1
|
Pierre PM, Preyanka M, Zachary H, Zhang L, Lukas B, Matias GF, Kian F, Callum G, Wolfgang B. Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:632-646. [PMID: 37871136 PMCID: PMC10841685 DOI: 10.1111/tpj.16493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/22/2023] [Indexed: 10/25/2023]
Abstract
Plants are sessile organisms that constantly adapt to their changing environment. The root is exposed to numerous environmental signals ranging from nutrients and water to microbial molecular patterns. These signals can trigger distinct responses including the rapid increase or decrease of root growth. Consequently, using root growth as a readout for signal perception can help decipher which external cues are perceived by roots, and how these signals are integrated. To date, studies measuring root growth responses using large numbers of roots have been limited by a lack of high-throughput image acquisition, poor scalability of analytical methods, or low spatiotemporal resolution. Here, we developed the Root Walker pipeline, which uses automated microscopes to acquire time-series images of many roots exposed to controlled treatments with high spatiotemporal resolution, in conjunction with fast and automated image analysis software. We demonstrate the power of Root Walker by quantifying root growth rate responses at different time and throughput scales upon treatment with natural auxin and two mitogen-associated protein kinase cascade inhibitors. We find a concentration-dependent root growth response to auxin and reveal the specificity of one MAPK inhibitor. We further demonstrate the ability of Root Walker to conduct genetic screens by performing a genome-wide association study on 260 accessions in under 2 weeks, revealing known and unknown root growth regulators. Root Walker promises to be a useful toolkit for the plant science community, allowing large-scale screening of root growth dynamics for a variety of purposes, including genetic screens for root sensing and root growth response mechanisms.
Collapse
Affiliation(s)
- Platre Matthieu Pierre
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Mehta Preyanka
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Halvorson Zachary
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Ling Zhang
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Brent Lukas
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Gleason F. Matias
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Faizi Kian
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Goulding Callum
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Busch Wolfgang
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| |
Collapse
|
2
|
Schwenkert S, Lo WT, Szulc B, Yip CK, Pratt AI, Cusack SA, Brandt B, Leister D, Kunz HH. Probing the physiological role of the plastid outer-envelope membrane using the oemiR plasmid collection. G3 (BETHESDA, MD.) 2023; 13:jkad187. [PMID: 37572358 PMCID: PMC10542568 DOI: 10.1093/g3journal/jkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
Plastids are the site of complex biochemical pathways, most prominently photosynthesis. The organelle evolved through endosymbiosis with a cyanobacterium, which is exemplified by the outer envelope membrane that harbors more than 40 proteins in Arabidopsis. Their evolutionary conservation indicates high significance for plant cell function. While a few proteins are well-studied as part of the protein translocon complex the majority of outer envelope protein functions is unclear. Gaining a deeper functional understanding has been complicated by the lack of observable loss-of-function mutant phenotypes, which is often rooted in functional genetic redundancy. Therefore, we designed outer envelope-specific artificial micro RNAs (oemiRs) capable of downregulating transcripts from several loci simultaneously. We successfully tested oemiR function by performing a proof-of-concept screen for pale and cold-sensitive mutants. An in-depth analysis of pale mutant alleles deficient in the translocon component TOC75 using proteomics provided new insights into putative compensatory import pathways. The cold stress screen not only recapitulated 3 previously known phenotypes of cold-sensitive mutants but also identified 4 mutants of additional oemiR outer envelope loci. Altogether our study revealed a role of the outer envelope to tolerate cold conditions and showcasts the power of the oemiR collection to research the significance of outer envelope proteins.
