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Liu Y, Jackson E, Liu X, Huang X, van der Hoorn RAL, Zhang Y, Li X. Proteolysis in plant immunity. THE PLANT CELL 2024; 36:3099-3115. [PMID: 38723588 PMCID: PMC11371161 DOI: 10.1093/plcell/koae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/23/2024] [Indexed: 09/05/2024]
Abstract
Compared with transcription and translation, protein degradation machineries can act faster and be targeted to different subcellular compartments, enabling immediate regulation of signaling events. It is therefore not surprising that proteolysis has been used extensively to control homeostasis of key regulators in different biological processes and pathways. Over the past decades, numerous studies have shown that proteolysis, where proteins are broken down to peptides or amino acids through ubiquitin-mediated degradation systems and proteases, is a key regulatory mechanism to control plant immunity output. Here, we briefly summarize the roles various proteases play during defence activation, focusing on recent findings. We also update the latest progress of ubiquitin-mediated degradation systems in modulating immunity by targeting plant membrane-localized pattern recognition receptors, intracellular nucleotide-binding domain leucine-rich repeat receptors, and downstream signaling components. Additionally, we highlight recent studies showcasing the importance of proteolysis in maintaining broad-spectrum resistance without obvious yield reduction, opening new directions for engineering elite crops that are resistant to a wide range of pathogens with high yield.
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Affiliation(s)
- Yanan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Edan Jackson
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xueru Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xingchuan Huang
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan 641100, China
| | | | - Yuelin Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Ngwenya SP, Moloi SJ, Shargie NG, Brown AP, Chivasa S, Ngara R. Regulation of Proline Accumulation and Protein Secretion in Sorghum under Combined Osmotic and Heat Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1874. [PMID: 38999714 PMCID: PMC11244414 DOI: 10.3390/plants13131874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024]
Abstract
Plants reprogramme their proteome to alter cellular metabolism for effective stress adaptation. Intracellular proteomic responses have been extensively studied, and the extracellular matrix stands as a key hub where peptide signals are generated/processed to trigger critical adaptive signal transduction cascades inaugurated at the cell surface. Therefore, it is important to study the plant extracellular proteome to understand its role in plant development and stress response. This study examined changes in the soluble extracellular sub-proteome of sorghum cell cultures exposed to a combination of sorbitol-induced osmotic stress and heat at 40 °C. The combined stress significantly reduced metabolic activity and altered protein secretion. While cells treated with osmotic stress alone had elevated proline content, the osmoprotectant in the combined treatment remained unchanged, confirming that sorghum cells exposed to combined stress utilise adaptive processes distinct from those invoked by the single stresses applied separately. Reactive oxygen species (ROS)-metabolising proteins and proteases dominated differentially expressed proteins identified in cells subjected to combined stress. ROS-generating peroxidases were suppressed, while ROS-degrading proteins were upregulated for protection from oxidative damage. Overall, our study provides protein candidates that could be used to develop crops better suited for an increasingly hot and dry climate.
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Affiliation(s)
- Samkelisiwe P Ngwenya
- Department of Plant Sciences, University of the Free State, Qwaqwa Campus, P. Bag X13, Phuthaditjhaba 9866, South Africa
| | - Sellwane J Moloi
- Department of Plant Sciences, University of the Free State, Qwaqwa Campus, P. Bag X13, Phuthaditjhaba 9866, South Africa
| | - Nemera G Shargie
- Agricultural Research Council-Grain Crops Institute, P. Bag X1251, Potchefstroom 2520, South Africa
| | - 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 9866, South Africa
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Sedaghatmehr M, Balazadeh S. Autophagy: a key player in the recovery of plants from heat stress. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2246-2255. [PMID: 38236036 PMCID: PMC11016841 DOI: 10.1093/jxb/erae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/15/2024] [Indexed: 01/19/2024]
Abstract
Plants can be primed to withstand otherwise lethal heat stress (HS) through exposure to a preceding temporary and mild HS, commonly known as the 'thermopriming stimulus'. Plants have also evolved mechanisms to establish 'memories' of a previous stress encounter, or to reset their physiology to the original cellular state once the stress has ended. The priming stimulus triggers a widespread change of transcripts, proteins, and metabolites, which is crucial for maintaining the memory state but may not be required for growth and development under optimal conditions or may even be harmful. In such a scenario, recycling mechanisms such as autophagy are crucial for re-establishing cellular homeostasis and optimizing resource use for post-stress growth. While pivotal for eliminating heat-induced protein aggregates and protecting plants from the harmful impact of HS, recent evidence implies that autophagy also breaks down heat-induced protective macromolecules, including heat shock proteins, functioning as a resetting mechanism during the recovery from mild HS. This review provides an overview of the latest advances in understanding the multifaceted functions of autophagy in HS responses, with a specific emphasis on its roles in recovery from mild HS, and the modulation of HS memory.
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Affiliation(s)
- Mastoureh Sedaghatmehr
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Salma Balazadeh
- Leiden University, PO Box 9500, 2300 RA, Leiden, The Netherlands
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Ahkami AH. Systems biology of root development in Populus: Review and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111818. [PMID: 37567482 DOI: 10.1016/j.plantsci.2023.111818] [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: 02/06/2023] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.
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Affiliation(s)
- Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
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Moloi SJ, Ngara R. The roles of plant proteases and protease inhibitors in drought response: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1165845. [PMID: 37143877 PMCID: PMC10151539 DOI: 10.3389/fpls.2023.1165845] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/30/2023] [Indexed: 05/06/2023]
Abstract
Upon exposure to drought, plants undergo complex signal transduction events with concomitant changes in the expression of genes, proteins and metabolites. For example, proteomics studies continue to identify multitudes of drought-responsive proteins with diverse roles in drought adaptation. Among these are protein degradation processes that activate enzymes and signalling peptides, recycle nitrogen sources, and maintain protein turnover and homeostasis under stressful environments. Here, we review the differential expression and functional activities of plant protease and protease inhibitor proteins under drought stress, mainly focusing on comparative studies involving genotypes of contrasting drought phenotypes. We further explore studies of transgenic plants either overexpressing or repressing proteases or their inhibitors under drought conditions and discuss the potential roles of these transgenes in drought response. Overall, the review highlights the integral role of protein degradation during plant survival under water deficits, irrespective of the genotypes' level of drought resilience. However, drought-sensitive genotypes exhibit higher proteolytic activities, while drought-tolerant genotypes tend to protect proteins from degradation by expressing more protease inhibitors. In addition, transgenic plant biology studies implicate proteases and protease inhibitors in various other physiological functions under drought stress. These include the regulation of stomatal closure, maintenance of relative water content, phytohormonal signalling systems including abscisic acid (ABA) signalling, and the induction of ABA-related stress genes, all of which are essential for maintaining cellular homeostasis under water deficits. Therefore, more validation studies are required to explore the various functions of proteases and their inhibitors under water limitation and their contributions towards drought adaptation.
