain PS-4 that is unable to ferment sucrose on a thiosulfate citrate bile salt sucrose (TCBS) agar medium. This bacterium was isolated from the skin mucus of a freshwater pufferfish. The genome of strain PS-4 was sequenced to understand the sucrose nonfermenting phenotype. The gene encoding the sucrose-specific phosphotransferase system IIB (sucR) was absent, resulting in the defective sucrose fermenting phenotype. In contrast, genes encoding the glucose-specific transport system IIB (ptsG) and fructose-specific transport system IIB (fruA) showed acid production while growing with respective sugars. The overall genome relatedness indices (OGRI), such as in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and average amino acid identity (AAI), were above the threshold value, that is, 70% and 95 to 96%, respectively. Phylogenomic analysis based on genome-wide core genes and the nonrecombinant core genes showed that strain PS-4 clustered with Vibrio cholerae ATCC 14035T. Further, genes encoding cholera toxin (ctx), zonula occludens toxin (zot), accessory cholera enterotoxin (ace), toxin-coregulated pilus (tcp), and lipopolysaccharide biosynthesis (rfb) were absent. PS-4 showed hemolytic activity and reacted strongly to the R antibody. Therefore, the Vibrio cholerae from the pufferfish adds a new ecological niche of this bacterium. IMPORTANCE Vibrio cholerae is native of aquatic environments. In general, V. cholerae ferments sucrose on thiosulfate citrate bile salt sucrose (TCBS) agar and produces yellow colonies. V. cholerae strain PS-4 described in this study is a sucrose nonfermenting variant associated with pufferfish skin and does not produce yellow colonies on TCBS agar. Genes encoding sucrose-specific phosphotransferase system IIB (sucR) were absent. The observed phenotype in the distinct metabolic pathway indicates niche-specific adaptive evolution for this bacterium. Our study suggests that the nonfermenting phenotype of V. cholerae strains on TCBS agar may not always be considered for species delineation.
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Affiliation(s)
- Lipika Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center of Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Sushanta Deb
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, India
| | - Eiji Arakawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinji Yamasaki
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Subrata K. Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center of Biotechnology, NCR Biotech Science Cluster, Faridabad, India
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45
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Yang X, Yin X, Liu J, Niu Z, Yang J, Shen B. Essential role of pyrophosphate homeostasis mediated by the pyrophosphate-dependent phosphofructokinase in Toxoplasma gondii. PLoS Pathog 2022; 18:e1010293. [PMID: 35104280 PMCID: PMC8836295 DOI: 10.1371/journal.ppat.1010293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/11/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022] Open
Abstract
Many biosynthetic pathways produce pyrophosphate (PPi) as a by-product, which is cytotoxic if accumulated at high levels. Pyrophosphatases play pivotal roles in PPi detoxification by converting PPi to inorganic phosphate. A number of apicomplexan parasites, including Toxoplasma gondii and Cryptosporidium parvum, express a PPi-dependent phosphofructokinase (PPi-PFK) that consumes PPi to power the phosphorylation of fructose-6-phosphate. However, the physiological roles of PPi-PFKs in these organisms are not known. Here, we report that Toxoplasma expresses both ATP- and PPi-dependent phosphofructokinases in the cytoplasm. Nonetheless, only PPi-PFK was indispensable for parasite growth, whereas the deletion of ATP-PFK did not affect parasite proliferation or virulence. The conditional depletion of PPi-PFK completely arrested parasite growth, but it did not affect the ATP level and only modestly reduced the flux of central carbon metabolism. However, PPi-PFK depletion caused a significant increase in cellular PPi and decreased the rates of nascent protein synthesis. The expression of a cytosolic pyrophosphatase in the PPi-PFK depletion mutant reduced its PPi level and increased the protein synthesis rate, therefore partially rescuing its growth. These results suggest that PPi-PFK has a major role in maintaining pyrophosphate homeostasis in T. gondii. This role may allow PPi-PFK to fine-tune the balance of catabolism and anabolism and maximize the utilization efficiency for carbon nutrients derived from host cells, increasing the success of parasitism. Moreover, PPi-PFK is essential for parasite propagation and virulence in vivo but it is not present in human hosts, making it a potential drug target to combat toxoplasmosis. Different from classic ATP-dependent phosphofructokinases, PPi-PFKs use pyrophosphate consumption to power the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate, the committed step of glycolysis. PPi-PFK is found in diverse organisms including archaea, bacteria, protists and plants. However, half a century after its first discovery, the physiological functions of PPi-PFK are still not well defined. Using the Toxoplasma gondii parasite as a model, here we show that PPi-PFK has a coordinator function to assure matched activities of anabolism and catabolism. This is achieved by maintaining the homeostasis of PPi, which is a byproduct, as well as an inhibitor of many biosynthetic reactions. PPi-PFK hydrolyzes PPi to promote anabolism, meanwhile being a glycolytic enzyme involved in catabolism. As such, it gauges the anabolic and catabolic activities in parasites to maximize the utilization efficiency of acquired nutrients. This work provides important insights to understand the physiological significance of PPi-PFK in Toxoplasma and other organisms.