Collapse
Affiliation(s)
- Serena Schwenkert
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Wing Tung Lo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Beata Szulc
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Chun Kwan Yip
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Anna I Pratt
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | | | - Benjamin Brandt
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| |
Collapse
|
3
|
Shi J, Jiang M, Wang H, Luo Z, Guo Y, Chen Y, Zhao X, Qiang S, Strasser RJ, Kalaji HM, Chen S. Effects of Mycotoxin Fumagillin, Mevastatin, Radicicol, and Wortmannin on Photosynthesis of Chlamydomonas reinhardtii. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030665. [PMID: 36771749 PMCID: PMC9920790 DOI: 10.3390/plants12030665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 05/12/2023]
Abstract
Mycotoxins are one of the most important sources for the discovery of new pesticides and drugs because of their chemical structural diversity and fascinating bioactivity as well as unique novel targets. Here, the effects of four mycotoxins, fumagillin, mevastatin, radicicol, and wortmannin, on photosynthesis were investigated to identify their precise sites of action on the photosynthetic apparatus of Chlamydomonas reinhardtii. Our results showed that these four mycotoxins have multiple targets, acting mainly on photosystem II (PSII). Their mode of action is similar to that of diuron, inhibiting electron flow beyond the primary quinone electron acceptor (QA) by binding to the secondary quinone electron acceptor (QB) site of the D1 protein, thereby affecting photosynthesis. The results of PSII oxygen evolution rate and chlorophyll (Chl) a fluorescence imaging suggested that fumagillin strongly inhibited overall PSII activity; the other three toxins also exhibited a negative influence at the high concentration. Chl a fluorescence kinetics and the JIP test showed that the inhibition of electron transport beyond QA was the most significant feature of the four mycotoxins. Fumagillin decreased the rate of O2 evolution by interrupting electron transfer on the PSII acceptor side, and had multiple negative effects on the primary photochemical reaction and PSII antenna size. Mevastatin caused a decrease in photosynthetic activity, mainly due to the inhibition of electron transport. Both radicicol and wortmannin decreased photosynthetic efficiency, mainly by inhibiting the electron transport efficiency of the PSII acceptor side and the activity of the PSII reaction centers. In addition, radicicol reduced the primary photochemical reaction efficiency and antenna size. The simulated molecular model of the four mycotoxins' binding to C. reinhardtii D1 protein indicated that the residue D1-Phe265 is their common site at the QB site. This is a novel target site different from those of commercial PSII herbicides. Thus, the interesting effects of the four mycotoxins on PSII suggested that they provide new ideas for the design of novel and efficient herbicide molecules.
Collapse
Affiliation(s)
- Jiale Shi
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengyun Jiang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - He Wang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Luo
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanjing Guo
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Chen
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoxi Zhao
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Sheng Qiang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Reto Jörg Strasser
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
- Bioenergetics Laboratory, University of Geneva, CH-1254 Jussy, Geneva, Switzerland
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Shiguo Chen
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
| |
Collapse
|
4
|
Ashley IA, Kitchen SA, Gorman LM, Grossman AR, Oakley CA, Suggett DJ, Weis VM, Rosset SL, Davy SK. Genomic conservation and putative downstream functionality of the phosphatidylinositol signalling pathway in the cnidarian-dinoflagellate symbiosis. Front Microbiol 2023; 13:1094255. [PMID: 36777026 PMCID: PMC9909359 DOI: 10.3389/fmicb.2022.1094255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/28/2022] [Indexed: 01/28/2023] Open
Abstract
The mutualistic cnidarian-dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon revealed a broad range of functions, including compelling links to processes putatively involved in symbiosis regulation. This analysis establishes a baseline for current understanding of the PI pathway across anthozoans and Symbiodiniaceae, and thus a framework to target future research.
Collapse
Affiliation(s)
- Immy A. Ashley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Sheila A. Kitchen
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Lucy M. Gorman
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA, United States
| | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - David J. Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Sabrina L. Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand,*Correspondence: Simon K. Davy,
| |
Collapse
|
5
|