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Yang K, Xiao W. Functions and mechanisms of the Ubc13-UEV complex and lysine 63-linked polyubiquitination in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5372-5387. [PMID: 35640002 DOI: 10.1093/jxb/erac239] [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: 02/02/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitination is one of the best-known post-translational modifications in eukaryotes, in which different linkage types of polyubiquitination result in different outputs of the target proteins. Distinct from the well-characterized K48-linked polyubiquitination that usually serves as a signal for degradation of the target protein, K63-linked polyubiquitination often requires a unique E2 heterodimer Ubc13-UEV and alters the target protein activity instead of marking it for degradation. This review focuses on recent advances on the roles of Ubc13-UEV-mediated K63-linked polyubiquitination in plant growth, development, and response to environmental stresses.
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Affiliation(s)
- Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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Schiavon M, Nardi S, Pilon-Smits EAH, Dall’Acqua S. Foliar selenium fertilization alters the content of dietary phytochemicals in two rocket species. FRONTIERS IN PLANT SCIENCE 2022; 13:987935. [PMID: 36119625 PMCID: PMC9470978 DOI: 10.3389/fpls.2022.987935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Biofortification is the process that aims to enrich crops in micronutrients and valuable compounds. Selenium (Se) biofortification has particularly attracted increasing interest in recent times due to the growing number of individuals suffering from Se deficiency. Selenate and selenite are the Se forms most frequently administered to crops. In this study, Se was applied foliarly as selenate at 2.5, 5, or 10 mg per plant to two rocket species, Diplotaxis tenuifolia and Eruca sativa, grown in soil and the effects in terms of Se enrichment and content of primary and secondary metabolites were comparatively analyzed. We also compared our results with those obtained previously when selenate was supplied to the same species in hydroponics by addition to the nutrient solution. In most cases, the results were the opposite. In E. sativa, foliar Se treatment was more effective in promoting Se accumulation, sulfur (S), cysteine, and glucosinolates. No significant effect of Se was evident on total phenolic content, but there were individual phenols. Among amino acids, the content of proline was increased by Se, perhaps to counteract osmotic stress due to high Se accumulation. In D. tenuifolia, the content of S and cysteine decreased under Se treatment, but the amount of glutathione was steady, suggesting a preferred assimilation of cysteine toward the synthesis of this antioxidant. Consistent, the content of methionine and glucosinolates was reduced. The content of total phenolics was enhanced only by the low Se dosage. In both species, selenocysteine (SeCys) was identified, the content of which was higher compared to plants grown hydroponically. Concluding, most metabolic differences between rocket species were observed at high Se supplementation. Low Se foliar fertilization was effective in an enriching rocket in Se without affecting other phytochemicals. However, the Se dosages sufficient for biofortification could be even lower, as the Se concentration in rocket treated with 2.5 mg Se per plant was still very high and the edible part should not be eaten undiluted. Also, a single method of Se supplementation does not appear to be optimal for all plant species or the same species, as the metabolic responses could be very different.
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Affiliation(s)
- Michela Schiavon
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Grugliasco, TO, Italy
| | - Serenella Nardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy
| | | | - Stefano Dall’Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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Li Y, Liu S, Shawky E, Tao M, Liu A, Sulaiman K, Tian J, Zhu W. SWATH-based quantitative proteomic analysis of Morus alba L. leaves after exposure to ultraviolet-B radiation and incubation in the dark. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 230:112443. [PMID: 35429828 DOI: 10.1016/j.jphotobiol.2022.112443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/23/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Morus alba is a woody shrub of the family Moraceae and used as traditional Chinese medicine for a long history. Ultraviolet-B (UV-B) radiation, as a kind of abiotic stress factor, affected the growth and secondary metabolism in M. alba. Previous studies indicated that the contents of several secondary metabolites such as moracin N, chalcomaricin were significantly increased under high level UV-B radiation and dark incubation in M. alba leaves. To reveal the response mechanism under UV-B radiation and dark incubation in M. alba leaves, SWATH-based quantitative proteomic analysis was performed. Totally, 716 proteins were identified and quantified in the control, UVB, and UVD groups. Among them, 123 proteins and 96 proteins were identified as differentially abundant proteins in UVB group and UVD groups, respectively. Proteins related to photosynthesis, amino acid biosynthesis, and tocopherol biosynthesis were significantly altered in UVB group, while proteins related to the biosynthesis of phenolic compounds were significantly altered in UVD group. In addition, the abundances of proteins involved in the ubiquitin-proteasome system (UPS) were significantly increased in both UVB and UVD groups, indicating that UPS combined with secondary mechanism participated in the resistance to UV-B radiation and dark incubation. The obtained results provide novel insight into the effects of high level UV-B radiation on M. alba leaves and on the strategies used for maximizing the chemical constituents and the medicinal value of the M. alba leaves.
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Affiliation(s)
- Yaohan Li
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Eman Shawky
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Minglei Tao
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Kaisa Sulaiman
- The Xinjiang Uygur Autonomous Region National Institute of Traditional Chinese Medicine, Urumchi 830092, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
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Soltabayeva A, Bekturova A, Kurmanbayeva A, Oshanova D, Nurbekova Z, Srivastava S, Standing D, Sagi M. Ureides are accumulated similarly in response to UV-C irradiation and wounding in Arabidopsis leaves but are remobilized differently during recovery. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1016-1032. [PMID: 34606608 DOI: 10.1093/jxb/erab441] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Purine degradation products have been shown to play roles in plant response to stresses such as drought, salinity, extended dark, nitrogen deficiency, and pathogen infection. In this study, we used Arabidopsis wild-type (WT) and an Atxdh1-knockout mutant defective in xanthine dehydrogenase1 (XDH1) to examine the role of degraded purine metabolites in the responses to wounding or UV-C stress applied to the middle leaves of the plant. Wounding or UV-C stress in the mutant resulted in lower fresh-weight, increased senescence symptoms, and increased cell death compared to WT plants. In addition, WT plants exhibited lower levels of oxidative stress indicators, reactive oxygen species, and malondialdehyde in their leaves than the mutant. Notably, transcripts and proteins functioning in the purine degradation pathway were regulated in such a way that it led to enhanced ureide levels in WT leaves 24h after applying the UV-C or wound stress. However, different remobilization of the accumulated ureides was observed after 72h of stress. In plants treated with UV-C, the concentration of allantoin was highest in young leaves, whereas in wounded plants it was lowest in these leaves and instead accumulated mainly in the middle leaves that had been wounded. These results indicated that in WT plants treated with UV-C, ureides were remobilized from the lower older and damaged leaves to support young leaf growth during the recovery period from stress. After wounding, however, whilst some ureides were remobilized to the young leaves, more remained in the wounded middle leaves to function as antioxidants and/or healing agents.
