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Muthego D, Moloi SJ, Brown AP, Goche T, Chivasa S, Ngara R. Exogenous abscisic acid treatment regulates protein secretion in sorghum cell suspension cultures. PLANT SIGNALING & BEHAVIOR 2023; 18:2291618. [PMID: 38100609 PMCID: PMC10730228 DOI: 10.1080/15592324.2023.2291618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Drought stress adversely affects plant growth, often leading to total crop failure. Upon sensing soil water deficits, plants switch on biosynthesis of abscisic acid (ABA), a stress hormone for drought adaptation. Here, we used exogenous ABA application to dark-grown sorghum cell suspension cultures as an experimental system to understand how a drought-tolerant crop responds to ABA. We evaluated intracellular and secreted proteins using isobaric tags for relative and absolute quantification. While the abundance of only ~ 7% (46 proteins) intracellular proteins changed in response to ABA, ~32% (82 proteins) of secreted proteins identified in this study were ABA responsive. This shows that the extracellular matrix is disproportionately targeted and suggests it plays a vital role in sorghum adaptation to drought. Extracellular proteins responsive to ABA were predominantly defense/detoxification and cell wall-modifying enzymes. We confirmed that sorghum plants exposed to drought stress activate genes encoding the same proteins identified in the in vitro cell culture system with ABA. Our results suggest that ABA activates defense and cell wall remodeling systems during stress response. This could underpin the success of sorghum adaptation to drought stress.
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Affiliation(s)
- Dakalo Muthego
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | - Sellwane J. Moloi
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | | | - Tatenda Goche
- Department of Biosciences, Durham University, Durham, UK
- Department of Crop Science, Bindura University of Science Education, Bindura, Zimbabwe
| | | | - Rudo Ngara
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
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2
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Burke R, McCabe A, Sonawane NR, Rathod MH, Whelan CV, McCabe PF, Kacprzyk J. Arabidopsis cell suspension culture and RNA sequencing reveal regulatory networks underlying plant-programmed cell death. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1465-1485. [PMID: 37531399 DOI: 10.1111/tpj.16407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023]
Abstract
Programmed cell death (PCD) facilitates selective, genetically controlled elimination of redundant, damaged, or infected cells. In plants, PCD is often an essential component of normal development and can mediate responses to abiotic and biotic stress stimuli. However, studying the transcriptional regulation of PCD is hindered by difficulties in sampling small groups of dying cells that are often buried within the bulk of living plant tissue. We addressed this challenge by using RNA sequencing and Arabidopsis thaliana suspension cells, a model system that allows precise monitoring of PCD rates. The use of three PCD-inducing treatments (salicylic acid, heat, and critical dilution), in combination with three cell death modulators (3-methyladenine, lanthanum chloride, and conditioned medium), enabled isolation of candidate core- and stimuli-specific PCD genes, inference of underlying regulatory networks and identification of putative transcriptional regulators of PCD in plants. This analysis underscored a disturbance of the cell cycle and mitochondrial retrograde signaling, and repression of pro-survival stress responses, as key elements of the PCD-associated transcriptional signature. Further, phenotyping of Arabidopsis T-DNA insertion mutants in selected candidate genes validated the potential of generated resources to identify novel genes involved in plant PCD pathways and/or stress tolerance.
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Affiliation(s)
- Rory Burke
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Aideen McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Neetu Ramesh Sonawane
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Meet Hasmukh Rathod
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Conor V Whelan
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Paul F McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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3
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Le Provost G, Brachi B, Lesur I, Lalanne C, Labadie K, Aury JM, Da Silva C, Postolache D, Leroy T, Plomion C. Gene expression and genetic divergence in oak species highlight adaptive genes to soil water constraints. PLANT PHYSIOLOGY 2022; 190:2466-2483. [PMID: 36066428 PMCID: PMC9706432 DOI: 10.1093/plphys/kiac420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Drought and waterlogging impede tree growth and may even lead to tree death. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species, pedunculate (PO; Quercus robur L.) and sessile oak (SO; Quercus petraea Matt. Lieb), have overlapping ranges, but their respective distribution are highly constrained by local soil conditions. These contrasting ecological preferences between two closely related and frequently hybridizing species constitute a powerful model to explore the functional bases of the adaptive responses in oak. We exposed oak seedlings to waterlogging and drought, conditions typically encountered by the two species in their respective habitats, and studied changes in gene expression in roots using RNA-seq. We identified genes that change in expression between treatments differentially depending on species. These "species × environment"-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with different expression between species independently of water conditions imposed. Surprisingly, this category included genes with functions consistent with a role in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the expressional candidate genes included numerous highly differentiated genetic markers between the two species. By combining transcriptomic analysis, gene annotation, pathway analyses, as well as genome scan for genetic differentiation among species, we were able to highlight loci likely involved in adaptation of the two species to their respective ecological niches.
