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Quinn O, Kumar M, Turner S. The role of lipid-modified proteins in cell wall synthesis and signaling. PLANT PHYSIOLOGY 2023; 194:51-66. [PMID: 37682865 PMCID: PMC10756762 DOI: 10.1093/plphys/kiad491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
The plant cell wall is a complex and dynamic extracellular matrix. Plant primary cell walls are the first line of defense against pathogens and regulate cell expansion. Specialized cells deposit a secondary cell wall that provides support and permits water transport. The composition and organization of the cell wall varies between cell types and species, contributing to the extensibility, stiffness, and hydrophobicity required for its proper function. Recently, many of the proteins involved in the biosynthesis, maintenance, and remodeling of the cell wall have been identified as being post-translationally modified with lipids. These modifications exhibit diverse structures and attach to proteins at different sites, which defines the specific role played by each lipid modification. The introduction of relatively hydrophobic lipid moieties promotes the interaction of proteins with membranes and can act as sorting signals, allowing targeted delivery to the plasma membrane regions and secretion into the apoplast. Disruption of lipid modification results in aberrant deposition of cell wall components and defective cell wall remodeling in response to stresses, demonstrating the essential nature of these modifications. Although much is known about which proteins bear lipid modifications, many questions remain regarding the contribution of lipid-driven membrane domain localization and lipid heterogeneity to protein function in cell wall metabolism. In this update, we highlight the contribution of lipid modifications to proteins involved in the formation and maintenance of plant cell walls, with a focus on the addition of glycosylphosphatidylinositol anchors, N-myristoylation, prenylation, and S-acylation.
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Affiliation(s)
- Oliver Quinn
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Simon Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
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2
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Yue N, Jiang Z, Zhang X, Li Z, Wang X, Wen Z, Gao Z, Pi Q, Zhang Y, Wang X, Han C, Yu J, Li D. Palmitoylation of γb protein directs a dynamic switch between Barley stripe mosaic virus replication and movement. EMBO J 2022; 41:e110060. [PMID: 35642376 PMCID: PMC9251889 DOI: 10.15252/embj.2021110060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Viral replication and movement are intimately linked; however, the molecular mechanisms regulating the transition between replication and subsequent movement remain largely unknown. We previously demonstrated that the Barley stripe mosaic virus (BSMV) γb protein promotes viral replication and movement by interacting with the αa replicase and TGB1 movement proteins. Here, we found that γb is palmitoylated at Cys-10, Cys-19, and Cys-60 in Nicotiana benthamiana, which supports BSMV infection. Intriguingly, non-palmitoylated γb is anchored to chloroplast replication sites and enhances BSMV replication, whereas palmitoylated γb protein recruits TGB1 to the chloroplasts and forms viral replication-movement intermediate complexes. At the late stages of replication, γb interacts with NbPAT15 and NbPAT21 and is palmitoylated at the chloroplast periphery, thereby shifting viral replication to intracellular and intercellular movement. We also show that palmitoylated γb promotes virus cell-to-cell movement by interacting with NbREM1 to inhibit callose deposition at the plasmodesmata. Altogether, our experiments reveal a model whereby palmitoylation of γb directs a dynamic switch between BSMV replication and movement events during infection.
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Affiliation(s)
- Ning Yue
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhihao Jiang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xuan Zhang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhenggang Li
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xueting Wang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhiyan Wen
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zongyu Gao
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Qinglin Pi
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yongliang Zhang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xian‐Bing Wang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chenggui Han
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jialin Yu
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dawei Li
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
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3
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Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022. [PMID: 35681017 DOI: 10.1101/2020.05.12.090415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
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Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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4
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Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022; 8:670-681. [PMID: 35681017 DOI: 10.1038/s41477-022-01164-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/04/2022] [Indexed: 05/28/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
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Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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5
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Li X, Shen L, Xu Z, Liu W, Li A, Xu J. Protein Palmitoylation Modification During Viral Infection and Detection Methods of Palmitoylated Proteins. Front Cell Infect Microbiol 2022; 12:821596. [PMID: 35155279 PMCID: PMC8829041 DOI: 10.3389/fcimb.2022.821596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 01/31/2023] Open
Abstract
Protein palmitoylation—a lipid modification in which one or more cysteine thiols on a substrate protein are modified to form a thioester with a palmitoyl group—is a significant post-translational biological process. This process regulates the trafficking, subcellular localization, and stability of different proteins in cells. Since palmitoylation participates in various biological processes, it is related to the occurrence and development of multiple diseases. It has been well evidenced that the proteins whose functions are palmitoylation-dependent or directly involved in key proteins’ palmitoylation/depalmitoylation cycle may be a potential source of novel therapeutic drugs for the related diseases. Many researchers have reported palmitoylation of proteins, which are crucial for host-virus interactions during viral infection. Quite a few explorations have focused on figuring out whether targeting the acylation of viral or host proteins might be a strategy to combat viral diseases. All these remarkable achievements in protein palmitoylation have been made to technological advances. This paper gives an overview of protein palmitoylation modification during viral infection and the methods for palmitoylated protein detection. Future challenges and potential developments are proposed.
