1
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Xiao Z, Nian Z, Zhang M, Liu Z, Zhang P, Zhang Z. Single-cell and bulk RNA-sequencing reveal SPP1 and CXCL12 as cell-to-cell communication markers to predict prognosis in lung adenocarcinoma. Environ Toxicol 2024. [PMID: 38622884 DOI: 10.1002/tox.24297] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
Lung adenocarcinoma (LUAD) generally presents as an immunosuppressive microenvironment. The characteristics of cell-to-cell communication in the LUAD microenvironment has been unclear. In this study, the LUAD bulk RNA-seq data and single-cell RNA-seq data were retrieved from public dataset. Differential expression genes (DEGs) between LUAD tumor and adjacent non-tumor tissues were calculated by limma algorithm, and then detected by PPI, KEGG, and GO analysis. Cell-cell interactions were explored using the single-cell RNA-seq data. Finally, the first 15 CytoHubba genes were used to establish related pathways and these pathways were used to characterize the immune-related ligands and their receptors in LUAD. Our analyses showed that monocytes or macrophages interact with tissue stem cells and NK cells via SPP1 signaling pathway and tissue stem cells interact with T and B cells via CXCL signaling pathway in different states. Hub genes of SPP1 participated in SPP1 signaling pathway, which was negatively correlated with CD4+ T cell and CD8+ T cell. The expression of SPP1 in LUAD tumor tissues was negatively correlated with the prognosis. While CXCL12 participated in CXCL signaling pathway, which was positively correlated with CD4+ T cell and CD8+ T cell. The role of CXCL12 in LUAD tumor tissues exhibits an opposite effect to that of SPP1. This study reveals that tumor-associated monocytes or macrophages may affect tumor progression. Moreover, the SPP1 and CXCL12 may be the critic genes of cell-to-cell communication in LUAD, and targeting these pathways may provide a new molecular mechanism for the treatment of LUAD.
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Affiliation(s)
- Zengtuan Xiao
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Zhe Nian
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Mengzhe Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Zuo Liu
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Pengpeng Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Zhenfa Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
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2
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Wu J, Bisaro DM. Cell-cell communication and initial population composition shape the structure of potato spindle tuber viroid quasispecies. Plant Cell 2024; 36:1036-1055. [PMID: 38252648 PMCID: PMC10980348 DOI: 10.1093/plcell/koae012] [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] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
RNA viruses and viroids replicate with high mutation rates, forming quasispecies, population of variants centered around dominant sequences. The mechanisms governing quasispecies remain unclear. Plasmodesmata regulate viroid movement and were hypothesized to impact viroid quasispecies. Here, we sequenced the progeny of potato spindle tuber viroid intermediate (PSTVd-I) strain from mature guard cells lacking plasmodesmal connections and from in vitro-cultivated mesophyll cell protoplasts from systemic leaves of early-infected tomato (Solanum lycopersicum) plants. Remarkably, more variants accumulated in guard cells compared to whole leaves. Similarly, after extended cell culture, we observed more variants in cultivated mesophyll protoplasts. Coinfection and single-cell sequencing experiments demonstrated that the same plant cell can be infected multiple times by the same or different PSTVd sequences. To study the impact of initial population composition on PSTVd-I quasispecies, we conducted coinfections with PSTVd-I and variants. Two inoculum ratios (10:1 or 1:10) established quasispecies with or without PSTVd-I as the master sequence. In the absence of the master sequence, the percentage of novel variants initially increased. Moreover, a 1:1 PSTVd-I/variant RNA ratio resulted in PSTVd-I dominating (>50%), while the variants reached 20%. After PSTVd-I-only infection, the variants reached around 10%, while after variant-only infection, the variants were significantly more than 10%. These results emphasize the role of cell-to-cell communication and initial population composition in shaping PSTVd quasispecies.