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Affiliation(s)
- Aigerim Soltabayeva
- Biology Department, School of Science and Humanities, Nazarbayev University, Nur Sultan, Z05H0P9, Kazakhstan
| | - Aizat Bekturova
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Assylay Kurmanbayeva
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Dinara Oshanova
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Zhadyrassyn Nurbekova
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Sudhakar Srivastava
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Dominic Standing
- The Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Moshe Sagi
- The Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
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TMT-based comparative proteomic analysis of the male-sterile mutant ms01 sheds light on sporopollenin production and pollen development in wucai (Brassica campestris L.). J Proteomics 2022; 254:104475. [PMID: 35007766 DOI: 10.1016/j.jprot.2021.104475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/21/2022]
Abstract
A spontaneous male-sterile mutant ms01 was discovered from the excellent high-generation inbred line 'hx12-6-3' in wucai. Compared with wild-type 'hx12-6-3', ms01 displayed complete male sterility with degenerated stamens and no pollen. In this study, cytological observation revealed that the tapetum of the anthers of ms01 had degraded in advance, and microspore development had stagnated in the mononuclear stage, ultimately resulting in completely aborted pollen. Genetic analysis indicated that the sterility of ms01 was controlled by a single recessive nuclear gene. In the differential proteomic analysis of 'hx12-6-3' and ms01 flower buds using a tandem mass tags-based approach, a comparison of two stages (stage a and stage e) revealed 1272 differentially abundant proteins (DAPs). The abnormal variation of the anther cuticle, pollen coat, and sporopollenin production were effected by lipid metabolism and phenylpropanoid biosynthesis in the mutant ms01. Further analysis elucidated that pollen development was associated with amino acid metabolism, protein synthesis and degradation, carbohydrate metabolism, flavonoid biosynthesis and glutathione metabolism. These results provide novel insights into the molecular mechanism of GMS (genic male sterility) in wucai. SIGNIFICANCE: ms01, as the first indentified spontaneous male-sterile mutant in wucai, plays a significant role in the initial study of GMS (genic male sterility). In our study, the key DAPs related to anther and pollen development were obtained by TMT-based comparative proteomic analysis. We found that the abnormal accumulation of H2O2 might induce premature degradation of the tapetum, causing anther metabolism disorder and pollen abortion. This process involved multiple DAPs and formed a complex regulatory network that generated a series of physiological metabolic alterations, ultimately leading to male sterility. Our results provide a theoretical foundation for further research on the complex anther and pollen development process.
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Yang Y, Xiang Y, Niu Y. An Overview of the Molecular Mechanisms and Functions of Autophagic Pathways in Plants. PLANT SIGNALING & BEHAVIOR 2021; 16:1977527. [PMID: 34617497 PMCID: PMC9208794 DOI: 10.1080/15592324.2021.1977527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Autophagy is an evolutionarily conserved pathway for the degradation of damaged or toxic components. Under normal conditions, autophagy maintains cellular homeostasis. It can be triggered by senescence and various stresses. In the process of autophagy, autophagy-related (ATG) proteins not only function as central signal regulators but also participate in the development of complex survival mechanisms when plants suffer from adverse environments. Therefore, ATGs play significant roles in metabolism, development and stress tolerance. In the past decade, both the molecular mechanisms of autophagy and a large number of components involved in the assembly of autophagic vesicles have been identified. In recent studies, an increasing number of components, mechanisms, and receptors have appeared in the autophagy pathway. In this paper, we mainly review the recent progress of research on the molecular mechanisms of plant autophagy, as well as its function under biotic stress and abiotic stress.
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Affiliation(s)
- Yang Yang
- Moe Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences,Lanzhou University, Lanzhou, China
| | - Yun Xiang
- Moe Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences,Lanzhou University, Lanzhou, China
| | - Yue Niu
- Moe Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences,Lanzhou University, Lanzhou, China
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Sun Y, Guo J, Zeng X, Chen R, Feng Y, Chen S, Yang K. Chromosome-scale genome assembly of Castanopsis tibetana provides a powerful comparative framework to study the evolution and adaptation of Fagaceae trees. Mol Ecol Resour 2021; 22:1178-1189. [PMID: 34689424 DOI: 10.1111/1755-0998.13539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/27/2022]
Abstract
Fagaceae species are increasingly used as models to elucidate the process and mechanism of adaptation and speciation by integrating ecology, evolution and genomics. The genus Castanopsis belongs to the family Fagaceae and is mainly distributed across subtropical and tropical Asia. In the present study, we reported the first chromosome-scale genome assembly of Castanopsis tibetana, a common species of evergreen broadleaved forests in subtropical China. The combination of Nanopore sequencing and Hi-C technologies enabled a high-quality genome assembly. The final assembled genome size of C. tibetana was 878.6 Mb (97.6% of the estimated genome size), consisting of 477 contigs with an N50 length of 3.3 Mb. The benchmarking universal single-copy orthologue (BUSCO) assessment indicated a completeness of 93.0%. Hi-C scaffolding generated 12 pseudochromosomes, representing 98.7% of the assembled genome. Subsequently, 40,937 protein-coding genes were predicted and 90.04% of them were functionally annotated. More than 476.9 Mb of repetitive sequences (54.3% of the genome) were identified, and the percentage of the genome covered by TE elements was 39.98%. Comparative genomics analysis revealed that C. tibetana was most closely related to Castanea mollissima and diverged at 18.48 Ma, and that C. tibetana has undergone considerable gene family expansion and contraction. Evidence of positive selection was detected in 53 genes, which showed different arrangement pattern compared to Quercus robur. The chromosome-scale genome assembly of C. tibetana will expand Fagaceae genome resources across the family and provide a powerful comparative framework to study the adaptation and evolution of Fagaceae trees.
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Affiliation(s)
- Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jianling Guo
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiaorong Zeng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Risheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yi Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shuang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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13
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Patipong T, Kageyama H, Waditee-Sirisattha R. Insights into the phylogeny and transcriptional response of serine proteases in a halotolerant cyanobacterium Halothece sp. PCC7418. PLANT SIGNALING & BEHAVIOR 2021; 16:1913556. [PMID: 34184613 PMCID: PMC8281059 DOI: 10.1080/15592324.2021.1913556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 06/13/2023]
Abstract
Serine proteases are a class of versatile proteolytic enzymes. They are necessary for protein catabolism, intracellular amino acid turnover, and regulation of proteins involved in diverse molecular and cellular processes across taxa. In this study, bioinformatic analyses revealed a significantly large number of serine proteases in the halotolerant cyanobacterium Halothece sp. PCC7418 (hereafter referred to as Halothece 7418) compared to the model freshwater cyanobacterium Synechococcus elongatus PCC7942 (hereafter referred to as S. elongatus 7942). The cyanobacterial serine proteases are likely derived from different linages since no conserved motifs were detected. The presence of highly diverse serine proteases in Halothece 7418 implicated an evolutionary-mediated modification of several proteases, which may play numerous physiological roles. We also examined the gene expression patterns of 34 serine protease encoding genes in Halothece 7418 exposed to salt stress. Our results revealed that several serine protease genes were drastically up-regulated under salt with high concentration but remained unchanged under salt with low concentration. All four clp genes (H1996, H1997, H0950, and H3375) and H3553 gene (which encodes a putative HtrA protease) were significantly induced upon salt stress. These responses support the roles of the housekeeping pathways in both the degradation of damaged proteins induced by salt stress and regulation of proteins involved in the molecular recovery from salt stress. Since serine proteases share several biochemical features and physiological functions, the results from this study provide an insight into diversification of serine proteases in cyanobacteria. Further, these results will increase our understanding of several mechanisms at the subcellular level.