Phosphatidylinositol-4-phosphate controls autophagosome formation in Arabidopsis thaliana. Nat Commun 2022; 13:4385. [PMID: 35902598 PMCID: PMC9334301 DOI: 10.1038/s41467-022-32109-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Autophagy is an intracellular degradation mechanism critical for plant acclimation to environmental stresses. Central to autophagy is the formation of specialized vesicles, the autophagosomes, which target and deliver cargo to the lytic vacuole. How autophagosomes form in plant cells remains poorly understood. Here, we uncover the importance of the lipid phosphatidylinositol-4-phosphate in autophagy using pharmacological and genetical approaches. Combining biochemical and live-microscopy analyses, we show that PI4K activity is required for early stages of autophagosome formation. Further, our results show that the plasma membrane-localized PI4Kα1 is involved in autophagy and that a substantial portion of autophagy structures are found in proximity to the PI4P-enriched plasma membrane. Together, our study unravels critical insights into the molecular determinants of autophagy, proposing a model whereby the plasma membrane provides PI4P to support the proper assembly and expansion of the phagophore thus governing autophagosome formation in Arabidopsis. Autophagosomes are specialized vesicles that target and deliver cargo to the lytic vacuole. Here the authors show that plasma-membrane derived lipid phosphatidylinositol-4-phosphate supports the assembly and expansion of autophagosomes in Arabidopsis
Collapse
|
6
|
Lin F, Zheng J, Xie Y, Jing W, Zhang Q, Zhang W. Emerging roles of phosphoinositide-associated membrane trafficking in plant stress responses. J Genet Genomics 2022; 49:726-734. [DOI: 10.1016/j.jgg.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 10/18/2022]
|
7
|
Noack LC, Bayle V, Armengot L, Rozier F, Mamode-Cassim A, Stevens FD, Caillaud MC, Munnik T, Mongrand S, Pleskot R, Jaillais Y. A nanodomain-anchored scaffolding complex is required for the function and localization of phosphatidylinositol 4-kinase alpha in plants. THE PLANT CELL 2022; 34:302-332. [PMID: 34010411 PMCID: PMC8774046 DOI: 10.1093/plcell/koab135] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/10/2021] [Indexed: 05/24/2023]
Abstract
Phosphoinositides are low-abundant lipids that participate in the acquisition of membrane identity through their spatiotemporal enrichment in specific compartments. Phosphatidylinositol 4-phosphate (PI4P) accumulates at the plant plasma membrane driving its high electrostatic potential, and thereby facilitating interactions with polybasic regions of proteins. PI4Kα1 has been suggested to produce PI4P at the plasma membrane, but how it is recruited to this compartment is unknown. Here, we pin-point the mechanism that tethers Arabidopsis thaliana phosphatidylinositol 4-kinase alpha1 (PI4Kα1) to the plasma membrane via a nanodomain-anchored scaffolding complex. We established that PI4Kα1 is part of a complex composed of proteins from the NO-POLLEN-GERMINATION, EFR3-OF-PLANTS, and HYCCIN-CONTAINING families. Comprehensive knockout and knockdown strategies revealed that subunits of the PI4Kα1 complex are essential for pollen, embryonic, and post-embryonic development. We further found that the PI4Kα1 complex is immobilized in plasma membrane nanodomains. Using synthetic mis-targeting strategies, we demonstrate that a combination of lipid anchoring and scaffolding localizes PI4Kα1 to the plasma membrane, which is essential for its function. Together, this work opens perspectives on the mechanisms and function of plasma membrane nanopatterning by lipid kinases.
Collapse
Affiliation(s)
- Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Frédérique Rozier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Adiilah Mamode-Cassim
- Laboratoire de Biogenèse Membranaire, UMR5200, Université de Bordeaux, CNRS, 33140 Villenave d’Ornon, France
- Agroécologie, AgroSup Dijon, CNRS, INRA, University Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Floris D Stevens
- Research Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1090 GE, The Netherlands
| | - Marie-Cécile Caillaud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Teun Munnik
- Research Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1090 GE, The Netherlands
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, UMR5200, Université de Bordeaux, CNRS, 33140 Villenave d’Ornon, France
| | - Roman Pleskot
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 16502 Prague 6, Czech Republic
| | | |
Collapse
|
8
|
Gao M, He Y, Yin X, Zhong X, Yan B, Wu Y, Chen J, Li X, Zhai K, Huang Y, Gong X, Chang H, Xie S, Liu J, Yue J, Xu J, Zhang G, Deng Y, Wang E, Tharreau D, Wang GL, Yang W, He Z. Ca 2+ sensor-mediated ROS scavenging suppresses rice immunity and is exploited by a fungal effector. Cell 2021; 184:5391-5404.e17. [PMID: 34597584 DOI: 10.1016/j.cell.2021.09.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/23/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Plant immunity is activated upon pathogen perception and often affects growth and yield when it is constitutively active. How plants fine-tune immune homeostasis in their natural habitats remains elusive. Here, we discover a conserved immune suppression network in cereals that orchestrates immune homeostasis, centering on a Ca2+-sensor, RESISTANCE OF RICE TO DISEASES1 (ROD1). ROD1 promotes reactive oxygen species (ROS) scavenging by stimulating catalase activity, and its protein stability is regulated by ubiquitination. ROD1 disruption confers resistance to multiple pathogens, whereas a natural ROD1 allele prevalent in indica rice with agroecology-specific distribution enhances resistance without yield penalty. The fungal effector AvrPiz-t structurally mimics ROD1 and activates the same ROS-scavenging cascade to suppress host immunity and promote virulence. We thus reveal a molecular framework adopted by both host and pathogen that integrates Ca2+ sensing and ROS homeostasis to suppress plant immunity, suggesting a principle for breeding disease-resistant, high-yield crops.