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Affiliation(s)
- Xuke Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiaojiao Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zhipeng Niu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jichao Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Bang Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- * E-mail:
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46
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Zhong S, Li L, Wang Z, Ge Z, Li Q, Bleckmann A, Wang J, Song Z, Shi Y, Liu T, Li L, Zhou H, Wang Y, Zhang L, Wu HM, Lai L, Gu H, Dong J, Cheung AY, Dresselhaus T, Qu LJ. RALF peptide signaling controls the polytubey block in Arabidopsis. Science 2022; 375:290-296. [PMID: 35050671 PMCID: PMC9040003 DOI: 10.1126/science.abl4683] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fertilization of an egg by multiple sperm (polyspermy) leads to lethal genome imbalance and chromosome segregation defects. In Arabidopsis thaliana, the block to polyspermy is facilitated by a mechanism that prevents polytubey (the arrival of multiple pollen tubes to one ovule). We show here that FERONIA, ANJEA, and HERCULES RECEPTOR KINASE 1 receptor-like kinases located at the septum interact with pollen tube-specific RALF6, 7, 16, 36, and 37 peptide ligands to establish this polytubey block. The same combination of RALF (rapid alkalinization factor) peptides and receptor complexes controls pollen tube reception and rupture inside the targeted ovule. Pollen tube rupture releases the polytubey block at the septum, which allows the emergence of secondary pollen tubes upon fertilization failure. Thus, orchestrated steps in the fertilization process in Arabidopsis are coordinated by the same signaling components to guarantee and optimize reproductive success.
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Affiliation(s)
- Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Ling Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Zhijuan Wang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Zengxiang Ge
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qiyun Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Jizong Wang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Zihan Song
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Yihao Shi
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Tianxu Liu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Luhan Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Huabin Zhou
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Yanyan Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Li Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Hen-Ming Wu
- Department of Biochemistry and Molecular Biology, Molecular and Cell Biology Program, Plant Biology Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Luhua Lai
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- The National Plant Gene Research Center (Beijing), Beijing 100101, People’s Republic of China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alice Y. Cheung
- Department of Biochemistry and Molecular Biology, Molecular and Cell Biology Program, Plant Biology Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- The National Plant Gene Research Center (Beijing), Beijing 100101, People’s Republic of China
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Zhang YQ, Ma LZ, Gao Y, Qin Q, Li J, Lou J, Zhang MM, Xue XF, Kan B, Gao H. Master Quorum Sensing Regulator HapR Acts as A Repressor of the Mannitol Phosphotransferase System Operon in Vibrio cholerae. Biomed Environ Sci 2022; 35:69-72. [PMID: 35078564 DOI: 10.3967/bes2022.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Yi Quan Zhang
- Department of Clinical Laboratory, Nantong Third Hospital Affiliated to Nantong University, Nantong 212006, Jiangsu, China
| | - Li Zhi Ma
- Medical Risk Management Section, Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100039, China
| | - Yue Gao
- First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Qin Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Miao Miao Zhang
- Department of Clinical Laboratory, Nantong Third Hospital Affiliated to Nantong University, Nantong 212006, Jiangsu, China;School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xing Fan Xue
- Department of Clinical Laboratory, Nantong Third Hospital Affiliated to Nantong University, Nantong 212006, Jiangsu, China;School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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48
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Yu J, Zhang L, Peng J, Ward R, Hao P, Wang J, Zhang N, Yang Y, Guo X, Xiang C, An S, Xu TR. Dictamnine, a novel c-Met inhibitor, suppresses the proliferation of lung cancer cells by downregulating the PI3K/AKT/mTOR and MAPK signaling pathways. Biochem Pharmacol 2022; 195:114864. [PMID: 34861243 DOI: 10.1016/j.bcp.2021.114864] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 01/19/2023]
Abstract