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Affiliation(s)
- Xiaoling Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lingyi Shen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhao Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Aihua Li
- Clinical Lab, Henan Provincial Chest Hospital, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Jun Xu, ;
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6
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Xu Y, Shi Z, Bao L. An expanding repertoire of protein acylations. Mol Cell Proteomics 2022; 21:100193. [PMID: 34999219 PMCID: PMC8933697 DOI: 10.1016/j.mcpro.2022.100193] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023] Open
Abstract
Protein post-translational modifications play key roles in multiple cellular processes by allowing rapid reprogramming of individual protein functions. Acylation, one of the most important post-translational modifications, is involved in different physiological activities including cell differentiation and energy metabolism. In recent years, the progression in technologies, especially the antibodies against acylation and the highly sensitive and effective mass spectrometry–based proteomics, as well as optimized functional studies, greatly deepen our understanding of protein acylation. In this review, we give a general overview of the 12 main protein acylations (formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, glutarylation, palmitoylation, myristoylation, benzoylation, crotonylation, and 2-hydroxyisobutyrylation), including their substrates (histones and nonhistone proteins), regulatory enzymes (writers, readers, and erasers), biological functions (transcriptional regulation, metabolic regulation, subcellular targeting, protein–membrane interactions, protein stability, and folding), and related diseases (cancer, diabetes, heart disease, neurodegenerative disease, and viral infection), to present a complete picture of protein acylations and highlight their functional significance in future research. Provide a general overview of the 12 main protein acylations. Acylation of viral proteins promotes viral integration and infection. Hyperacylation of histone has antitumous and neuroprotective effects. MS is widely used in the identification of acylation but has its challenges.
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Affiliation(s)
- Yuxuan Xu
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Zhenyu Shi
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Li Bao
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China.
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Li H, Qiu L, Wang M. Informed Attentive Predictors: A Generalisable Architecture for Prior Knowledge-Based Assisted Diagnosis of Cancers. SENSORS 2021; 21:s21196484. [PMID: 34640802 PMCID: PMC8512568 DOI: 10.3390/s21196484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022]
Abstract
Due to the high mortality of many cancers and their related diseases, the prediction and prognosis techniques of cancers are being extensively studied to assist doctors in making diagnoses. Many machine-learning-based cancer predictors have been put forward, but many of them have failed to become widely utilised due to some crucial problems. For example, most methods require too much training data, which is not always applicable to institutes, and the complicated genetic mutual effects of cancers are generally ignored in many proposed methods. Moreover, a majority of these assist models are actually not safe to use, as they are generally built on black-box machine learners that lack references from related field knowledge. We observe that few machine-learning-based cancer predictors are capable of employing prior knowledge (PrK) to mitigate these issues. Therefore, in this paper, we propose a generalisable informed machine learning architecture named the Informed Attentive Predictor (IAP) to make PrK available to the predictor’s decision-making phases and apply it to the field of cancer prediction. Specifically, we make several implementations of the IAP and evaluate its performance on six TCGA datasets to demonstrate the effectiveness of our architecture as an assist system framework for actual clinical usage. The experimental results show a noticeable improvement in IAP models on accuracies, f1-scores and recall rates compared to their non-IAP counterparts (i.e., basic predictors).