Collapse
Affiliation(s)
- Mingjun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Yin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbin Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Bingxiao Yan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yue Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoyuan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Keran Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yifeng Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiangyu Gong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huizhong Chang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shenghan Xie
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiaxing Yue
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jianlong Xu
- Insititute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guiquan Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Didier Tharreau
- PHIM, CIRAD, INRAE, IRD, Montpellier SupAgro, MUSE, Montpellier Cedex 05, France
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, OH 43210, USA
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CAS-JIC Center of Excellence for Plant and Microbial Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| |
Collapse
|
9
|
Membrane Profiling by Free Flow Electrophoresis and SWATH-MS to Characterize Subcellular Compartment Proteomes in Mesembryanthemum crystallinum. Int J Mol Sci 2021; 22:ijms22095020. [PMID: 34065142 PMCID: PMC8126025 DOI: 10.3390/ijms22095020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/11/2023] Open
Abstract
The study of subcellular membrane structure and function facilitates investigations into how biological processes are divided within the cell. However, work in this area has been hampered by the limited techniques available to fractionate the different membranes. Free Flow Electrophoresis (FFE) allows for the fractionation of membranes based on their different surface charges, a property made up primarily of their varied lipid and protein compositions. In this study, high-resolution plant membrane fractionation by FFE, combined with mass spectrometry-based proteomics, allowed the simultaneous profiling of multiple cellular membranes from the leaf tissue of the plant Mesembryanthemum crystallinum. Comparisons of the fractionated membranes’ protein profile to that of known markers for specific cellular compartments sheds light on the functions of proteins, as well as provides new evidence for multiple subcellular localization of several proteins, including those involved in lipid metabolism.
Collapse
|
10
|
Dubois GA, Jaillais Y. Anionic phospholipid gradients: an uncharacterized frontier of the plant endomembrane network. PLANT PHYSIOLOGY 2021; 185:577-592. [PMID: 33793905 PMCID: PMC8133617 DOI: 10.1093/plphys/kiaa056] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/16/2020] [Indexed: 05/19/2023]
Abstract
Anionic phospholipids include phosphatidic acid (PA), phosphatidylserine (PS), phosphatidylinositol (PI), and its phosphorylated derivatives the phosphoinositides (e.g. phosphatidylinositol-4-phosphate [PI4P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]). Although anionic phospholipids are low-abundant lipids, they are particularly important for membrane functions. In particular, anionic lipids act as biochemical and biophysical landmarks that contribute to the establishment of membrane identity, signaling activities, and compartment morphodynamics. Each anionic lipid accumulates in different endomembranes according to a unique subcellular pattern, where they locally provide docking platforms for proteins. As such, they are mostly believed to act in the compartments in which they accumulate. However, mounting evidence throughout eukaryotes suggests that anionic lipids are not as compartment-specific as initially thought and that they are instead organized as concentration gradients across different organelles. In this update, we review the evidence for the existence of anionic lipid gradients in plants. We then discuss the possible implication of these gradients in lipid dynamics and homeostasis, and also in coordinating subcellular activities. Finally, we introduce the notion that anionic lipid gradients at the cellular scale may translate into gradients at the tissue level, which could have implications for plant development.
Collapse
Affiliation(s)
- Gwennogan A Dubois
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
- Author for communication:
| |
Collapse
|
11
|
Zhao CY, Xue HW. PI4Kγ2 Interacts with E3 Ligase MIEL1 to Regulate Auxin Metabolism and Root Development. PLANT PHYSIOLOGY 2020; 184:933-944. [PMID: 32788299 PMCID: PMC7536656 DOI: 10.1104/pp.20.00799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/20/2020] [Indexed: 05/07/2023]
Abstract
Root development is important for normal plant growth and nutrient absorption. Studies have revealed the involvement of various factors in this complex process, improving our understanding of the relevant regulatory mechanisms. Here, we functionally characterize the role of Arabidopsis (Arabidopsis thaliana) phosphatidylinositol 4-kinase γ2 (PI4Kγ2) in root elongation regulation, which functions to modulate stability of the RING-type E3 ligase MYB30-INTERACTING E3 LIGASE1 (MIEL1) and auxin metabolism. Mutant plants deficient in PI4Kγ2 (pi4kγ2) exhibited a shortened root length and elongation zone due to reduced auxin level. PI4Kγ2 was shown to interact with MIEL1, regulating its degradation and furthering the stability of transcription factor MYB30 (which suppresses auxin metabolism by directly binding to promoter regions of GH3 2 and GH3 6). Interestingly, pi4kγ2 plants presented altered hypersensitive response, indicating that PI4Kγ2 regulates synergetic growth and defense of plants through modulating auxin metabolism. These results reveal the importance of protein interaction in regulating ubiquitin-mediated protein degradation in eukaryotic cells, and illustrate a mechanism coordinating plant growth and biotic stress response.