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Affiliation(s)
| | | | - Isabelle Lesur
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, F-33610, France
- Helix Venture, Mérignac, F-33700, France
| | | | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Dragos Postolache
- National Institute for Research and Development in Forestry “Marin Drăcea”, Cluj Napoca Research Station, Cluj-Napoca, 400202, Romania
| | - Thibault Leroy
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, F-33610, France
- IRHS-UMR1345, Université d’Angers, INRAE, Institut Agro, Beaucouzé, 49071, France
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4
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Goodman HL, Kroon JTM, Tomé DFA, Hamilton JMU, Alqarni AO, Chivasa S. Extracellular ATP targets Arabidopsis RIBONUCLEASE 1 to suppress mycotoxin stress-induced cell death. THE NEW PHYTOLOGIST 2022; 235:1531-1542. [PMID: 35524456 PMCID: PMC9545236 DOI: 10.1111/nph.18211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Extracellular ATP is a purinergic signal with important functions in regulating plant growth and stress-adaptive responses, including programmed cell death. While signalling events proximate to receptor activation at the plasma membrane have been characterised, downstream protein targets and the mechanism of cell death activation/regulation are unknown. We designed a proteomic screen to identify ATP-responsive proteins in Arabidopsis cell cultures exposed to mycotoxin stress via fumonisin B1 (FB1) application. Arabidopsis RIBONUCLEASE 1 (RNS1) was identified by the screen, and transgenic plants overexpressing native RNS1 showed greater susceptibility to FB1, while a gene knockout rns1 mutant and antisense RNS1 transgenic plants were resistant to FB1-induced cell death. Native RNS1 complemented rns1 mutants and restored the cell death response to FB1, while a catalytically inactive version of the ribonuclease could not. The FB1 resistance of salicylic acid (SA)-depleted nahG-expressing plants was abolished by transformation with native RNS1, but not the catalytically dead version. The mechanism of FB1-induced cell death is activation of RNS1-dependent RNA cleavage, which is blocked by ATP via RNS1 suppression, or enhanced by SA through induction of RNS1 expression. Our study reveals RNS1 as a previously unknown convergence point of ATP and SA signalling in the regulation of stress-induced cell death.
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Affiliation(s)
| | | | | | | | - Ali O. Alqarni
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Stephen Chivasa
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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5
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Wang X, Yan K, Fu M, Liang S, Zhao H, Fu C, Yang L, Song Z, Sun D, Wan C. EspF of Enterohemorrhagic Escherichia coli Enhances Apoptosis via Endoplasmic Reticulum Stress in Intestinal Epithelial Cells: An Isobaric Tags for Relative and Absolute Quantitation-Based Comparative Proteomic Analysis. Front Microbiol 2022; 13:900919. [PMID: 35847082 PMCID: PMC9279134 DOI: 10.3389/fmicb.2022.900919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
There have been large foodborne outbreaks related to Enterohemorrhagic Escherichia coli (EHEC) around the world. Among its virulence proteins, the EspF encoded by locus of enterocyte effacement is one of the most known functional effector proteins. In this research, we infected the HT-29 cells with the EHEC wild type strain and EspF-deficient EHEC strain. Via the emerging technique isobaric tags for relative and absolute quantitation (iTRAQ), we explored the pathogenic characteristics of EspF within host cells. Our data showed that the differences regarding cellular responses mainly contained immune regulation, protein synthesis, signal transduction, cellular assembly and organization, endoplasmic reticulum (ER) stress, and apoptosis. Notably, compared with the EspF-deficient strain, the protein processing in the ER and ribosome were upregulated during wild type (WT) infection. Our findings proved that the EspF of Enterohemorrhagic Escherichia coli induced ER stress in intestinal epithelial cells; the ER stress-dependent apoptosis pathway was also activated within the host cells. This study provides insight into the virulence mechanism of protein EspF, which will deepen our general understanding of A/E pathogens and their interaction with host proteins.