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Affiliation(s)
- Tanutcha Patipong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Thailand
| | - Hakuto Kageyama
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Japan
- Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Japan
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14
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Basu R, Dutta S, Pal A, Sengupta M, Chattopadhyay S. Calmodulin7: recent insights into emerging roles in plant development and stress. PLANT MOLECULAR BIOLOGY 2021; 107:1-20. [PMID: 34398355 DOI: 10.1007/s11103-021-01177-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/27/2021] [Indexed: 05/25/2023]
Abstract
Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca2+-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca2+ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.
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Affiliation(s)
- Riya Basu
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Siddhartha Dutta
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
- Department of Biotechnology, University of Engineering and Management, University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Abhideep Pal
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Mandar Sengupta
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Sudip Chattopadhyay
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India.
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15
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Atallah I, Quinodoz M, Campos-Xavier B, Peter VG, Fouriki A, Bonvin C, Bottani A, Kumps C, Angelini F, Bellutti Enders F, Christen-Zaech S, Rizzi M, Renella R, Beck-Popovic M, Poloni C, Frossard V, Blouin JL, Rivolta C, Riccio O, Candotti F, Hofer M, Unger S, Superti-Furga A. Immune deficiency, autoimmune disease and intellectual disability: A pleiotropic disorder caused by biallelic variants in the TPP2 gene. Clin Genet 2021; 99:780-788. [PMID: 33586135 DOI: 10.1111/cge.13942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022]
Abstract
Four individuals from two families presented with a multisystemic condition of suspected genetic origin that was diagnosed only after genome analysis. The main phenotypic features were immune system dysregulation (severe immunodeficiency with autoimmunity) and intellectual disability. The four individuals were found to be homozygous for a 4.4 Kb deletion removing exons 20-23 (NM_003291.4) of the TPP2 gene, predicting a frameshift with premature termination of the protein. The deletion was located on a shared chromosome 13 haplotype indicating a Swiss founder mutation. Tripeptidyl peptidase 2 (TPP2) is a protease involved in HLA/antigen complex processing and amino acid homeostasis. Biallelic variants in TPP2 have been described in 10 individuals with variable features including immune deficiency, autoimmune cytopenias, and intellectual disability or chronic sterile brain inflammation mimicking multiple sclerosis. Our observations further delineate this severe condition not yet included in the OMIM catalog. Timely recognition of TPP2 deficiency is crucial since (1) immune surveillance is needed and hematopoietic stem cell transplantation may be necessary, and (2) for provision of genetic counselling. Additionally, enzyme replacement therapy, as already established for TPP1 deficiency, might be an option in the future.
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Affiliation(s)
- Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Belinda Campos-Xavier
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Athina Fouriki
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Christophe Bonvin
- Division of Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Armand Bottani
- Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Camille Kumps
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Federica Angelini
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Felicitas Bellutti Enders
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Mattia Rizzi
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Raffaele Renella
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Maja Beck-Popovic
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Claudia Poloni
- Pediatric Neurology Unit, Sion Hospital, Sion, Switzerland
| | | | - Jean-Louis Blouin
- Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Orbicia Riccio
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Michael Hofer
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Sheila Unger
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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16
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da Silva MF, Gonçalves MC, Brito MDS, Medeiros CN, Harakava R, Landell MGDA, Pinto LR. Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes. PLoS One 2020; 15:e0241493. [PMID: 33166323 PMCID: PMC7652275 DOI: 10.1371/journal.pone.0241493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.
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Affiliation(s)
- Marcel Fernando da Silva
- Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
| | | | - Michael dos Santos Brito
- Departamento de Ciência e Tecnologia, Instituto de Ciência e Tecnologia da Universidade Federal de São Paulo, São José dos Campos, São Paulo, Brazil
| | | | - Ricardo Harakava
- Crop Protection Research Centre, Instituto Biológico, São Paulo, Brazil
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17
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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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18
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Detto M, Xu X. Optimal leaf life strategies determine V c,max dynamic during ontogeny. THE NEW PHYTOLOGIST 2020; 228:361-375. [PMID: 32473028 DOI: 10.1111/nph.16712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/12/2020] [Indexed: 05/26/2023]
Abstract
Leaf photosynthetic properties, for example the maximum carboxylation velocity or Vc,max , change with leaf age due to ontogenetic processes. This study introduces an optimal dynamic allocation scheme to model changes in leaf-level photosynthetic capacity as a function of leaf biochemical constraints (costs of synthesis and defence), nitrogen availability and other environmental factors (e.g. light). The model consists of a system of equations describing RuBisCO synthesis and degradation within chloroplasts, defence and ageing at leaf levels, nitrogen transfer and carbon budget at plant levels. Model results show that optimal allocation principles explained RuBisCO dynamics with leaf age. An approximated analytical solution can reproduce the basic pattern of RuBisCO and Vc,max in rice and in two tropical tree species. The model also reveals leaf life complementarities that remained unexplained in previous approaches, as the interplay between Vc,max at maturation, life span and the decline in photosynthetic capacity with age. Furthermore, it explores the role of defence, which is not implemented in current models. This framework covers some of the existing gaps in integrating multiple processes across plant organs (chloroplast, leaf and whole plant) and is a first-step towards representing mechanistically leaf ontogenetic processes into physiological and ecosystem models.
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Affiliation(s)
- Matteo Detto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
- Smithsonian Tropical Research Institute, Balboa, 0843-03092, Republic of Panama
| | - Xiangtao Xu
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
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19
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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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20
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Martinez-Garcia M, Fernández-Jiménez N, Santos JL, Pradillo M. Duplication and divergence: New insights into AXR1 and AXL functions in DNA repair and meiosis. Sci Rep 2020; 10:8860. [PMID: 32483285 PMCID: PMC7264244 DOI: 10.1038/s41598-020-65734-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/20/2020] [Indexed: 01/08/2023] Open
Abstract
Rubylation is a conserved regulatory pathway similar to ubiquitination and essential in the response to the plant hormone auxin. In Arabidopsis thaliana, AUXIN RESISTANT1 (AXR1) functions as the E1-ligase in the rubylation pathway. The gene AXR1-LIKE (AXL), generated by a relatively recent duplication event, can partially replace AXR1 in this pathway. We have analysed mutants deficient for both proteins and complementation lines (with the AXR1 promoter and either AXR1 or AXL coding sequences) to further study the extent of functional redundancy between both genes regarding two processes: meiosis and DNA repair. Here we report that whereas AXR1 is essential to ensure the obligatory chiasma, AXL seems to be dispensable during meiosis, although its absence slightly alters chiasma distribution. In addition, expression of key DNA repair and meiotic genes is altered when either AXR1 or AXL are absent. Furthermore, our results support a significant role for both genes in DNA repair that was not previously described. These findings highlight that AXR1 and AXL show a functional divergence in relation to their involvement in homologous recombination, exemplifying a duplicate retention model in which one copy tends to have more sub-functions than its paralog.