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Affiliation(s)
- Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
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3
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Versini R, Sritharan S, Aykac Fas B, Tubiana T, Aimeur SZ, Henri J, Erard M, Nüsse O, Andreani J, Baaden M, Fuchs P, Galochkina T, Chatzigoulas A, Cournia Z, Santuz H, Sacquin-Mora S, Taly A. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model 2024; 64:26-41. [PMID: 38124369 DOI: 10.1021/acs.jcim.3c01361] [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: 12/23/2023]
Abstract
AlphaFold2 (AF2) and RoseTTaFold (RF) have revolutionized structural biology, serving as highly reliable and effective methods for predicting protein structures. This article explores their impact and limitations, focusing on their integration into experimental pipelines and their application in diverse protein classes, including membrane proteins, intrinsically disordered proteins (IDPs), and oligomers. In experimental pipelines, AF2 models help X-ray crystallography in resolving the phase problem, while complementarity with mass spectrometry and NMR data enhances structure determination and protein flexibility prediction. Predicting the structure of membrane proteins remains challenging for both AF2 and RF due to difficulties in capturing conformational ensembles and interactions with the membrane. Improvements in incorporating membrane-specific features and predicting the structural effect of mutations are crucial. For intrinsically disordered proteins, AF2's confidence score (pLDDT) serves as a competitive disorder predictor, but integrative approaches including molecular dynamics (MD) simulations or hydrophobic cluster analyses are advocated for accurate dynamics representation. AF2 and RF show promising results for oligomeric models, outperforming traditional docking methods, with AlphaFold-Multimer showing improved performance. However, some caveats remain in particular for membrane proteins. Real-life examples demonstrate AF2's predictive capabilities in unknown protein structures, but models should be evaluated for their agreement with experimental data. Furthermore, AF2 models can be used complementarily with MD simulations. In this Perspective, we propose a "wish list" for improving deep-learning-based protein folding prediction models, including using experimental data as constraints and modifying models with binding partners or post-translational modifications. Additionally, a meta-tool for ranking and suggesting composite models is suggested, driving future advancements in this rapidly evolving field.
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Affiliation(s)
- Raphaelle Versini
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Sujith Sritharan
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Burcu Aykac Fas
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sana Zineb Aimeur
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Julien Henri
- Sorbonne Université, CNRS, Laboratoire de Biologie, Computationnelle et Quantitative UMR 7238, Institut de Biologie Paris-Seine, 4 Place Jussieu, F-75005 Paris, France
| | - Marie Erard
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Oliver Nüsse
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Patrick Fuchs
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Université de Paris, UFR Sciences du Vivant, 75013 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Hubert Santuz
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
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4
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Luo KR, Huang NC, Chang YH, Jan YW, Yu TS. Arabidopsis cyclophilins direct intracellular transport of mobile mRNA via organelle hitchhiking. Nat Plants 2024; 10:161-171. [PMID: 38177664 DOI: 10.1038/s41477-023-01597-5] [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] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/24/2023] [Indexed: 01/06/2024]
Abstract
Plants convert external cues into mobile mRNAs to synchronize meristematic differentiation with environmental dynamics. These mRNAs are selectively transported to intercellular pores, plasmodesmata (PD), for cell-to-cell movement. However, how plants recognize and deliver mobile mRNAs to PD remains unknown. Here we show that mobile mRNAs hitchhike on organelle trafficking to transport towards PD. Perturbed cytoskeleton organization or organelle trafficking severely disrupts the subcellular distribution of mobile mRNAs. Arabidopsis rotamase cyclophilins (ROCs), which are organelle-localized RNA-binding proteins, specifically bind mobile mRNAs on the surface of organelles to direct intracellular transport. Arabidopsis roc mutants exhibit phenotype alterations and disruptions in the transport of mobile mRNAs. These findings suggest that ROCs play a crucial role in facilitating the systemic delivery of mobile mRNAs. Our results highlight that an RNA-binding protein-mediated hitchhiking system is specifically recruited to orient plant mobile mRNAs for intercellular transport.