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Affiliation(s)
- Xiangyu Wang
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Kaina Yan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Muqing Fu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Song Liang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Haiyi Zhao
- Genecreate Biological Engineering Co., Ltd., National Bio-industry Base, Wuhan, China
| | - Changzhu Fu
- MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Lan Yang
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Zhihong Song
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Dayong Sun
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- *Correspondence: Dayong Sun,
| | - Chengsong Wan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Chengsong Wan,
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6
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Huerta-Olalde AM, Hernández-García A, López-Gómez R, Fernández-Pavía SP, Zavala-Páramo MG, Salgado-Garciglia R. In vitro selection of blackberry ( Rubus fruticosus 'Tupy') plants resistant to Botrytis cinerea using gamma ray-irradiated shoot tips. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:165-171. [PMID: 35937526 PMCID: PMC9300433 DOI: 10.5511/plantbiotechnology.22.0312b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/12/2022] [Indexed: 06/15/2023]
Abstract
Blackberry is an economically important crop in Mexico, and its yield is substantially reduced by gray mold, a disease caused by Botrytis cinerea. One of the means to obtain B. cinerea-resistant plants is gamma irradiation. Shoot tips of in vitro-micropropagated blackberry plants (Rubus fruticosus 'Tupy') were irradiated with five doses of Cobalt-60 gamma radiation (0, 15, 30, 45, and 60 Gy) and cultured on Murashige and Skoog basal medium containing 1.0 mg l-1 benzylaminopurine and 0.06 mg l-1 indole-3-butyric acid (MSB medium). After 28 days of culture, survival was evaluated to determine mean lethal dose (LD50), and 200 shoots were further irradiated at the determined LD50 (30.8 Gy). After 28 days, the surviving shoots were micropropagated on MSB medium for 60 days. Non-irradiated shoots were screened for the in vitro selection of resistant B. cinerea, exposing them to different concentrations of sterile culture filtrate of B. cinerea (0, 2, 4, 6, 8, and 10 g l-1) for 28 days to determine mean lethal concentration (LC50), and the irradiated surviving shoots were further exposed to the determined LC50 (4.6 g l-1). Three surviving lines (rfgum5, rfgum6, and rfgum17) that did not present changes compared with the control shoots were micropropagated to obtain plantlets, which were further subjected to in vitro resistance assays using detached leaves inoculated with B. cinerea (1×103 spores ml-1). Plants of rfgum5 and rfgum6 mutant lines were highly resistant and presented similar growth to control plants. Therefore, this methodology is useful to obtain B. cinerea-resistant blackberry plants.
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Affiliation(s)
- Ana Maria Huerta-Olalde
- Instituto de Investigaciones Químico-Biológicas, Edif. B3, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Ciudad Universitaria, Ave. Francisco. J. Múgica S/N, C.P. 58030, Morelia, Michoacán, México
| | - Alejandra Hernández-García
- Instituto de Investigaciones Químico-Biológicas, Edif. B3, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Ciudad Universitaria, Ave. Francisco. J. Múgica S/N, C.P. 58030, Morelia, Michoacán, México
| | - Rodolfo López-Gómez
- Instituto de Investigaciones Químico-Biológicas, Edif. B3, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Ciudad Universitaria, Ave. Francisco. J. Múgica S/N, C.P. 58030, Morelia, Michoacán, México
| | - Sylvia Patricia Fernández-Pavía
- Instituto de Investigaciones Agropecuarias y Forestales, UMSNH, Km. 9.5 Carretera Morelia-Zinapécuaro, C.P. 58880, Tarímbaro, Michoacán, México
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, UMSNH, C.P. 58194, Morelia, Michoacán, México
| | - Rafael Salgado-Garciglia
- Instituto de Investigaciones Químico-Biológicas, Edif. B3, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Ciudad Universitaria, Ave. Francisco. J. Múgica S/N, C.P. 58030, Morelia, Michoacán, México
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7
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Smith SJ, Goodman H, Kroon JTM, Brown AP, Simon WJ, Chivasa S. Isolation of Arabidopsis extracellular ATP binding proteins by affinity proteomics and identification of PHOSPHOLIPASE C-LIKE 1 as an extracellular protein essential for fumonisin B1 toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1387-1400. [PMID: 33735457 DOI: 10.1111/tpj.15243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 05/21/2023]
Abstract