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8
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The molecular basis of plant cellulose synthase complex organisation and assembly. Biochem Soc Trans 2021; 49:379-391. [PMID: 33616627 DOI: 10.1042/bst20200697] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 02/02/2023]
Abstract
The material properties of cellulose are heavily influenced by the organisation of β-1,4-glucan chains into a microfibril. It is likely that the structure of this microfibril is determined by the spatial arrangement of catalytic cellulose synthase (CESA) proteins within the cellulose synthase complex (CSC). In land plants, CESA proteins form a large complex composed of a hexamer of trimeric lobes termed the rosette. Each rosette synthesises a single microfibril likely composed of 18 glucan chains. In this review, the biochemical events leading to plant CESA protein assembly into the rosette are explored. The protein interfaces responsible for CESA trimerization are formed by regions that define rosette-forming CESA proteins. As a consequence, these regions are absent from the ancestral bacterial cellulose synthases (BcsAs) that do not form rosettes. CSC assembly occurs within the context of the endomembrane system, however the site of CESA assembly into trimers and rosettes is not determined. Both the N-Terminal Domain and Class Specific Region of CESA proteins are intrinsically disordered and contain all of the identified phosphorylation sites, making both regions candidates as sites for protein-protein interactions and inter-lobe interface formation. We propose a sequential assembly model, whereby CESA proteins form stable trimers shortly after native folding, followed by sequential recruitment of lobes into a rosette, possibly assisted by Golgi-localised STELLO proteins. A comprehensive understanding of CESA assembly into the CSC will enable directed engineering of CESA protein spatial arrangements, allowing changes in cellulose crystal packing that alter its material properties.
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9
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H 2S signaling in plants and applications in agriculture. J Adv Res 2020; 24:131-137. [PMID: 32292600 PMCID: PMC7150428 DOI: 10.1016/j.jare.2020.03.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Hydrogen sulfide (H2S) plays a signaling role in higher plants. It mediates persulfidation, a post-translational modification. It regulates physiological functions ranging from seed germination to fruit ripening. The beneficial effects of exogenous H2S are mainly caused by the stimulation of antioxidant systems.
The signaling properties of the gasotransmitter molecule hydrogen sulfide (H2S), which is endogenously generated in plant cells, are mainly observed during persulfidation, a protein post-translational modification (PTM) that affects redox-sensitive cysteine residues. There is growing experimental evidence that H2S in higher plants may function as a mechanism of response to environmental stress conditions. In addition, exogenous applications of H2S to plants appear to provide additional protection against stresses, such as salinity, drought, extreme temperatures and heavy metals, mainly through the induction of antioxidant systems, in order to palliate oxidative cellular damage. H2S also appears to be involved in regulating physiological functions, such as seed germination, stomatal movement and fruit ripening, as well as molecules that maintain post-harvest quality and rhizobium–legume symbiosis. These properties of H2S open up new challenges in plant research to better understand its functions as well as new opportunities for biotechnological treatments in agriculture in a changing environment.
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10
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Zhu W, Xie L, Han J, Guo X. The Application of Deep Learning in Cancer Prognosis Prediction. Cancers (Basel) 2020; 12:E603. [PMID: 32150991 PMCID: PMC7139576 DOI: 10.3390/cancers12030603] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Deep learning has been applied to many areas in health care, including imaging diagnosis, digital pathology, prediction of hospital admission, drug design, classification of cancer and stromal cells, doctor assistance, etc. Cancer prognosis is to estimate the fate of cancer, probabilities of cancer recurrence and progression, and to provide survival estimation to the patients. The accuracy of cancer prognosis prediction will greatly benefit clinical management of cancer patients. The improvement of biomedical translational research and the application of advanced statistical analysis and machine learning methods are the driving forces to improve cancer prognosis prediction. Recent years, there is a significant increase of computational power and rapid advancement in the technology of artificial intelligence, particularly in deep learning. In addition, the cost reduction in large scale next-generation sequencing, and the availability of such data through open source databases (e.g., TCGA and GEO databases) offer us opportunities to possibly build more powerful and accurate models to predict cancer prognosis more accurately. In this review, we reviewed the most recent published works that used deep learning to build models for cancer prognosis prediction. Deep learning has been suggested to be a more generic model, requires less data engineering, and achieves more accurate prediction when working with large amounts of data. The application of deep learning in cancer prognosis has been shown to be equivalent or better than current approaches, such as Cox-PH. With the burst of multi-omics data, including genomics data, transcriptomics data and clinical information in cancer studies, we believe that deep learning would potentially improve cancer prognosis.