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Affiliation(s)
- Kai-Ren Luo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Nien-Chen Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsin Chang
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Wen Jan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Tien-Shin Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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5
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Mamun MAA, Cao W, Nakamura S, Maruyama JI. Large-scale identification of genes involved in septal pore plugging in multicellular fungi. Nat Commun 2023; 14:1418. [PMID: 36932089 PMCID: PMC10023807 DOI: 10.1038/s41467-023-36925-y] [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: 01/20/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Multicellular filamentous fungi have septal pores that allow cytoplasmic exchange, and thus connectivity, between neighboring cells in the filament. Hyphal wounding and other stress conditions induce septal pore closure to minimize cytoplasmic loss. However, the composition of the septal pore and the mechanisms underlying its function are not well understood. Here, we set out to identify new septal components by determining the subcellular localization of 776 uncharacterized proteins in a multicellular ascomycete, Aspergillus oryzae. The set of 776 uncharacterized proteins was selected on the basis that their genes were present in the genomes of multicellular, septal pore-bearing ascomycetes (three Aspergillus species, in subdivision Pezizomycotina) and absent/divergent in the genomes of septal pore-lacking ascomycetes (yeasts). Upon determining their subcellular localization, 62 proteins were found to localize to the septum or septal pore. Deletion of the encoding genes revealed that 23 proteins are involved in regulating septal pore plugging upon hyphal wounding. Thus, this study determines the subcellular localization of many uncharacterized proteins in A. oryzae and, in particular, identifies a set of proteins involved in septal pore function.
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Affiliation(s)
| | - Wei Cao
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shugo Nakamura
- Department of Information Networking for Innovation and Design, Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan
| | - Jun-Ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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6
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Ma T, Fu S, Wang K, Wang Y, Wu J, Zhou X. Palmitoylation Is Indispensable for Remorin to Restrict Tobacco Mosaic Virus Cell-to-Cell Movement in Nicotiana benthamiana. Viruses 2022; 14:1324. [PMID: 35746795 PMCID: PMC9227848 DOI: 10.3390/v14061324] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
Remorin (REM) is a plant-specific plasma membrane-associated protein regulating plasmodesmata plasticity and restricting viral cell-to-cell movement. Here, we show that palmitoylation is broadly present in group 1 remorin proteins in Nicotiana benthamiana and is crucial for plasma membrane localization and accumulation. By screening the four members of N. benthamiana group 1 remorin proteins, we found that only NbREM1.5 could significantly hamper tobacco mosaic virus (TMV) cell-to-cell movement. We further showed that NbREM1.5 interacts with the movement protein of TMV in vivo and interferes with its function of expanding the plasmodesmata size exclusion limit. We also demonstrated that palmitoylation is indispensable for NbREM1.5 to hamper plasmodesmata permeability and inhibit TMV cell-to-cell movement.
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Affiliation(s)
- Tingting Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Kun Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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7
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Yan Y, Ham BK. The Mobile Small RNAs: Important Messengers for Long-Distance Communication in Plants. Front Plant Sci 2022; 13:928729. [PMID: 35783973 PMCID: PMC9247610 DOI: 10.3389/fpls.2022.928729] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/25/2022] [Indexed: 06/06/2023]
Abstract
Various species of small RNAs (sRNAs), notably microRNAs and small interfering RNAs (siRNAs), have been characterized as the major effectors of RNA interference in plants. Growing evidence supports a model in which sRNAs move, intercellularly, systemically, and between cross-species. These non-coding sRNAs can traffic cell-to-cell through plasmodesmata (PD), in a symplasmic manner, as well as from source to sink tissues, via the phloem, to trigger gene silencing in their target cells. Such mobile sRNAs function in non-cell-autonomous communication pathways, to regulate various biological processes, such as plant development, reproduction, and plant defense. In this review, we summarize recent progress supporting the roles of mobile sRNA in plants, and discuss mechanisms of sRNA transport, signal amplification, and the plant's response, in terms of RNAi activity, within the recipient tissues. We also discuss potential research directions and their likely impact on engineering of crops with traits for achieving food security.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Byung-Kook Ham