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Affiliation(s)
- Marina Martinez-Garcia
- Departamento de Genética, Fisiología y Microbiología. Facultad de Biología, Universidad Complutense de Madrid, Madrid, 28040, Spain.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nadia Fernández-Jiménez
- Departamento de Genética, Fisiología y Microbiología. Facultad de Biología, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Juan L Santos
- Departamento de Genética, Fisiología y Microbiología. Facultad de Biología, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología. Facultad de Biología, Universidad Complutense de Madrid, Madrid, 28040, Spain.
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21
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Shen T, Wang Q, Li C, Zhou B, Li Y, Liu Y. Transcriptome sequencing analysis reveals silver nanoparticles antifungal molecular mechanism of the soil fungi Fusarium solani species complex. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:122063. [PMID: 31972432 DOI: 10.1016/j.jhazmat.2020.122063] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Silver nanoparticles (AgNPs) have been widely used in various fields due to their antimicrobial activities. However, the antimicrobial mechanisms of AgNPs against fungi, especially on transcriptional level, are still unclear. In this study, the inhibitory property of AgNPs against Fusarium solani species complex was investigated. Transmission electron microscopes were used to observe the alterations in morphology and cellular structure of fungal hyphae treated with AgNPs. Disturbances in the cell walls and membranes, as well as empty space in the cytoplasm were observed. The transcriptome sequencing of F. solani species complex mycelia was performed using the Illumina NextSeq 500 ribonucleic acid sequencing (RNA-Seq) platform. In the RNA-Seq study, AgNPs treatment resulted in 2503 differentially expressed genes (DEGs). Gene Ontology (GO) analysis revealed that the DEGs were mainly involved in 6 different terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis also revealed that energy and substance metabolism, signal transduction and genetic information processing were the most highly enriched pathways for these DEGs. In addition, RNA-seq results were validated by quantitative polymerase chain reactions (qPCRs). Our findings enhanced the understanding of the antifungal activities of AgNPs and the underlying molecular mechanisms, and provided a new perspective for investigating this novel antifungal agent.
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Affiliation(s)
- Tianlin Shen
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qiushuang Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Chengliang Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuhuan Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yanli Liu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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22
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Savić J, Nikolić R, Banjac N, Zdravković-Korać S, Stupar S, Cingel A, Ćosić T, Raspor M, Smigocki A, Ninković S. Beneficial implications of sugar beet proteinase inhibitor BvSTI on plant architecture and salt stress tolerance in Lotus corniculatus L. JOURNAL OF PLANT PHYSIOLOGY 2019; 243:153055. [PMID: 31639537 DOI: 10.1016/j.jplph.2019.153055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Food demands of increasing human population dictate intensification of livestock production, however, environmental stresses could jeopardize producers' efforts. Forage legumes suffer from yield losses and poor nutritional status due to salinity increase of agricultural soils. As tools aimed to reduce negative impacts of biotic or abiotic stresses, proteinase inhibitors (PIs) have been promoted for biotechnological improvements. In order to increase tolerance of Lotus corniculatus L. to salt stress, serine PI, BvSTI, was introduced into this legume using Agrobacterium rhizogenes, with final transformation efficiency of 4.57%. PCR, DNA gel-blot, RT-PCR and in-gel protein activity assays confirmed the presence and activity of BvSTI products in transformed lines. Plants from three selected transgenic lines (21, 73 and 109) showed significant alterations in overall phenotypic appearance, corresponding to differences in BvSTI accumulation. Lines 73 and 109 showed up to 7.3-fold higher number of tillers and massive, up to 5.8-fold heavier roots than in nontransformed controls (NTC). Line 21 was phenotypically similar to NTC, accumulated less BvSTI transcripts and did not exhibit an additional band of recombinant trypsin inhibitor as seen in lines 73 and 109. Exposure of the transgenic lines to NaCl revealed different levels of salt stress susceptibility. The NaCl sensitivity index, based on morphological appearance and chlorophyll concentrations showed that lines 73 and 109 were significantly less affected by salinity than NTC or line 21. High level of BvSTI altered morphology and delayed salt stress related senescence, implicating BvSTI gene as a promising tool for salinity tolerance improvement trials in L. corniculatus.
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Affiliation(s)
- Jelena Savić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia.
| | - Radomirka Nikolić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Nevena Banjac
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Snežana Zdravković-Korać
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Sofija Stupar
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Aleksandar Cingel
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Tatjana Ćosić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Martin Raspor
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Ann Smigocki
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Slavica Ninković
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
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Li Y, Zhai L, Fan J, Ren J, Gong W, Wang X, Huang J. Genome-wide identification, phylogenetic and expression analysis of the maize HECT E3 ubiquitin ligase genes. Genetica 2019; 147:391-400. [PMID: 31741104 DOI: 10.1007/s10709-019-00080-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/13/2019] [Indexed: 11/27/2022]
Abstract
HECT (homologous to the E6AP carboxyl terminus) ubiquitin ligase genes (E3s) are enzymes with diverse functions influencing plant growth, development, and responses to abiotic stresses. However, there is relatively little information available regarding the maize HECT E3 gene family. In the present study, 12 maize HECT E3 genes (ZmUPL1 to ZmUPL12) were identified at the whole-genome level. The phylogenetic relationships, structures, and expression levels of the maize HECT E3 genes were then analyzed. On the basis of the constructed maximum likelihood phylogenetic tree, the HECT E3 genes were divided into six groups. The quantitative real-time polymerase chain reaction assay results revealed that all of the maize ZmUPL genes were expressed in most of the examined tissues and were responsive to three abiotic stresses. Considered together, the study results may provide a useful foundation for future investigations of maize stress-tolerance genes as well as functional analyses of the E3 enzymes in diverse agriculturally important crop species.
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Affiliation(s)
- Yunfeng Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lihong Zhai
- Medical College, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Jingsheng Fan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaxin Ren
- Medical College, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Wenrong Gong
- Medical College, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Xin Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jun Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China. .,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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New Aspects of HECT-E3 Ligases in Cell Senescence and Cell Death of Plants. PLANTS 2019; 8:plants8110483. [PMID: 31717304 PMCID: PMC6918304 DOI: 10.3390/plants8110483] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 01/17/2023]
Abstract
Plant cells undergo massive orderly changes in structure, biochemistry, and gene expression during cell senescence. These changes cannot be distinguished from the hydrolysis/degradation function controlled by the ubiquitination pathway, autophagy, and various hydrolases in cells. In this mini-review, we summarized current research progress that the human HECT (homologous to the E6AP carboxyl terminus)-type ubiquitin E3 ligases have non-redundant functions in regulating specific signaling pathways, involved in a number of human diseases, especially aging-related diseases, through the influence of DNA repair, protein stability, and removal efficiency of damaged proteins or organelles. We further compared HECT E3 ligases’ structure and functions between plant and mammalian cells, and speculated new aspects acting as degrading signals and regulating signals of HECT E3 ligase in cell senescence and the cell death of plants.