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Affiliation(s)
- Wan Zhu
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics center, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
- Department of Anesthesia, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Longxiang Xie
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics center, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
| | - Jianye Han
- Department of Computer Science, University of Illinois, Urbana Champions, IL 61820, USA;
| | - Xiangqian Guo
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics center, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
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Gadalla MR, Veit M. Toward the identification of ZDHHC enzymes required for palmitoylation of viral protein as potential drug targets. Expert Opin Drug Discov 2019; 15:159-177. [PMID: 31809605 DOI: 10.1080/17460441.2020.1696306] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Introduction: S-acylation is the attachment of fatty acids not only to cysteines of cellular, but also of viral proteins. The modification is often crucial for the protein´s function and hence for virus replication. Transfer of fatty acids is mediated by one or several of the 23 members of the ZDHHC family of proteins. Since their genes are linked to various human diseases, they represent drug targets.Areas covered: The authors explore whether targeting acylation of viral proteins might be a strategy to combat viral diseases. Many human pathogens contain S-acylated proteins; the ZDHHCs involved in their acylation are currently identified. Based on the 3D structure of two ZDHHCs, the regulation and the biochemistry of the palmitolyation reaction and the lipid and protein substrate specificities are discussed. The authors then speculate how ZDHHCs might recognize S-acylated membrane proteins of Influenza virus.Expert opinion: Although many viral diseases can now be treated, the available drugs bind to viral proteins that rapidly mutate and become resistant. To develop inhibitors for the genetically more stable cellular ZDHHCs, their binding sites for viral substrates need to be identified. If only a few cellular proteins are recognized by the same binding site, development of specific inhibitors may have therapeutic potential.
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Affiliation(s)
- Mohamed Rasheed Gadalla
- Institute of Virology, Free University Berlin, Berlin, Germany.,Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Michael Veit
- Institute of Virology, Free University Berlin, Berlin, Germany
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12
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Amraee L, Rahmani F, Abdollahi Mandoulakani B. 24-Epibrassinolide alters DNA cytosine methylation of Linum usitatissimum L. under salinity stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:478-484. [PMID: 31005823 DOI: 10.1016/j.plaphy.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Salinity is a common environmental challenge limiting worldwide agricultural crop yield. Plants employ epigenetic regulatory strategies, such as DNA methylation which relatively allows rapid adaptation to new conditions in response to environmental stresses. Brassinosteroids (BRs) are a novel group of phytohormones recognized as transcription and translation regulators which are able to mitigate the impact of environmental stresses on the plants. In the current investigation, the influence of salinity and 24-epibrassinolide (24-epiBL) was investigated on the extent and pattern of cytosine DNA methylation using methylation-sensitive amplified polymorphisms (MSAP) technique in flax. Upon NaCl (150 mM) exposure, total methylation of CCGG sequences was decreased in comparison to control plants, while 24-epiBL (10-8 M) induced total methylation under salinity stress. Sequencing and analysis of six randomly selected MSAP fragments detected genes involved in various biological and molecular processes such as vitamine B1 biosynthesis, protein targeting and localization, post-translational modification and gene regulation. In conclusion, 24-epiBL seed priming could play critical role in regulation of cellular and biological processes in response to salt stress by epigenetic modification and induction of methylation.