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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8
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Kirk P, Amsbury S, German L, Gaudioso-Pedraza R, Benitez-Alfonso Y. A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species. BMC Biol 2022; 20:128. [PMID: 35655273 PMCID: PMC9164936 DOI: 10.1186/s12915-022-01331-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/16/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND A major route for cell-to-cell signalling in plants is mediated by cell wall-embedded pores termed plasmodesmata forming the symplasm. Plasmodesmata regulate the plant development and responses to the environment; however, our understanding of what factors or regulatory cues affect their structure and permeability is still limited. In this paper, a meta-analysis was carried out for the identification of conditions affecting plasmodesmata transport and for the in silico prediction of plasmodesmata proteins in species for which the plasmodesmata proteome has not been experimentally determined. RESULTS Using the information obtained from experimental proteomes, an analysis pipeline (named plasmodesmata in silico proteome 1 or PIP1) was developed to rapidly generate candidate plasmodesmata proteomes for 22 plant species. Using the in silico proteomes to interrogate published transcriptomes, gene interaction networks were identified pointing to conditions likely affecting plasmodesmata transport capacity. High salinity, drought and osmotic stress regulate the expression of clusters enriched in genes encoding plasmodesmata proteins, including those involved in the metabolism of the cell wall polysaccharide callose. Experimental determinations showed restriction in the intercellular transport of the symplasmic reporter GFP and enhanced callose deposition in Arabidopsis roots exposed to 75-mM NaCl and 3% PEG (polyethylene glycol). Using PIP1 and transcriptome meta-analyses, candidate plasmodesmata proteins for the legume Medicago truncatula were generated, leading to the identification of Medtr1g073320, a novel receptor-like protein that localises at plasmodesmata. Expression of Medtr1g073320 affects callose deposition and the root response to infection with the soil-borne bacteria rhizobia in the presence of nitrate. CONCLUSIONS Our study shows that combining proteomic meta-analysis and transcriptomic data can be a valuable tool for the identification of new proteins and regulatory mechanisms affecting plasmodesmata function. We have created the freely accessible pipeline PIP1 as a resource for the screening of experimental proteomes and for the in silico prediction of PD proteins in diverse plant species.
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Affiliation(s)
- Philip Kirk
- Centre for Plant Science, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sam Amsbury
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Liam German
- Centre for Plant Science, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
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9
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Kitagawa M, Jackson D. A Forward Genetic Approach to Identify Plasmodesmal Trafficking Regulators Based on Trichome Rescue. Methods Mol Biol 2022; 2457:393-407. [PMID: 35349156 DOI: 10.1007/978-1-0716-2132-5_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Plasmodesmata (PD) are channels in the walls of plant cells which enable cell-to-cell information transfer. This includes the selective transport of specific transcription factors that control cell fate during plant development. KNOTTED1 (KN1) homeobox (KNOX) family transcription factors that are essential for the maintenance and function of stem cells in shoot meristems use this trafficking pathway, but its mechanism is largely unknown. Here we describe a forward genetic approach to the identification of regulators of selective KN1 trafficking through PD, using a trichome rescue system that permits simple visual analysis in Arabidopsis leaves. A KN1 trafficking regulator identified in this approach had the capacity to regulate the transport not only of KN1 but also of another mobile regulatory protein, TRANSPARENT TESTA GLABRA1 (TTG1). Our system could be easily adapted to reveal the mechanism underlying the selective transport of additional mobile signals through PD.
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10
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Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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11
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Kang BH, Anderson CT, Arimura SI, Bayer E, Bezanilla M, Botella MA, Brandizzi F, Burch-Smith TM, Chapman KD, Dünser K, Gu Y, Jaillais Y, Kirchhoff H, Otegui MS, Rosado A, Tang Y, Kleine-Vehn J, Wang P, Zolman BK. A glossary of plant cell structures: Current insights and future questions. Plant Cell 2022; 34:10-52. [PMID: 34633455 PMCID: PMC8846186 DOI: 10.1093/plcell/koab247] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 05/03/2023]
Abstract
In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.