ATP is secreted to the extracellular matrix, where it activates plasma membrane receptors for controlling plant growth and stress-adaptive processes. DOES NOT RESPOND TO NUCLEOTIDES 1 (DORN1), was the first plant ATP receptor to be identified but key downstream proteins remain sought after. Here, we identified 120 proteins secreted by Arabidopsis cell cultures and screened them for putative stress-responsive proteins using ATP-affinity purification. We report three Arabidopsis proteins isolated by ATP-affinity: PEROXIDASE 52, SUBTILASE-LIKE SERINE PROTEASE 1.7 and PHOSPHOLIPASE C-LIKE 1. In wild-type Arabidopsis, the expression of genes encoding all three proteins responded to fumonisin B1, a cell death-activating mycotoxin. The expression of PEROXIDASE 52 and PHOSPHOLIPASE C-LIKE 1 was altered in fumonisin B1-resistant salicylic acid induction-deficient (sid2) mutants. Exposure to fumonisin B1 suppressed PHOSPHOLIPASE C-LIKE 1 expression in sid2 mutants, suggesting that the inactivation of this gene might provide mycotoxin tolerance. Accordingly, gene knockout mutants of PHOSPHOLIPASE C-LIKE 1 were resistant to fumonisin B1-induced death. The activation of PHOSPHOLIPASE C-LIKE 1 gene expression by exogenous ATP was not blocked in dorn1 loss-of-function mutants, indicating that DORN1 is not required. Furthermore, exogenous ATP rescued both the wild type and the dorn1 mutants from fumonisin-B1 toxicity, suggesting that different ATP receptor(s) are operational in this process. Our results point to the existence of additional plant ATP receptor(s) and provide crucial downstream targets for use in designing screens to identify these receptors. Finally, PHOSPHOLIPASE C-LIKE 1 serves as a convergence point for fumonisin B1 and extracellular ATP signalling, and functions in the Arabidopsis stress response to fumonisin B1.
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Affiliation(s)
- Sarah J Smith
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Heather Goodman
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Johan T M Kroon
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Adrian P Brown
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - William J Simon
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Stephen Chivasa
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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8
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Zeng HY, Li CY, Yao N. Fumonisin B1: A Tool for Exploring the Multiple Functions of Sphingolipids in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:600458. [PMID: 33193556 PMCID: PMC7652989 DOI: 10.3389/fpls.2020.600458] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/05/2020] [Indexed: 05/25/2023]
Abstract
Fumonisin toxins are produced by Fusarium fungal pathogens. Fumonisins are structural analogs of sphingosine and potent inhibitors of ceramide synthases (CerSs); they disrupt sphingolipid metabolism and cause disease in plants and animals. Over the past three decades, researchers have used fumonisin B1 (FB1), the most common fumonisin, as a probe to investigate sphingolipid metabolism in yeast and animals. Although the physiological effects of FB1 in plants have yet to be investigated in detail, forward and reverse genetic approaches have revealed many genes involved in these processes. In this review, we discuss the intricate network of signaling pathways affected by FB1, including changes in sphingolipid metabolism and the effects of these changes, with a focus on our current understanding of the multiple effects of FB1 on plant cell death and plant growth. We analyze the major findings that highlight the connections between sphingolipid metabolism and FB1-induced signaling, and we point out where additional research is needed to fill the gaps in our understanding of FB1-induced signaling pathways in plants.
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Affiliation(s)
- Hong-Yun Zeng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chun-Yu Li
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Nan Yao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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9
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Ngcala MG, Goche T, Brown AP, Chivasa S, Ngara R. Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures. Proteomes 2020; 8:29. [PMID: 33105781 PMCID: PMC7709130 DOI: 10.3390/proteomes8040029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 01/13/2023] Open
Abstract
Plants reprogram gene expression as an adaptive response to survive high temperatures. While the identity and functions of intracellular heat stress-responsive proteins have been extensively studied, the heat response of proteins secreted to the extracellular matrix is unknown. Here, we used Sorghum bicolor, a species adapted for growth in hot climates, to investigate the extracellular heat-induced responses. When exposed to 40 C for 72 h, heat-sensitive Arabidopsis cell suspension cultures died, while ICSB338 sorghum cell cultures survived by activation of a transcriptional response characterized by the induction of HSP70 and HSP90 genes. Quantitative proteomic analysis of proteins recovered from cell culture medium revealed specific heat stress-induced protein accumulation within the sorghum secretome. Of the 265 secreted proteins identified, 31 responded to heat (2-fold change), with 84% possessing a predicted signal peptide for targeting to the classical secretory pathway. The differentially accumulated proteins have putative functions in metabolism, detoxification, and protein modifications. A germin (SORBI_3003G427700) was highly heat-inducible at both protein and gene level. Overall, our study reveals new insights into sorghum responses to heat and provides a useful resource of extracellular proteins that could serve as targets for developing thermotolerant crops. Data are available via ProteomeXchange with identifier PXD021536.