Collapse
Affiliation(s)
- Chun-Yan Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Wei Xue
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
12
|
Lu H, Yuan G, Strauss SH, Tschaplinski TJ, Tuskan GA, Chen JG, Yang X. Reconfiguring Plant Metabolism for Biodegradable Plastic Production. BIODESIGN RESEARCH 2020; 2020:9078303. [PMID: 37849903 PMCID: PMC10530661 DOI: 10.34133/2020/9078303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/11/2020] [Indexed: 10/19/2023] Open
Abstract
For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.
Collapse
Affiliation(s)
- Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
13
|
Hertle AP, García-Cerdán JG, Armbruster U, Shih R, Lee JJ, Wong W, Niyogi KK. A Sec14 domain protein is required for photoautotrophic growth and chloroplast vesicle formation in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:9101-9111. [PMID: 32245810 PMCID: PMC7183190 DOI: 10.1073/pnas.1916946117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In eukaryotic photosynthetic organisms, the conversion of solar into chemical energy occurs in thylakoid membranes in the chloroplast. How thylakoid membranes are formed and maintained is poorly understood. However, previous observations of vesicles adjacent to the stromal side of the inner envelope membrane of the chloroplast suggest a possible role of membrane transport via vesicle trafficking from the inner envelope to the thylakoids. Here we show that the model plant Arabidopsis thaliana has a chloroplast-localized Sec14-like protein (CPSFL1) that is necessary for photoautotrophic growth and vesicle formation at the inner envelope membrane of the chloroplast. The cpsfl1 mutants are seedling lethal, show a defect in thylakoid structure, and lack chloroplast vesicles. Sec14 domain proteins are found only in eukaryotes and have been well characterized in yeast, where they regulate vesicle budding at the trans-Golgi network. Like the yeast Sec14p, CPSFL1 binds phosphatidylinositol phosphates (PIPs) and phosphatidic acid (PA) and acts as a phosphatidylinositol transfer protein in vitro, and expression of Arabidopsis CPSFL1 can complement the yeast sec14 mutation. CPSFL1 can transfer PIP into PA-rich membrane bilayers in vitro, suggesting that CPSFL1 potentially facilitates vesicle formation by trafficking PA and/or PIP, known regulators of membrane trafficking between organellar subcompartments. These results underscore the role of vesicles in thylakoid biogenesis and/or maintenance. CPSFL1 appears to be an example of a eukaryotic cytosolic protein that has been coopted for a function in the chloroplast, an organelle derived from endosymbiosis of a cyanobacterium.
Collapse
Affiliation(s)
- Alexander P Hertle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
| | - José G García-Cerdán
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Ute Armbruster
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Robert Shih
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jimmy J Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Winnie Wong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| |
Collapse
|
14
|
Guo T, Chen HC, Lu ZQ, Diao M, Chen K, Dong NQ, Shan JX, Ye WW, Huang S, Lin HX. A SAC Phosphoinositide Phosphatase Controls Rice Development via Hydrolyzing PI4P and PI(4,5)P 2. PLANT PHYSIOLOGY 2020; 182:1346-1358. [PMID: 31882455 PMCID: PMC7054871 DOI: 10.1104/pp.19.01131] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/12/2019] [Indexed: 05/06/2023]
Abstract
Phosphoinositides (PIs) as regulatory membrane lipids play essential roles in multiple cellular processes. Although the exact molecular targets of PI-dependent modulation remain largely elusive, the effects of disturbed PI metabolism could be employed to identify regulatory modules associated with particular downstream targets of PIs. Here, we identified the role of GRAIN NUMBER AND PLANT HEIGHT1 (GH1), which encodes a suppressor of actin (SAC) domain-containing phosphatase with unknown function in rice (Oryza sativa). Endoplasmic reticulum-localized GH1 specifically dephosphorylated and hydrolyzed phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Inactivation of GH1 resulted in massive accumulation of both PI4P and PI(4,5)P2, while excessive GH1 caused their depletion. Notably, superabundant PI4P and PI(4,5)P2 could both disrupt actin cytoskeleton organization and suppress cell elongation. Interestingly, both PI4P and PI(4,5)P2 inhibited actin-related protein2 and -3 (Arp2/3) complex-nucleated actin-branching networks in vitro, whereas PI(4,5)P2 showed more dramatic effects in a dose-dependent manner. Overall, the overaccumulation of PI(4,5)P2 resulting from dysfunction of SAC phosphatase possibly perturbs Arp2/3 complex-mediated actin polymerization, thereby disordering cell development. These findings imply that the Arp2/3 complex might be the potential molecular target of PI(4,5)P2-dependent modulation in eukaryotes, thereby providing insights into the relationship between PI homeostasis and plant growth and development.