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Affiliation(s)
- Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Charles T Anderson
- Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Emmanuelle Bayer
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Villenave d'Ornon F-33140, France
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortifruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 29071, Spain
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Kai Dünser
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Yangnan Gu
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Abel Rosado
- Department of Botany, University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yu Tang
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Jürgen Kleine-Vehn
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri, St. Louis, St. Louis, Missouri 63121, USA
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12
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Blümke P, Howe V, Simon R. Studying Protein-Protein Interactions at Plasmodesmata by Measuring Förster Resonance Energy Transfer. Methods Mol Biol 2022; 2457:219-232. [PMID: 35349143 DOI: 10.1007/978-1-0716-2132-5_14] [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: 06/14/2023]
Abstract
Plasmodesmata (PD) provide interconnectivity between plant cells to enable the intercellular transport and communication that is requisite to multicellularity. Being at the interface of the apoplast, plasma membrane (PM), endoplasmic reticulum (ER), and symplast, PD are uniquely positioned to integrate exogenously and endogenously derived signals with plant developmental and physiological responses. The distinct membrane curvature and composition of PD allow them to function as microdomains to facilitate dynamic protein-protein interactions. Förster resonance energy transfer (FRET) combined with fluorescence lifetime imaging microscopy (FLIM) and fluorescence anisotropic decay measurements provides valuable tools to analyze these interactions in vivo and in planta. Here we describe a detailed methodology to perform FRET-FLIM and fluorescence anisotropy measurements to analyze protein-protein interactions at PD in a transient expression system using Nicotiana benthamiana; however this can be adapted to other plant species and subcellular compartments.
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Affiliation(s)
- Patrick Blümke
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | - Vicky Howe
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany.
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13
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Godel-J Drychowska K, Kurczy Ska E. Qualitative and quantitative analyses of the plasmodesmata that accompany cell fate changes during the somatic embryogenesis of Arabidopsis thaliana. Funct Plant Biol 2022; 49:186-200. [PMID: 34838155 DOI: 10.1071/fp21243] [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] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Plasmodesmata (PD) are cytoplasmic and membrane-lined microchannels that enable symplasmic communication in plants, which is involved in the regulation of cell differentiation. The presented results emphasise the qualitative and quantitative analyses of PD, which are the basis of the symplasmic communication. The cells that initiate various development programmes create symplasmic domains that are characterised by different degrees of symplasmic communication. Changes in symplasmic communication are caused by the presence or absence of PD and/or the ability of signals to move through them. In the presented studies, somatic embryogenesis was used to describe the characteristics of the PD within and between the symplasmic domains in explants of the Arabidopsis thaliana (L.) Heynh ecotype Columbia-0 and 35S:BBM transgenic line. Transmission electron microscopy was used to describe the cells that regain totipotency/pluripotency during somatic embryogenesis, as well as the number and shape of the PD in the different symplasmic domains of the explants and somatic embryos. Array tomography was used to create a 3D reconstruction of the protodermal cells of the somatic embryos with particular emphasis on the PD distribution in the cell walls. The results showed that there were different frequencies of the PD within and between the symplasmic domain that emerges during somatic embryogenesis and between the Col-0 and 35S:BBM somatic embryos with regard to the differences in the shape of the PD.
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Affiliation(s)
- Kamila Godel-J Drychowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, The University of Silesia, 28 Jagiellonska Street, 40-032 Katowice, Poland
| | - Ewa Kurczy Ska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, The University of Silesia, 28 Jagiellonska Street, 40-032 Katowice, Poland
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14
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Tomkins M, Hughes A, Morris RJ. An update on passive transport in and out of plant cells. Plant Physiol 2021; 187:1973-1984. [PMID: 35235675 PMCID: PMC8644452 DOI: 10.1093/plphys/kiab406] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/30/2021] [Indexed: 05/09/2023]
Abstract
Transport across membranes is critical for plant survival. Membranes are the interfaces at which plants interact with their environment. The transmission of energy and molecules into cells provides plants with the source material and power to grow, develop, defend, and move. An appreciation of the physical forces that drive transport processes is thus important for understanding the plant growth and development. We focus on the passive transport of molecules, describing the fundamental concepts and demonstrating how different levels of abstraction can lead to different interpretations of the driving forces. We summarize recent developments on quantitative frameworks for describing diffusive and bulk flow transport processes in and out of cells, with a more detailed focus on plasmodesmata, and outline open questions and challenges.