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Affiliation(s)
- Mamosa G. Ngcala
- Department of Plant Sciences, Qwaqwa campus, University of the Free State, Phuthadithjaba 9866, South Africa;
| | - Tatenda Goche
- Department of Crop Sciences, Epoch Mine Campus, Gwanda State University, Filabusi, Zimbabwe;
| | - Adrian P. Brown
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (A.P.B.); (S.C.)
| | - Stephen Chivasa
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (A.P.B.); (S.C.)
| | - Rudo Ngara
- Department of Plant Sciences, Qwaqwa campus, University of the Free State, Phuthadithjaba 9866, South Africa;
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10
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Goche T, Shargie NG, Cummins I, Brown AP, Chivasa S, Ngara R. Comparative physiological and root proteome analyses of two sorghum varieties responding to water limitation. Sci Rep 2020; 10:11835. [PMID: 32678202 PMCID: PMC7366710 DOI: 10.1038/s41598-020-68735-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/09/2020] [Indexed: 01/31/2023] Open
Abstract
When exposed to drought stress many plants reprogram their gene expression to activate adaptive biochemical and physiological responses for survival. However, most of the well-studied adaptive responses are common between drought-sensitive and drought-tolerant species, making it difficult to identify the key mechanisms underpinning successful drought tolerance in crops. We developed a sorghum experimental system that compares between drought-sensitive (ICSB338) and enhanced drought-tolerant (SA1441) varieties. We show that sorghum activates a swift and robust stomatal shutdown to preserve leaf water content when water stress has been sensed. Water uptake is enhanced via increasing root cell water potential through the rapid biosynthesis of predominantly glycine betaine and an increased root-to-shoot ratio to explore more soil volume for water. In addition to stomatal responses, there is a prompt accumulation of proline in leaves and effective protection of chlorophyll during periods of water limitation. Root and stomatal functions rapidly recover from water limitation (within 24 h of re-watering) in the drought-tolerant variety, but recovery is impaired in the drought-sensitive sorghum variety. Analysis of the root proteome revealed complex protein networks that possibly underpin sorghum responses to water limitation. Common and unique protein changes between the two sorghum varieties provide new targets for future use in investigating sorghum drought tolerance.
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Affiliation(s)
- Tatenda Goche
- Department of Plant Sciences, University of the Free State, Qwaqwa Campus, P. Bag X13, Phuthaditjhaba, South Africa
| | - Nemera G Shargie
- Agricultural Research Council-Grain Crops Institute, P. Bag X1251, Potchefstroom, 2520, South Africa
| | - Ian Cummins
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Adrian P Brown
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Stephen Chivasa
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Rudo Ngara
- Department of Plant Sciences, University of the Free State, Qwaqwa Campus, P. Bag X13, Phuthaditjhaba, South Africa.
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11
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Chivasa S, Goodman HL. Stress-adaptive gene discovery by exploiting collective decision-making of decentralized plant response systems. THE NEW PHYTOLOGIST 2020; 225:2307-2313. [PMID: 31625607 DOI: 10.1111/nph.16273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Despite having a network of cytoplasmic interconnections (plasmodesmata) facilitating rapid exchange of metabolites and signal molecules, plant cells use the extracellular matrix as an alternative route for cell-cell communication. The need for extracellular signalling in plasmodesmata-networked tissues is baffling. A hypothesis is proposed that this phenomenon defines the plant extracellular matrix as a 'democratic space' for collective decision-making in a decentralized system, similar to quorum-sensing in bacteria. Extracellular communication enables signal integration and coordination across several cell layers through ligand-activated plasma membrane receptors. Recent results from drought stress-adaptive responses and light-mediated signalling in cell death activation show operational utility of this decision-making process. Opportunities are discussed for new innovations in drought gene discovery using platforms targeting the extracellular matrix.