Collapse
Affiliation(s)
- Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Hua-Chang Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Min Diao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Shanjin Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
15
|
Rubilar-Hernández C, Osorio-Navarro C, Cabello F, Norambuena L. PI4KIII β Activity Regulates Lateral Root Formation Driven by Endocytic Trafficking to the Vacuole. PLANT PHYSIOLOGY 2019; 181:112-126. [PMID: 31285293 PMCID: PMC6716240 DOI: 10.1104/pp.19.00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 06/01/2023]
Abstract
Lateral roots (LRs) increase the contact area of the root with the rhizosphere and thereby improve water and nutrient uptake from the soil. LRs are generated either via a developmentally controlled mechanism or through induction by external stimuli, such as water and nutrient availability. Auxin regulates LR organogenesis via transcriptional activation by an auxin complex receptor. Endocytic trafficking to the vacuole positively regulates LR organogenesis independently of the auxin complex receptor in Arabidopsis (Arabidopsis thaliana). Here, we demonstrate that phosphatidylinositol 4-phosphate (PI4P) biosynthesis regulated by the phosphatidylinositol 4-kinases PI4KIIIβ1 and PI4KIIIβ2 is essential for the LR organogenesis driven by endocytic trafficking to the vacuole. Stimulation with Sortin2, a biomodulator that promotes protein targeting to the vacuole, altered PI4P abundance at both the plasma membrane and endosomal compartments, a process dependent on PI4K activity. These findings suggest that endocytic trafficking to the vacuole regulated by the enzymatic activities of PI4KIIIβ1 and PI4KIIIβ2 participates in a mechanism independent of the auxin complex receptor that regulates LR organogenesis in Arabidopsis. Surprisingly, loss-of-function of PI4KIIIβ1 and PI4KIIIβ2 induced both LR primordium formation and endocytic trafficking toward the vacuole. This LR primordium induction was alleviated by exogenous PI4P, suggesting that PI4KIIIβ1 and PI4KIIIβ2 activity constitutively negatively regulates LR primordium formation. Overall, this research demonstrates a dual role of PI4KIIIβ1 and PI4KIIIβ2 in LR primordium formation in Arabidopsis.
Collapse
Affiliation(s)
- Carlos Rubilar-Hernández
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Claudio Osorio-Navarro
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Francisca Cabello
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| |
Collapse
|
16
|
VIPP1 rods engulf membranes containing phosphatidylinositol phosphates. Sci Rep 2019; 9:8725. [PMID: 31217458 PMCID: PMC6584618 DOI: 10.1038/s41598-019-44259-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 05/14/2019] [Indexed: 12/15/2022] Open
Abstract
In cyanobacteria and plants, VIPP1 plays crucial roles in the biogenesis and repair of thylakoid membrane protein complexes and in coping with chloroplast membrane stress. In chloroplasts, VIPP1 localizes in distinct patterns at or close to envelope and thylakoid membranes. In vitro, VIPP1 forms higher-order oligomers of >1 MDa that organize into rings and rods. However, it remains unknown how VIPP1 oligomerization is related to function. Using time-resolved fluorescence anisotropy and sucrose density gradient centrifugation, we show here that Chlamydomonas reinhardtii VIPP1 binds strongly to liposomal membranes containing phosphatidylinositol-4-phosphate (PI4P). Cryo-electron tomography reveals that VIPP1 oligomerizes into rods that can engulf liposomal membranes containing PI4P. These findings place VIPP1 into a group of membrane-shaping proteins including epsin and BAR domain proteins. Moreover, they point to a potential role of phosphatidylinositols in directing the shaping of chloroplast membranes.