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Affiliation(s)
- Melissa Tomkins
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, UK
| | - Aoife Hughes
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, UK
| | - Richard J Morris
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, UK
- Author for communication:
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15
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Sorkin ML, Nusinow DA. Time Will Tell: Intercellular Communication in the Plant Clock. Trends Plant Sci 2021; 26:706-719. [PMID: 33468432 DOI: 10.1016/j.tplants.2020.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/14/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 05/17/2023]
Abstract
Multicellular organisms have evolved local and long-distance signaling mechanisms to synchronize development and response to stimuli among a complex network of cells, tissues, and organs. Biological timekeeping is one such activity that is suggested to be coordinated within an organism to anticipate and respond to daily and seasonal patterns in the environment. New research into the plant clock suggests circadian rhythms are communicated between cells and across long distances. However, further clarity is required on the nature of the signaling molecules and the mechanisms underlying signal translocation. Here we summarize the roles and properties of tissue-specific circadian rhythms, discuss the evidence for local and long-distance clock communication, and evaluate the potential signaling molecules and transport mechanisms involved in this system.
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Affiliation(s)
- Maria L Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
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16
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Godel-Jędrychowska K, Kulińska-Łukaszek K, Kurczyńska E. Similarities and Differences in the GFP Movement in the Zygotic and Somatic Embryos of Arabidopsis. Front Plant Sci 2021; 12:649806. [PMID: 34122474 PMCID: PMC8194063 DOI: 10.3389/fpls.2021.649806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Intercellular signaling during embryo patterning is not well understood and the role of symplasmic communication has been poorly considered. The correlation between the symplasmic domains and the development of the embryo organs/tissues during zygotic embryogenesis has only been described for a few examples, including Arabidopsis. How this process occurs during the development of somatic embryos (SEs) is still unknown. The aim of these studies was to answer the question: do SEs have a restriction in symplasmic transport depending on the developmental stage that is similar to their zygotic counterparts? The studies included an analysis of the GFP distribution pattern as expressed under diverse promoters in zygotic embryos (ZEs) and SEs. The results of the GFP distribution in the ZEs and SEs showed that 1/the symplasmic domains between the embryo organs and tissues in the SEs was similar to those in the ZEs and 2/the restriction in symplasmic transport in the SEs was correlated with the developmental stage and was similar to the one in their zygotic counterparts, however, with the spatio-temporal differences and different PDs SEL value between these two types of embryos.
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17
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Chen C, Vanneste S, Chen X. Review: Membrane tethers control plasmodesmal function and formation. Plant Sci 2021; 304:110800. [PMID: 33568299 DOI: 10.1016/j.plantsci.2020.110800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/29/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Cell-to-cell communication is crucial in coordinating diverse biological processes in multicellular organisms. In plants, communication between adjacent cells occurs via nanotubular passages called plasmodesmata (PD). The PD passage is composed of an appressed endoplasmic reticulum (ER) internally, and plasma membrane (PM) externally, that traverses the cell wall, and associates with the actin-cytoskeleton. The coordination of the ER, PM and cytoskeleton plays a potential role in maintaining the architecture and conductivity of PD. Many data suggest that PD-associated proteins can serve as tethers that connect these structures in a functional PD, to regulate cell-to-cell communication. In this review, we summarize the organization and regulation of PD activity via tethering proteins, and discuss the importance of PD-mediated cell-to-cell communication in plant development and defense against environmental stress.