Dictamnine (Dic), a naturally occurring small-molecule furoquinoline alkaloid isolated from the root bark of Dictamnus dasycarpus Turcz., is reported to display anticancer properties. However, little is known about the direct target proteins and anticancer mechanisms of Dic. In the current study, Dic was found to suppress the growth of lung cancer cells in vitro and in vivo, and to attenuate the activation of PI3K/AKT/mTOR and mitogen-activated protein kinase (MAPK) signaling pathways by inhibiting the phosphorylation and activation of receptor tyrosine kinase c-Met. Moreover, the binding of Dic to c-Met was confirmed by using cellular thermal shift assay (CETSA) and drug affinity responsive target stability (DARTS) assay. Among all cancer cell lines tested, Dic inhibited the proliferation of c-Met-dependent EBC-1 cells with the greatest potency (IC50 = 2.811 μM). Notably, Dic was shown to synergistically improve the chemo-sensitivity of epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI)-resistant lung cancer cells to gefitinib and osimertinib. These results suggest that Dic is a c-Met inhibitor that can serve as a potential therapeutic agent in the treatment of lung cancer, especially against EGFR TKI-resistant and c-Met-dependent lung cancer.
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Affiliation(s)
- Jiaojiao Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Lijing Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun Peng
- Department of Thoracic Surgery, the First People's Hospital of Yunnan Province, Kunming 650032, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China
| | - Richard Ward
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Peiqi Hao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jiwei Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Na Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiaoxi Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Cheng Xiang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Su An
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China.
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China.
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49
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Karabiyik C, Rubinsztein DC. Protocol for determining the regulation of lipid kinases and changes in phospholipids in vitro. STAR Protoc 2021; 2:100926. [PMID: 34766030 PMCID: PMC8571518 DOI: 10.1016/j.xpro.2021.100926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The regulation of lipid kinases has remained elusive given the difficulties of assessing changes in lipid levels. Here, we describe the isolation of protein and lipid kinases to determine the regulation of lipid kinases in vitro. This can be followed by analysis of effects of regulators on lipid kinase-mediated changes in phospholipids without the use of radioactivity, with a specific focus on PI(5)P generation by the enzyme PIKfyve. For complete details on the use and execution of this protocol, please refer to Karabiyik et al. (2021).
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Affiliation(s)
- Cansu Karabiyik
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, Cambridge, UK
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, 3227 Broadway, Manhattan, NY 10027, USA
| | - David C. Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, Cambridge, UK
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50
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Dankwa S, Dols MM, Wei L, Glennon EKK, Kain HS, Kaushansky A, Smith JD. Exploiting polypharmacology to dissect host kinases and kinase inhibitors that modulate endothelial barrier integrity. Cell Chem Biol 2021; 28:1679-1692.e4. [PMID: 34216546 PMCID: PMC8688180 DOI: 10.1016/j.chembiol.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/29/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Kinase inhibitors are promising drugs to stabilize the endothelial barrier following inflammatory damage. However, our limited knowledge of how kinase signaling activates barrier-restorative pathways and the complexity of multi-target drugs have hindered drug discovery and repurposing efforts. Here, we apply a kinase regression approach that exploits drug polypharmacology to investigate endothelial barrier regulation. A screen of 28 kinase inhibitors identified multiple inhibitors that promote endothelial barrier integrity and revealed divergent barrier phenotypes for BCR-ABL drugs. Target deconvolution predicted 50 barrier-regulating kinases from diverse kinase families. Using gene knockdowns, we identified kinases with a role in endothelial barrier regulation and dissected different mechanisms of action of barrier-protective kinase inhibitors. These results demonstrate the importance of polypharmacology in the endothelial barrier phenotype of kinase inhibitors and provide promising new leads for barrier-strengthening therapies.
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Affiliation(s)
- Selasi Dankwa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Mary-Margaret Dols
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Ling Wei
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Elizabeth K K Glennon
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Heather S Kain
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA.
| | - Joseph D Smith
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA.
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