Collapse
|
17
|
Khadka B, Gupta RS. Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family. Genes (Basel) 2019; 10:genes10040312. [PMID: 31010098 PMCID: PMC6523245 DOI: 10.3390/genes10040312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023] Open
Abstract
Members of the PIP4K/PIP5K family of proteins, which generate the highly important secondary messenger phosphatidylinositol-4,5-bisphosphate, play central roles in regulating diverse signaling pathways. In eukaryotic organisms, multiple isozymes and subfamilies of PIP4K/PIP5K proteins are found and it is of much interest to understand their evolution and species distribution and what unique molecular and biochemical characteristics distinguish specific isozymes and subfamilies of proteins. We report here the species distribution of different PIP4K/PIP5K family of proteins in eukaryotic organisms and phylogenetic analysis based on their protein sequences. Our results indicate that the distinct homologs of both PIP4K and PIP5K are found in different organisms belonging to the Holozoa clade of eukaryotes, which comprises of various metazoan phyla as well as their close unicellular relatives Choanoflagellates and Filasterea. In contrast, the deeper-branching eukaryotic lineages, as well as plants and fungi, contain only a single homolog of the PIP4K/PIP5K proteins. In parallel, our comparative analyses of PIP4K/PIP5K protein sequences have identified six highly-specific molecular markers consisting of conserved signature indels (CSIs) that are uniquely shared by either the PIP4K or PIP5K proteins, or both, or specific subfamilies of these proteins. Of these molecular markers, 2 CSIs are distinctive characteristics of all PIP4K homologs, 1 CSI distinguishes the PIP4K and PIP5K homologs from the Holozoa clade of species from the ancestral form of PIP4K/PIP5K found in deeper-branching eukaryotic lineages. The remaining three CSIs are specific for the PIP5Kα, PIP5Kβ, and PIP4Kγ subfamilies of proteins from vertebrate species. These molecular markers provide important means for distinguishing different PIP4K/PIP5K isozymes as well as some of their subfamilies. In addition, the distribution patterns of these markers in different isozymes provide important insights into the evolutionary divergence of PIP4K/PIP5K proteins. Our results support the view that the Holozoa clade of eukaryotic organisms shared a common ancestor exclusive of the other eukaryotic lineages and that the initial gene duplication event leading to the divergence of distinct types of PIP4K and PIP5K homologs occurred in a common ancestor of this clade. Based on the results gleaned from different studies presented here, a model for the evolutionary divergence of the PIP4K/PIP5K family of proteins is presented.
Collapse
Affiliation(s)
- Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
| |
Collapse
|
18
|
Physiological Functions of Phosphoinositide-Modifying Enzymes and Their Interacting Proteins in Arabidopsis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [PMID: 30499079 DOI: 10.1007/5584_2018_295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The integrity of cellular membranes is maintained not only by structural phospholipids such as phosphatidylcholine and phosphatidylethanolamine, but also by regulatory phospholipids, phosphatidylinositol phosphates (phosphoinositides). Although phosphoinositides constitute minor membrane phospholipids, they exert a wide variety of regulatory functions in all eukaryotic cells. They act as key markers of membrane surfaces that determine the biological integrity of cellular compartments to recruit various phosphoinositide-binding proteins. This review focuses on recent progress on the significance of phosphoinositides, their modifying enzymes, and phosphoinositide-binding proteins in Arabidopsis.
Collapse
|
19
|
Chen C, MacCready JS, Ducat DC, Osteryoung KW. The Molecular Machinery of Chloroplast Division. PLANT PHYSIOLOGY 2018; 176:138-151. [PMID: 29079653 PMCID: PMC5761817 DOI: 10.1104/pp.17.01272] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/09/2017] [Indexed: 05/17/2023]
Abstract
Recent studies advance understanding of the mechanisms, spatial control, and regulation of chloroplast division, but many questions remain.
Collapse
Affiliation(s)
- Cheng Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Joshua S MacCready
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Daniel C Ducat
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | | |
Collapse
|
20
|
Kf de Campos M, Schaaf G. The regulation of cell polarity by lipid transfer proteins of the SEC14 family. CURRENT OPINION IN PLANT BIOLOGY 2017; 40:158-168. [PMID: 29017091 DOI: 10.1016/j.pbi.2017.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
SEC14 lipid transfer proteins are important regulators of phospholipid metabolism. Structural, genetic and cell biological studies in yeast suggest that they help phosphatidylinositol (PtdIns)/phosphoinositide (PIP) kinases to overcome their intrinsic inefficiency to recognize membrane-embedded substrate, thereby playing a key role in PIP homeostasis. Genomes of higher plants encode a high number and diversity of SEC14 proteins, often in combination with other domains. The Arabidopsis SEC14-Nlj16 protein AtSFH1, an important regulator of root hair development, plays an important role in the establishment of PIP microdomains. Key to this mechanism is a highly specific interaction of the Nlj16 domain with PtdIns(4,5)P2 and an interaction-triggered oligomerization of the protein. Nlj16/PtdIns(4,5)P2 interaction depends on a polybasic motif similar to those identified in other regulatory proteins.