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Affiliation(s)
- Chaofan Chen
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China; FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Department of Plants and Crops, Ghent University, Coupure links 653, 9000 Ghent, Belgium; Lab of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, 119, Yeonsu-gu, Incheon 21985, Republic of Korea
| | - Xu Chen
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
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18
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Fichman Y, Myers RJ, Grant DG, Mittler R. Plasmodesmata-localized proteins and ROS orchestrate light-induced rapid systemic signaling in Arabidopsis. Sci Signal 2021; 14:14/671/eabf0322. [PMID: 33622982 DOI: 10.1126/scisignal.abf0322] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Systemic signaling and systemic acquired acclimation (SAA) are key to the survival of plants during episodes of abiotic stress. These processes depend on a continuous chain of cell-to-cell signaling events that extends from the initial tissue that senses the stress (the local tissue) to the entire plant (systemic tissues). Reactive oxygen species (ROS) and Ca2+ are key signaling molecules thought to be involved in this cell-to-cell mechanism. Here, we report that the systemic response of Arabidopsis thaliana to a local treatment of high light stress, which resulted in local ROS accumulation, required ROS generated by respiratory burst oxidase homolog D (RBOHD). ROS increased cell-to-cell transport and plasmodesmata (PD) pore size in a manner dependent on PD-localized protein 1 (PDLP1) and PDLP5, and this process was required for the propagation of the systemic ROS signals and SAA. Furthermore, aquaporins and several Ca2+-permeable channels in the glutamate receptor-like (GLR), mechanosensitive small conductance-like (MSL), and cyclic nucleotide-gated (CNGC) families were involved in this systemic signaling process. However, we determined that these channels were required primarily to amplify the systemic signal in each cell along the path of the systemic ROS wave, as well as to establish local and systemic acclimation. Thus, PD and RBOHD-generated ROS orchestrate light stress-induced rapid cell-to-cell spread of systemic signals in Arabidopsis.
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Affiliation(s)
- Yosef Fichman
- The Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO 65201, USA
| | - Ronald J Myers
- The Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO 65201, USA
| | - DeAna G Grant
- Electron Microscopy Core Facility, University of Missouri, W136 Veterinary Medicine Building 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Ron Mittler
- The Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO 65201, USA. .,Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO 65201, USA
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19
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Peters WS, Jensen KH, Stone HA, Knoblauch M. Plasmodesmata and the problems with size: Interpreting the confusion. J Plant Physiol 2021; 257:153341. [PMID: 33388666 DOI: 10.1016/j.jplph.2020.153341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/20/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 05/14/2023]
Abstract
Plant tissues exhibit a symplasmic organization; the individual protoplasts are connected to their neighbors via cytoplasmic bridges that extend through pores in the cell walls. These bridges may have diameters of a micrometer or more, as in the sieve pores of the phloem, but in most cell types they are smaller. Historically, botanists referred to cytoplasmic bridges of all sizes as plasmodesmata. The meaning of the term began to shift when the transmission electron microscope (TEM) became the preferred tool for studying these structures. Today, a plasmodesma is widely understood to be a 'nano-scale' pore. Unfortunately, our understanding of these nanoscopic channels suffers from methodological limitations. This is exemplified by the fact that state-of-the-art EM techniques appear to reveal plasmodesmal pore structures that are much smaller than the tracer molecules known to diffuse through these pores. In general, transport processes in pores that have dimensions in the size range of the transported molecules are governed by different physical parameters than transport process in the macroscopic realm. This can lead to unexpected effects, as experience in nanofluidic technologies demonstrates. Our discussion of problems of size in plasmodesma research leads us to conclude that the field will benefit from technomimetic reasoning - the utilization of concepts developed in applied nanofluidics for the interpretation of biological systems.
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Affiliation(s)
- Winfried S Peters
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA; Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, 46805, USA.
| | - Kaare H Jensen
- Department of Physics, Technical University of Denmark, DK-2800 Kgs., Lyngby, Denmark.
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA.