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Affiliation(s)
- Stephen Chivasa
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
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12
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Zhou K. Glycosylphosphatidylinositol-Anchored Proteins in Arabidopsis and One of Their Common Roles in Signaling Transduction. FRONTIERS IN PLANT SCIENCE 2019; 10:1022. [PMID: 31555307 PMCID: PMC6726743 DOI: 10.3389/fpls.2019.01022] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/22/2019] [Indexed: 05/17/2023]
Abstract
Diverse proteins are found modified with glycosylphosphatidylinositol (GPI) at their carboxyl terminus in eukaryotes, which allows them to associate with membrane lipid bilayers and anchor on the external surface of the plasma membrane. GPI-anchored proteins (GPI-APs) play crucial roles in various processes, and more and more GPI-APs have been identified and studied. In this review, previous genomic and proteomic predictions of GPI-APs in Arabidopsis have been updated, which reveal their high abundance and complexity. From studies of individual GPI-APs in Arabidopsis, certain GPI-APs have been found associated with partner receptor-like kinases (RLKs), targeting RLKs to their subcellular localization and helping to recognize extracellular signaling polypeptide ligands. Interestingly, the association might also be involved in ligand selection. The analyses suggest that GPI-APs are essential and widely involved in signal transduction through association with RLKs.
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Gao F, Liu X, Shen Z, Jia X, He H, Gao J, Wu J, Jiang C, Zhou H, Wang Y. Andrographolide Sulfonate Attenuates Acute Lung Injury by Reducing Expression of Myeloperoxidase and Neutrophil-Derived Proteases in Mice. Front Physiol 2018; 9:939. [PMID: 30174607 PMCID: PMC6107831 DOI: 10.3389/fphys.2018.00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
Andrographolide sulfonate (Andro-S), a sulfonation derivative of andrographolide, is known to be effective in treating inflammation-related diseases, while the underlying mechanisms and global protein alterations in response to Andro-S remain unknown. This study aimed to investigate the pharmacological effects and potential targets of Andro-S in a murine model of acute lung injury (ALI). ALI was induced by aerosolized lipopolysaccharide (LPS) exposure before treatment with Andro-S. Inflammatory state of each treatment group was determined by histological analysis and quantification of inflammatory markers. Differentially expressed proteins in lung tissues were identified by an iTRAQ-based quantitative proteomic approach and further confirmed by immunohistochemistry analysis. Administration of Andro-S alleviated LPS-induced histological changes in the lung and reduced the expression of inflammatory markers in serum, bronchoalveolar fluid and lung tissues. Proteomic analysis identified 31 differentially expressed proteins from a total of 2,234 quantified proteins in the lung. According to bioinformatics analysis, neutrophil elastase (ELANE), cathepsin G (CTSG) and myeloperoxidase (MPO), three neutrophil-derived proteases related to immune system process and defense responses to fungi were chosen as potential targets of Andro-S. Further immunohistochemistry analysis confirmed the inhibitory effects of Andro-S on LPS-induced ELANE, CTSG and MPO up-regulation. These results indicate that Andro-S suppressed the severity of LPS-induced ALI, possibly by attenuating the expression of and neutrophil-derived proteases.
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Affiliation(s)
- Fei Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Ziying Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaohui Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Jianhong Wu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Chunhong Jiang
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Ganzhou, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Yiping Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
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14
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Identifying differentially expressed proteins in sorghum cell cultures exposed to osmotic stress. Sci Rep 2018; 8:8671. [PMID: 29875393 PMCID: PMC5989219 DOI: 10.1038/s41598-018-27003-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/15/2018] [Indexed: 11/28/2022] Open
Abstract
Drought stress triggers remarkable physiological changes and growth impediments, which significantly diminish plant biomass and crop yield. However, certain plant species show notable resilience, maintaining nearly normal yields under severe water deficits. For example, sorghum is a naturally drought-tolerant crop, which is ideal for studying plant adaptive responses to drought. Here we used sorbitol treatments to simulate drought-induced osmotic stress in sorghum cell suspension cultures and analysed fractions enriched for extracellular matrix proteins using isobaric tags for relative and absolute quantification technology. Sorbitol induced an overall increase in protein secretion, with putative redox proteins, proteases, and glycosyl hydrolases featuring prominently among the responsive proteins. Gene expression analysis of selected candidates revealed regulation at the transcriptional level. There was a notable differential gene expression between drought-tolerant and drought-sensitive sorghum varieties for some of the candidates. This study shows that protein secretion is a major component of the sorghum response to osmotic stress. Additionally, our data provide candidate genes, which may have putative functions in sorghum drought tolerance, and offer a pool of genes that could be developed as potential biomarkers for rapid identification of drought tolerant lines in plant breeding programs.