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25
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Pérez-Díaz J, Pérez-Díaz JR, Medeiros DB, Zuther E, Hong CY, Nunes-Nesi A, Hincha DK, Ruiz-Lara S, Casaretto JA. Transcriptome analysis reveals potential roles of a barley ASR gene that confers stress tolerance in transgenic rice. JOURNAL OF PLANT PHYSIOLOGY 2019; 238:29-39. [PMID: 31129469 DOI: 10.1016/j.jplph.2019.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 05/29/2023]
Abstract
Control of gene expression and induction of cellular protection mechanisms are two important processes that plants employ to protect themselves against abiotic stresses. ABA-, stress, and ripening-induced (ASR) proteins have been identified to participate in such responses. Previous studies have proposed that these proteins can act as transcription factors and as molecular chaperones protecting transgenic plants against stresses; however a gene network regulated by ASRs has not been explored. To expand our knowledge on the function of these proteins in cereals, we present the functional characterization of a barley ASR gene. Expression of HvASR5 was almost ubiquitous in different organs and responded to ABA and to different stress treatments. When expressed ectopically, HvASR5 was able to confer drought and salt stress tolerance to Arabidopsis thaliana and to improve growth performance of rice plants under stress conditions. A transcriptomic analysis with two transgenic rice lines overexpressing HvASR5 helped to identify potential downstream targets and understand ASR-regulated cellular processes. HvASR5 up-regulated the expression of a distinct set of genes associated with stress responses, metabolic processes (particularly carbohydrate metabolism), as well as reproduction and development. These data, together with the confirmed nuclear and cytoplasmic localization of HvASR5, further support the hypothesis that HvASR5 can also carry out roles as molecular protector and transcriptional regulator.
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Affiliation(s)
- Jorge Pérez-Díaz
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | - David B Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Chwan-Yang Hong
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Dirk K Hincha
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Simón Ruiz-Lara
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - José A Casaretto
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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26
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Influence of storage length and inoculation with Lactobacillus buchneri on the fermentation, aerobic stability, and ruminal degradability of high-moisture corn and rehydrated corn grain silage. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2019.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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27
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Plaxton WC. Avoiding Proteolysis during the Extraction and Purification of Active Plant Enzymes. PLANT & CELL PHYSIOLOGY 2019; 60:715-724. [PMID: 30753712 DOI: 10.1093/pcp/pcz028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/03/2019] [Indexed: 06/09/2023]
Abstract
The aim of this article is to discuss approaches to diagnose and prevent unwanted proteolysis during extraction and isolation of active enzymes from plant tissues. Enzymes are protein catalysts that require great care during sample processing in order to ensure that they remain intact and fully active. Preventing artifactual enzyme modifications ex planta is of utmost importance in order to obtain biologically relevant data. This is particularly problematic following enzyme extraction from plant tissues, which relative to microbes or animals contain relatively low protein amounts coupled with high concentrations of vacuolar proteases. Although cytoplasmic enzymes are not directly accessible to vacuolar proteases owing their physical segregation into different subcellular compartments, this compartmentation is destroyed during cell lysis. Unwanted proteolysis by endogenous proteases is an insidious problem because in many cases the enzyme of interest is only partially degraded and retains catalytic activity. This can not only lead to erroneous conclusions about an enzyme's size, subunit structure and post-translational modifications, but can also result in striking changes to its kinetic and regulatory (i.e. allosteric) properties. Furthermore, the routine addition of class-specific protease inhibitors and/or commercially available (and expensive) protease inhibitor cocktails to extraction and purification buffers does not necessarily preclude partial proteolysis of plant enzymes by endogenous proteases. When antibodies are available, plant scientists are advised to employ immunoblotting to diagnose potential in vitro proteolytic truncation of the enzymes that they wish to characterize, as well as to test the effectiveness of specific protease inhibitors in overcoming this recurrent issue.
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Affiliation(s)
- William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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28
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Zhong Y, Xu D, Hebelstrup KH, Yang D, Cai J, Wang X, Zhou Q, Cao W, Dai T, Jiang D. Nitrogen topdressing timing modifies free amino acids profiles and storage protein gene expression in wheat grain. BMC PLANT BIOLOGY 2018; 18:353. [PMID: 30545290 PMCID: PMC6293556 DOI: 10.1186/s12870-018-1563-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 11/22/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Nitrogen is one basic element of amino acids and grain protein in wheat. In field experiments, wheat plants were subjected to different timing of nitrogen topdressing treatments: at the stages of emergence of the top fifth leaf (TL5), top third leaf (TL3) and top first leaf (TL1) to test the regulatory effects of nitrogen topdressing timing on grain protein quality. The underlying mechanisms were elucidated by clarifying the relationship between proteolysis in vegetative organs and accumulation of amino acids in the endosperm cavity, conversion of amino acids, and storage protein synthesis in endosperm of wheat grain. RESULTS Delayed nitrogen topdressing up-regulated gene expression related to nitrogen metabolism and protease synthesis in the flag leaf, followed by more free amino acids being transported to both the cavity and the endosperm from 7 days after anthesis (DAA) to 13 DAA in TL1. TL1 enhanced the conversion between free amino acids in endosperm and upregulated the expression of genes encoding high molecular weight (HMW) and low molecular weight (LMW) subunits and protein disulfide isomerases-like (PDIL) proteins, indicating that the synthesis and folding of glutenin were enhanched by delayed nitrogen topdressing. As a consequense, the content of glutenin macropolymers (GMP) and glutenin increased with delaying nitrogen topdressing. CONCLUSIONS The results highlight the relationship between nitrogen remobilization and final grain protein production and suggest that the nitrogen remobilization processes could be a potential target for improving the quality of wheat grain. Additionally, specific gene expression related to nitrogen topdressing was identified, which conferred more detailed insights into underlying mechanism on the modification protein quality.
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Affiliation(s)
- Yingxin Zhong
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Dachao Xu
- National Laboratory of Plant Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Kim Henrik Hebelstrup
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Donglei Yang
- National Laboratory of Plant Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Jian Cai
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Xiao Wang
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Qin Zhou
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Weixing Cao
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Tingbo Dai
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production / Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture / National Engineering and technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
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29
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Mandal A, Sharma N, Muthamilarasan M, Prasad M. Ubiquitination: a tool for plant adaptation to changing environments. THE NUCLEUS 2018. [DOI: 10.1007/s13237-018-0255-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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30
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Dhanushkodi R, Matthew C, McManus MT, Dijkwel PP. Drought-induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels. THE NEW PHYTOLOGIST 2018; 220:196-208. [PMID: 29974467 DOI: 10.1111/nph.15298] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/20/2018] [Indexed: 05/09/2023]
Abstract
Drought is a major constraint for legume growth and yield. Senescence of nitrogen-fixing nodules is one of the early drought responses and may cause nutrient stress in addition to water stress in legumes. For nodule senescence to function as part of a drought-survival strategy, we propose that the intrinsically destructive senescence process must be tightly regulated. Medicago truncatula protease inhibitor and iron scavenger-encoding genes, possibly involved in controlling nodule senescence, were identified. RNA interference (RNAi) lines were constructed in which expression of a serpin or ferritins was knocked down. Both wild-type and RNAi lines were subjected to drought stress and nodule activity and plant physiological responses were measured. Drought caused M. truncatula to initiate nodule senescence before plant growth was affected and before an increase in papain-like proteolytic activity and free iron levels was apparent. Knock-down expression of serpin6 and ferritins caused increased protease activity, free iron levels, early nodule senescence and reduced plant growth. The results suggest that M. truncatula nodule-expressed serpin6 and ferritins mediate ordered drought-induced senescence by regulating papain-like cysteine protease activity and free iron levels. This strategy may allow the drought-stressed plants to benefit maximally from residual nitrogen fixation and nutrient recovery resulting from break down of macromolecules.