Collapse
Affiliation(s)
- Marília Kf de Campos
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115 Bonn, Germany.
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115 Bonn, Germany.
| |
Collapse
|
21
|
Abstract
The membranes of eukaryotic cells create hydrophobic barriers that control substance and information exchange between the inside and outside of cells and between cellular compartments. Besides their roles as membrane building blocks, some membrane lipids, such as phosphoinositides (PIs), also exert regulatory effects. Indeed, emerging evidence indicates that PIs play crucial roles in controlling polarity and growth in plants. Here, I highlight the key roles of PIs as important regulatory membrane lipids in plant development and function.
Collapse
Affiliation(s)
- Ingo Heilmann
- Department of Cellular Biochemistry, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06114, Germany
| |
Collapse
|
22
|
Gerth K, Lin F, Menzel W, Krishnamoorthy P, Stenzel I, Heilmann M, Heilmann I. Guilt by Association: A Phenotype-Based View of the Plant Phosphoinositide Network. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:349-374. [PMID: 28125287 DOI: 10.1146/annurev-arplant-042916-041022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Eukaryotic membranes contain small amounts of phospholipids that have regulatory effects on the physiological functions of cells, tissues, and organs. Phosphoinositides (PIs)-the phosphorylated derivatives of phosphatidylinositol-are one example of such regulatory lipids. Although PIs were described in plants decades ago, their contribution to the regulation of physiological processes in plants is not well understood. In the past few years, evidence has emerged that PIs are essential for plant function and development. Recently reported phenotypes associated with the perturbation of different PIs suggest that some subgroups of PIs influence specific processes. Although the molecular targets of PI-dependent regulation in plants are largely unknown, the effects of perturbed PI metabolism can be used to propose regulatory modules that involve particular downstream targets of PI regulation. This review summarizes phenotypes associated with the perturbation of the plant PI network to categorize functions and suggest possible downstream targets of plant PI regulation.
Collapse
Affiliation(s)
- Katharina Gerth
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| | - Feng Lin
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| | - Wilhelm Menzel
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| | - Praveen Krishnamoorthy
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| | - Irene Stenzel
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| | - Mareike Heilmann
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| | - Ingo Heilmann
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; , , , , , ,
| |
Collapse
|
23
|
Armengot L, Marquès-Bueno MM, Jaillais Y. Regulation of polar auxin transport by protein and lipid kinases. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4015-4037. [PMID: 27242371 PMCID: PMC4968656 DOI: 10.1093/jxb/erw216] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The directional transport of auxin, known as polar auxin transport (PAT), allows asymmetric distribution of this hormone in different cells and tissues. This system creates local auxin maxima, minima, and gradients that are instrumental in both organ initiation and shape determination. As such, PAT is crucial for all aspects of plant development but also for environmental interaction, notably in shaping plant architecture to its environment. Cell to cell auxin transport is mediated by a network of auxin carriers that are regulated at the transcriptional and post-translational levels. Here we review our current knowledge on some aspects of the 'non-genomic' regulation of auxin transport, placing an emphasis on how phosphorylation by protein and lipid kinases controls the polarity, intracellular trafficking, stability, and activity of auxin carriers. We describe the role of several AGC kinases, including PINOID, D6PK, and the blue light photoreceptor phot1, in phosphorylating auxin carriers from the PIN and ABCB families. We also highlight the function of some receptor-like kinases (RLKs) and two-component histidine kinase receptors in PAT, noting that there are probably RLKs involved in co-ordinating auxin distribution yet to be discovered. In addition, we describe the emerging role of phospholipid phosphorylation in polarity establishment and intracellular trafficking of PIN proteins. We outline these various phosphorylation mechanisms in the context of primary and lateral root development, leaf cell shape acquisition, as well as root gravitropism and shoot phototropism.
Collapse
Affiliation(s)
- Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Maria Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
- Correspondence to:
| |
Collapse
|
24
|
Okazaki K, Miyagishima SY, Wada H. Preparation of Chloroplast Lipid Membrane and Lipid-protein Interaction Assay. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
25
|
Okazaki K, Miyagishima SY, Wada H. Measurement of PI4P Levels in Intact Chloroplasts Isolated from Arabidopsis thaliana. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|