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15
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Chen W, Wan S, Shen L, Zhou Y, Huang C, Chu P, Guan R. Histological, Physiological, and Comparative Proteomic Analyses Provide Insights into Leaf Rolling in Brassica napus. J Proteome Res 2018; 17:1761-1772. [PMID: 29693398 DOI: 10.1021/acs.jproteome.7b00744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Moderate leaf rolling is important in ideotype breeding, as it improves photosynthetic efficiency and therefore increases crop yields. To understand the regulatory network of leaf rolling in Brassica napus, a down-curved leaf mutant ( Bndcl1) has been investigated. Physiological analyses indicated that the chlorophyll contents and antioxidant enzyme activities were remarkably increased and the photosynthetic performance was significantly improved in Bndcl1. Consistent with these findings, 943 differentially accumulated proteins (DAPs) were identified in the Bndcl1 mutant and its wild-type plants using iTRAQ-based comparative proteomic analyses. Enrichment analysis of proteins with higher abundance in Bndcl1 revealed that the functional category "photosynthesis" was significantly overrepresented. Moreover, proteins associated with oxidative stress response and photosystem II repairing were also up-accumulated in Bndcl1, which might help the mutant to sustain the photosynthetic efficiency under unfavorable conditions. Histological observation showed that the mutant displayed defects in adaxial-abaxial patterning. Important DAPs associated with leaf polarity establishment were detected in Bndcl1, including ribosomal proteins, proteins involved in post-transcriptional gene silencing, and proteins related to brassinosteroid. Together, our findings may help clarify the mechanisms underlying leaf rolling and its physiological effects on plants and may facilitate ideotype breeding in Brassica napus.
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Affiliation(s)
- Wenjing Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Linkui Shen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Ying Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Chengwei Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Pu Chu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
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16
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Huang R, Chen Z, He L, He N, Xi Z, Li Z, Deng Y, Zeng X. Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application. Theranostics 2017; 7:3559-3572. [PMID: 28912895 PMCID: PMC5596443 DOI: 10.7150/thno.20797] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
There is a critical need for the discovery of novel biomarkers for early detection and targeted therapy of cancer, a major cause of deaths worldwide. In this respect, proteomic technologies, such as mass spectrometry (MS), enable the identification of pathologically significant proteins in various types of samples. MS is capable of high-throughput profiling of complex biological samples including blood, tissues, urine, milk, and cells. MS-assisted proteomics has contributed to the development of cancer biomarkers that may form the foundation for new clinical tests. It can also aid in elucidating the molecular mechanisms underlying cancer. In this review, we discuss MS principles and instrumentation as well as approaches in MS-based proteomics, which have been employed in the development of potential biomarkers. Furthermore, the challenges in validation of MS biomarkers for their use in clinical practice are also reviewed.
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Affiliation(s)
- Rongrong Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongsi Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lei He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Zhijiang Xi
- School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Zhiyang Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Xin Zeng
- Nanjing Maternity and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
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17
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González-Torralva F, Brown AP, Chivasa S. Comparative proteomic analysis of horseweed (Conyza canadensis) biotypes identifies candidate proteins for glyphosate resistance. Sci Rep 2017; 7:42565. [PMID: 28198407 PMCID: PMC5309786 DOI: 10.1038/srep42565] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/10/2017] [Indexed: 12/31/2022] Open
Abstract
Emergence of glyphosate-resistant horseweed (Conyza canadensis) biotypes is an example of how unrelenting use of a single mode of action herbicide in agricultural weed control drives genetic adaptation in targeted species. While in other weeds glyphosate resistance arose from target site mutation or target gene amplification, the resistance mechanism in horseweed uses neither of these, being instead linked to reduced herbicide uptake and/or translocation. The molecular components underpinning horseweed glyphosate-resistance remain unknown. Here, we used an in vitro leaf disc system for comparative analysis of proteins extracted from control and glyphosate-treated tissues of glyphosate-resistant and glyphosate-susceptible biotypes. Analysis of shikimic acid accumulation, ABC-transporter gene expression, and cell death were used to select a suitable glyphosate concentration and sampling time for enriching proteins pivotal to glyphosate resistance. Protein gel analysis and mass spectrometry identified mainly chloroplast proteins differentially expressed between the biotypes before and after glyphosate treatment. Chloroplasts are the organelles in which the shikimate pathway, which is targeted by glyphosate, is located. Calvin cycle enzymes and proteins of unknown function were among the proteins identified. Our study provides candidate proteins that could be pivotal in engendering resistance and implicates chloroplasts as the primary sites driving glyphosate-resistance in horseweed.