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Affiliation(s)
- Ramadoss Dhanushkodi
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cory Matthew
- Institute of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Michael T McManus
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Guerrero J, Andrello M, Burgarella C, Manel S. Soil environment is a key driver of adaptation in Medicago truncatula: new insights from landscape genomics. THE NEW PHYTOLOGIST 2018; 219:378-390. [PMID: 29696659 DOI: 10.1111/nph.15171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/14/2018] [Indexed: 05/22/2023]
Abstract
Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome-environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD-MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume-rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD-MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle.
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Affiliation(s)
- Jimena Guerrero
- CEFE-CNRS, Centre D'Ecologie Fonctionelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Marco Andrello
- CEFE-CNRS, Centre D'Ecologie Fonctionelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Concetta Burgarella
- UMR DIADE Institut de Recherche pour le Developpement (IRD), Centre de Montpellier, BP 64501, Montpellier Cedex 5, France
- UMR AGAP Centre de Coopération International en Recherche Agronomique pour le Développement (CIRAD), Avenue Agropolis, 34398, Montpellier, France
| | - Stephanie Manel
- CEFE-CNRS, Centre D'Ecologie Fonctionelle et Evolutive, Route de Mende, 34090, Montpellier, France
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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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Lei C, Fan S, Li K, Meng Y, Mao J, Han M, Zhao C, Bao L, Zhang D. iTRAQ-Based Proteomic Analysis Reveals Potential Regulation Networks of IBA-Induced Adventitious Root Formation in Apple. Int J Mol Sci 2018; 19:ijms19030667. [PMID: 29495482 PMCID: PMC5877528 DOI: 10.3390/ijms19030667] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/14/2018] [Accepted: 02/22/2018] [Indexed: 01/19/2023] Open
Abstract
Adventitious root (AR) formation, which is controlled by endogenous and environmental factors, is indispensable for vegetative asexual propagation. However, comprehensive proteomic data on AR formation are still lacking. The aim of this work was to study indole-3-butyric acid (IBA)-induced AR formation in the dwarf apple rootstock 'T337'. In this study, the effect of IBA on AR formation was analysed. Subsequent to treatment with IBA, both the rooting rate and root length of 'T337' increased significantly. An assessment of hormone levels in basal stem cuttings suggested that auxin, abscisic acid, and brassinolide were higher in basal stem cuttings that received the exogenous IBA application; while zeatin riboside, gibberellins, and jasmonic acid were lower than non-treated basal stem cuttings. To explore the underlying molecular mechanism, an isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic technique was employed to identify the expression profiles of proteins at a key period of adventitious root induction (three days after IBA treatment). In total, 3355 differentially expressed proteins (DEPs) were identified. Many DEPs were closely related to carbohydrate metabolism and energy production, protein homeostasis, reactive oxygen and nitric oxide signaling, and cell wall remodeling biological processes; as well as the phytohormone signaling, which was the most critical process in response to IBA treatment. Further, RT-qPCR analysis was used to evaluate the expression level of nine genes that are involved in phytohormone signaling and their transcriptional levels were mostly in accordance with the protein patterns. Finally, a putative work model was proposed. Our study establishes a foundation for further research and sheds light on IBA-mediated AR formation in apple as well as other fruit rootstock cuttings.
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Affiliation(s)
- Chao Lei
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Ke Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Yuan Meng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Jiangping Mao
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Lu Bao
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Tevatia R, Oyler GA. Evolution of DDB1-binding WD40 (DWD) in the viridiplantae. PLoS One 2018; 13:e0190282. [PMID: 29293590 PMCID: PMC5749748 DOI: 10.1371/journal.pone.0190282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/11/2017] [Indexed: 12/16/2022] Open
Abstract
Damaged DNA Binding 1 (DDB1)—binding WD40 (DWD) proteins are highly conserved and involved in a plethora of developmental and physiological processes such as flowering time control, photomorphogenesis, and abiotic stress responses. The phylogeny of this family of proteins in plants and algae of viridiplante is a critical area to understand the emergence of this family in such important and diverse functions. We aimed to investigate the putative homologs of DWD in the viridiplante and establish a deeper DWD evolutionary grasp. The advancement in publicly available genomic data allowed us to perform an extensive genome-wide DWD retrieval. Using annotated Arabidopsis thaliana DWDs as the reference, we generated and characterized a comprehensive DWD database for the studied photoautotrophs. Further, a generic DWD classification system (Type A to K), based on (i) position of DWD motifs, (ii) number of DWD motifs, and (iii) presence/absence of other domains, was adopted. About 72–80% DWDs have one DWD motif, whereas 17–24% DWDs have two and 0.5–4.7% DWDs have three DWD motifs. Neighbor-joining phylogenetic construction of A. thaliana DWDs facilitated us to tune these substrate receptors into 15 groups. Though the DWD count increases from microalgae to higher land plants, the ratio of DWD to WD40 remained constant throughout the viridiplante. The DWD expansion appeared to be the consequence of consistent DWD genetic flow accompanied by several gene duplication events. The network, phylogenetic, and statistical analysis delineated DWD evolutionary relevance in the viridiplante.
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Affiliation(s)
- Rahul Tevatia
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (RT); (GAO)
| | - George A. Oyler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Synaptic Research LLC, Baltimore, Maryland, United States of America
- * E-mail: (RT); (GAO)
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Amorim LLB, Ferreira-Neto JRC, Bezerra-Neto JP, Pandolfi V, de Araújo FT, da Silva Matos MK, Santos MG, Kido EA, Benko-Iseppon AM. Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR. PLANT METHODS 2018; 14:88. [PMID: 30337949 PMCID: PMC6182843 DOI: 10.1186/s13007-018-0354-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Due to cowpea ability to fix nitrogen in poor soils and relative tolerance to drought and salt stresses, efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Real-time quantitative PCR (qPCR) has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. In the present study, nine candidate reference genes were rigorously tested for their application in normalization of qPCR data onto roots of four distinct cowpea accessions under two abiotic stresses: root dehydration and salt (NaCl, 100 mM). In addition, the regulation of four target transcripts, under the same referred conditions was also scrutinized. RESULTS geNorm, NormFinder, BestKeeper, and ΔCt method results indicated a set of three statistically validated RGs for each stress condition: (I) root dehydration (actin, ubiquitin-conjugating enzyme E2 variant 1D, and a Phaseolus vulgaris unknown gene-UNK), and (II) salt (ubiquitin-conjugating enzyme E2 variant 1D, F-box protein, and UNK). The expression profile of the target transcripts suggests that flavonoids are important players in the cowpea response to the abiotic stresses analyzed, since chalcone isomerase and chalcone synthase were up-regulated in the tolerant and sensitive accessions. A lipid transfer protein also participates in the cowpea tolerance mechanisms to root dehydration and salt stress. The referred transcript was up-regulated in the two tolerant accessions and presented no differential expression in the sensitive counterparts. Chitinase B, in turn, generally related to plant defense, was an important target transcript under salt stress, being up-regulated at the tolerant, and down-regulated in the sensitive accession. CONCLUSIONS Reference genes suitable for qPCR analyses in cowpea under root dehydration and salt stress were identified. This action will lead to a more accurate and reliable analysis of gene expression on this species. Additionally, the results obtained in this study may guide future research on gene expression in cowpea under other abiotic stress types that impose osmotic imbalance. The target genes analyzed, in turn, deserve functional evaluation due to their transcriptional regulation under stresses and biotechnological potential.