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
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20
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Lazareva EA, Lezzhov AA, Chergintsev DA, Golyshev SA, Dolja VV, Morozov SY, Heinlein M, Solovyev AG. Reticulon-like properties of a plant virus-encoded movement protein. New Phytol 2021; 229:1052-1066. [PMID: 32866987 DOI: 10.1111/nph.16905] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 06/26/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Plant viruses encode movement proteins (MPs) that ensure the transport of viral genomes through plasmodesmata (PD) and use cell endomembranes, mostly the endoplasmic reticulum (ER), for delivery of viral genomes to PD and formation of PD-anchored virus replication compartments. Here, we demonstrate that the Hibiscus green spot virus BMB2 MP, an integral ER protein, induces constrictions of ER tubules, decreases the mobility of ER luminal content, and exhibits an affinity to highly curved membranes. These properties are similar to those described for reticulons, cellular proteins that induce membrane curvature to shape the ER tubules. Similar to reticulons, BMB2 adopts a W-like topology within the ER membrane. BMB2 targets PD and increases their size exclusion limit, and these BMB2 activities correlate with the ability to induce constrictions of ER tubules. We propose that the induction of ER constrictions contributes to the BMB2-dependent increase in PD permeability and formation of the PD-associated replication compartments, therefore facilitating the virus intercellular spread. Furthermore, we show that the ER tubule constrictions also occur in cells expressing TGB2, one of the three MPs of Potato virus X (PVX), and in PVX-infected cells, suggesting that reticulon-like MPs are employed by diverse RNA viruses.
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Affiliation(s)
- Ekaterina A Lazareva
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119991, Russia
| | - Denis A Chergintsev
- Department of Plant Physiology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Sergei A Golyshev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Sergey Y Morozov
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
| | - Manfred Heinlein
- Institute for Plant Molecular Biology (IBMP-CNRS), University of Strasbourg, Strasbourg, 67000, France
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Moscow, 127550, Russia
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21
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Abstract
ABSTRACT
Fibroblast growth factor 2 (FGF2) and interleukin 1β (IL-1β) were among the earliest examples of a subclass of proteins with extracellular functions that were found to lack N-terminal secretory signal peptides and were shown to be secreted in an ER- and Golgi-independent manner. Many years later, a number of alternative secretory pathways have been discovered, processes collectively termed unconventional protein secretion (UPS). In the course of these studies, unconventional secretion of FGF2 and IL-1β were found to be based upon distinct pathways, mechanisms and molecular machineries. Following a concise introduction into various pathways mediating unconventional secretion and transcellular spreading of proteins, this Cell Science at a Glance poster article aims at a focused analysis of recent key discoveries providing unprecedented detail about the molecular mechanisms and machineries driving FGF2 and IL-1β secretion. These findings are also highly relevant for other unconventionally secreted cargoes that, like FGF2 and IL1β, exert fundamental biological functions in biomedically relevant processes, such as tumor-induced angiogenesis and inflammation.
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Affiliation(s)
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg 69120, Germany
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22
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Morozov SY, Solovyev AG. Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes. AIMS Microbiol 2020; 6:305-329. [PMID: 33134746 PMCID: PMC7595835 DOI: 10.3934/microbiol.2020019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022] Open
Abstract
Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. Moreover, it was found that small membrane MPs encoded by many viruses can be involved in coupling viral replication and cell-to-cell movement. Currently, the studies of evolutionary origin and functioning of small membrane MPs is regarded as an important pre-requisite for understanding of the evolution of the existing plant virus transport systems. This paper represents the first comprehensive review which describes the whole diversity of small membrane MPs and presents the current views on their role in plant virus movement.
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Affiliation(s)
- Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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23
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Li ZP, Paterlini A, Glavier M, Bayer EM. Intercellular trafficking via plasmodesmata: molecular layers of complexity. Cell Mol Life Sci 2021; 78:799-816. [PMID: 32920696 DOI: 10.1007/s00018-020-03622-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Plasmodesmata are intercellular pores connecting together most plant cells. These structures consist of a central constricted form of the endoplasmic reticulum, encircled by some cytoplasmic space, in turn delimited by the plasma membrane, itself ultimately surrounded by the cell wall. The presence and structure of plasmodesmata create multiple routes for intercellular trafficking of a large spectrum of molecules (encompassing RNAs, proteins, hormones and metabolites) and also enable local signalling events. Movement across plasmodesmata is finely controlled in order to balance processes requiring communication with those necessitating symplastic isolation. Here, we describe the identities and roles of the molecular components (specific sets of lipids, proteins and wall polysaccharides) that shape and define plasmodesmata structural and functional domains. We highlight the extensive and dynamic interactions that exist between the plasma/endoplasmic reticulum membranes, cytoplasm and cell wall domains, binding them together to effectively define plasmodesmata shapes and purposes.
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