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Affiliation(s)
| | - Adrian P. Brown
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Stephen Chivasa
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, United Kingdom
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18
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Dong CJ, Cao N, Li L, Shang QM. Quantitative Proteomic Profiling of Early and Late Responses to Salicylic Acid in Cucumber Leaves. PLoS One 2016; 11:e0161395. [PMID: 27551830 PMCID: PMC4995040 DOI: 10.1371/journal.pone.0161395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/04/2016] [Indexed: 11/18/2022] Open
Abstract
Salicylic acid (SA) is an important phytohormone that plays vital regulatory roles in plant growth, development, and stress responses. However, studies on the molecular mechanism of SA, especially during the early SA responses, are lagging behind. In this study, we initiated a comprehensive isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis to explore the early and late SA-responsive proteins in leaves of cucumber (Cucumis sativus L.) seedlings. Upon SA application through the roots, endogenous SA accumulated in cucumber leaves. By assaying the changes in marker gene expression and photosynthetic rate, we collected samples at 12 h and 72 h post treatment (hpt) to profile the early and late SA responsiveness, respectively. The iTRAQ assay followed by tandem mass spectrometry revealed 135 differentially expressed proteins (DEPs) at 12 hpt and 301 DEPs at 72 hpt. The functional categories for these SA-responsive proteins included in a variety of biochemical processes, including photosynthesis, redox homeostasis, carbohydrate and energy metabolism, lipid metabolism, transport, protein folding and modification, proteolysis, cell wall organization, and the secondary phenylpropanoid pathway. Conclusively, based on the abundant changes of these DEPs, together with their putative functions, we proposed a possible SA-responsive protein network. It appears that SA could elicit reactive oxygen species (ROS) production via enhancing the photosynthetic electron transferring, and then confer some growth-promoting and stress-priming effects on cells during the late phase, including enhanced photosynthesis and ROS scavenging, altered carbon metabolic flux for the biosynthesis of amino acids and nucleotides, and cell wall reorganization. Overall, the present iTRAQ assay provides higher proteome coverage and deepened our understanding of the molecular basis of SA-responses.
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Affiliation(s)
- Chun-Juan Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences,Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Beijing, 100081, P.R.China
- * E-mail: (CJD); (QMS)
| | - Ning Cao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences,Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Beijing, 100081, P.R.China
| | - Liang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences,Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Beijing, 100081, P.R.China
| | - Qing-Mao Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences,Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Beijing, 100081, P.R.China
- * E-mail: (CJD); (QMS)
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19
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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20
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Regulatory Proteolysis in Arabidopsis-Pathogen Interactions. Int J Mol Sci 2015; 16:23177-94. [PMID: 26404238 PMCID: PMC4632692 DOI: 10.3390/ijms161023177] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/07/2015] [Accepted: 09/15/2015] [Indexed: 11/16/2022] Open
Abstract
Approximately two and a half percent of protein coding genes in Arabidopsis encode enzymes with known or putative proteolytic activity. Proteases possess not only common housekeeping functions by recycling nonfunctional proteins. By irreversibly cleaving other proteins, they regulate crucial developmental processes and control responses to environmental changes. Regulatory proteolysis is also indispensable in interactions between plants and their microbial pathogens. Proteolytic cleavage is simultaneously used both by plant cells, to recognize and inactivate invading pathogens, and by microbes, to overcome the immune system of the plant and successfully colonize host cells. In this review, we present available results on the group of proteases in the model plant Arabidopsis thaliana whose functions in microbial pathogenesis were confirmed. Pathogen-derived proteolytic factors are also discussed when they are involved in the cleavage of host metabolites. Considering the wealth of review papers available in the field of the ubiquitin-26S proteasome system results on the ubiquitin cascade are not presented. Arabidopsis and its pathogens are conferred with abundant sets of proteases. This review compiles a list of those that are apparently involved in an interaction between the plant and its pathogens, also presenting their molecular partners when available.
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