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Affiliation(s)
- Leila Amraee
- Department of Biology, Faculty and Sciences, Urmia University, Urmia, Iran; Institute of Biotechnology, Urmia University, Urmia, Iran
| | - Fatemeh Rahmani
- Department of Biology, Faculty and Sciences, Urmia University, Urmia, Iran; Institute of Biotechnology, Urmia University, Urmia, Iran.
| | - Babak Abdollahi Mandoulakani
- Institute of Biotechnology, Urmia University, Urmia, Iran; Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
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13
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Shen J, Zhao Q, Wang X, Gao C, Zhu Y, Zeng Y, Jiang L. A plant Bro1 domain protein BRAF regulates multivesicular body biogenesis and membrane protein homeostasis. Nat Commun 2018; 9:3784. [PMID: 30224707 PMCID: PMC6141507 DOI: 10.1038/s41467-018-05913-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/06/2018] [Indexed: 02/07/2023] Open
Abstract
Plant development, defense, and many physiological processes rely on the endosomal sorting complex required for transport (ESCRT) machinery to control the homeostasis of membrane proteins by selective vacuolar degradation. Although ESCRT core components are conserved among higher eukaryotes, the regulators that control the function of the ESCRT machinery remain elusive. We recently identified a plant-specific ESCRT component, FREE1, that is essential for multivesicular body/prevacuolar compartment (MVB/PVC) biogenesis and vacuolar sorting of membrane proteins. Here we identify a plant-specific Bro1-domain protein BRAF, which regulates FREE1 recruitment to the MVB/PVC membrane by competitively binding to the ESCRT-I component Vps23. Altogether, we have successfully identified a role for BRAF, whose function as a unique evolutionary ESCRT regulator in orchestrating intraluminal vesicle formation in MVB/PVCs and the sorting of membrane proteins for degradation in plants makes it an important regulatory mechanism underlying the ESCRT machinery in higher eukaryotes.
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Affiliation(s)
- Jinbo Shen
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Linan, Hangzhou, 311300, China.
| | - Qiong Zhao
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xiangfeng Wang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Caiji Gao
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University (SCNU), Guangzhou, 510631, China
| | - Ying Zhu
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yonglun Zeng
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.
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14
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Carluccio AV, Prigigallo MI, Rosas-Diaz T, Lozano-Duran R, Stavolone L. S-acylation mediates Mungbean yellow mosaic virus AC4 localization to the plasma membrane and in turns gene silencing suppression. PLoS Pathog 2018; 14:e1007207. [PMID: 30067843 PMCID: PMC6089456 DOI: 10.1371/journal.ppat.1007207] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 08/13/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
RNA silencing plays a critical role in plant resistance against viruses. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that interfere with the cellular silencing machinery through various mechanisms not always well understood. We examined the role of Mungbean yellow mosaic virus (MYMV) AC4 and showed that it is essential for infectivity but not for virus replication. It acts as a determinant of pathogenicity and counteracts virus induced gene silencing by strongly suppressing the systemic phase of silencing whereas it does not interfere with local production of siRNA. We demonstrate the ability of AC4 to bind native 21-25 nt siRNAs in vitro by electrophoretic mobility shift assay. While most of the known VSRs have cytoplasmic localization, we observed that despite its hydrophilic nature and the absence of trans-membrane domain, MYMV AC4 specifically accumulates to the plasma membrane (PM). We show that AC4 binds to PM via S-palmitoylation, a process of post-translational modification regulating membrane-protein interactions, not known for plant viral protein before. When localized to the PM, AC4 strongly suppresses systemic silencing whereas its delocalization impairs VSR activity of the protein. We also show that AC4 interacts with the receptor-like kinase (RLK) BARELY ANY MERISTEM 1 (BAM1), a positive regulator of the cell-to-cell movement of RNAi. The absolute requirement of PM localization for direct silencing suppression activity of AC4 is novel and intriguing. We discuss a possible model of action: palmitoylated AC4 anchors to the PM by means of palmitate to acquire the optimal conformation to bind siRNAs, hinder their systemic movement and hence suppress the spread of the PTGS signal in the plant.
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Affiliation(s)
- Anna Vittoria Carluccio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle ricerche, Bari, Italia
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Maria Isabella Prigigallo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle ricerche, Bari, Italia
| | - Tabata Rosas-Diaz
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- Chinese Academy of Sciences–John Innes Centre Center of Excellence for Plant and Microbial Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Livia Stavolone
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle ricerche, Bari, Italia
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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15
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Murphy A. Plant membranes and border control. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3037-3040. [PMID: 28899083 PMCID: PMC5853494 DOI: 10.1093/jxb/erx229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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