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Affiliation(s)
- Lidiane Lindinalva Barbosa Amorim
- Instituto Federal de Educação, Ciência e Tecnologia do Piauí, Oeiras, Piauí Brazil
- Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
| | | | | | - Valesca Pandolfi
- Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
| | | | | | - Mauro Guida Santos
- Botany Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
| | - Ederson Akio Kido
- Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil
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Ligaba-Osena A, Hankoua B, DiMarco K, Pace R, Crocker M, McAtee J, Nagachar N, Tien M, Richard TL. Reducing biomass recalcitrance by heterologous expression of a bacterial peroxidase in tobacco (Nicotiana benthamiana). Sci Rep 2017; 7:17104. [PMID: 29213132 PMCID: PMC5719049 DOI: 10.1038/s41598-017-16909-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/25/2017] [Indexed: 11/13/2022] Open
Abstract
Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and extracts from transgenic leaves showed higher activity on classic peroxidase substrates than the control. Intriguingly, in situ DypB activation and subsequent saccharification released nearly 200% more fermentable sugars from transgenic lines than controls, which were not explained by variation in initial structural and non-structural carbohydrates and lignin content. Pyrolysis-GC-MS analysis showed more reduction in the level of lignin associated pyrolysates in the transgenic lines than the control primarily when the enzyme is activated prior to pyrolysis, consistent with increased lignin degradation and improved saccharification. The findings reveal for the first time that accumulation and in situ activation of a peroxidase improves biomass digestibility.
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Affiliation(s)
- Ayalew Ligaba-Osena
- College of Agriculture and Related Sciences, Delaware State University, 1200 N DuPont Highway, Dover, DE, 19901, USA
| | - Bertrand Hankoua
- College of Agriculture and Related Sciences, Delaware State University, 1200 N DuPont Highway, Dover, DE, 19901, USA.
| | - Kay DiMarco
- Agricultural and Biological Engineering, Pennsylvania State University, 111 Research Unit A, University Park, Pennsylvania, PA, 16802, USA
| | - Robert Pace
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY, 40511, USA
| | - Mark Crocker
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY, 40511, USA
| | - Jesse McAtee
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Nivedita Nagachar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania, PA, 16802, USA
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania, PA, 16802, USA
| | - Tom L Richard
- Agricultural and Biological Engineering, Pennsylvania State University, 111 Research Unit A, University Park, Pennsylvania, PA, 16802, USA
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Ararso Z, Ma C, Qi Y, Feng M, Han B, Hu H, Meng L, Li J. Proteome Comparisons between Hemolymph of Two Honeybee Strains (Apis mellifera ligustica) Reveal Divergent Molecular Basis in Driving Hemolymph Function and High Royal Jelly Secretion. J Proteome Res 2017; 17:402-419. [DOI: 10.1021/acs.jproteome.7b00621] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zewdu Ararso
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Ma
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuping Qi
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mao Feng
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Han
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Hu
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lifeng Meng
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianke Li
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yocgo RE, Geza E, Chimusa ER, Mazandu GK. A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. BMC PLANT BIOLOGY 2017; 17:218. [PMID: 29169324 PMCID: PMC5701366 DOI: 10.1186/s12870-017-1151-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Advances in forward and reverse genetic techniques have enabled the discovery and identification of several plant defence genes based on quantifiable disease phenotypes in mutant populations. Existing models for testing the effect of gene inactivation or genes causing these phenotypes do not take into account eventual uncertainty of these datasets and potential noise inherent in the biological experiment used, which may mask downstream analysis and limit the use of these datasets. Moreover, elucidating biological mechanisms driving the induced disease resistance and influencing these observable disease phenotypes has never been systematically tackled, eliciting the need for an efficient model to characterize completely the gene target under consideration. RESULTS We developed a post-gene silencing bioinformatics (post-GSB) protocol which accounts for potential biases related to the disease phenotype datasets in assessing the contribution of the gene target to the plant defence response. The post-GSB protocol uses Gene Ontology semantic similarity and pathway dataset to generate enriched process regulatory network based on the functional degeneracy of the plant proteome to help understand the induced plant defence response. We applied this protocol to investigate the effect of the NPR1 gene silencing to changes in Arabidopsis thaliana plants following Pseudomonas syringae pathovar tomato strain DC3000 infection. Results indicated that the presence of a functionally active NPR1 reduced the plant's susceptibility to the infection, with about 99% of variability in Pseudomonas spore growth between npr1 mutant and wild-type samples. Moreover, the post-GSB protocol has revealed the coordinate action of target-associated genes and pathways through an enriched process regulatory network, summarizing the potential target-based induced disease resistance mechanism. CONCLUSIONS This protocol can improve the characterization of the gene target and, potentially, elucidate induced defence response by more effectively utilizing available phenotype information and plant proteome functional knowledge.
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Affiliation(s)
- Rosita E. Yocgo
- African Institute for Mathematical Sciences (AIMS), AIMS South Africa and AIMS Ghana, Cape Town, South Africa
- Biomathematics Division, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Ephifania Geza
- African Institute for Mathematical Sciences (AIMS), AIMS South Africa and AIMS Ghana, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Anzio Road, Observatory, Cape Town, 7925 South Africa
| | - Emile R. Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Anzio Road, Observatory, Cape Town, 7925 South Africa
| | - Gaston K. Mazandu
- African Institute for Mathematical Sciences (AIMS), AIMS South Africa and AIMS Ghana, Cape Town, South Africa
- Biomathematics Division, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Anzio Road, Observatory, Cape Town, 7925 South Africa
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Junges D, Morais G, Spoto M, Santos P, Adesogan A, Nussio L, Daniel J. Short communication: Influence of various proteolytic sources during fermentation of reconstituted corn grain silages. J Dairy Sci 2017; 100:9048-9051. [DOI: 10.3168/jds.2017-12943] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/02/2017] [Indexed: 11/19/2022]
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Zhou H, Zhao J, Cai J, Patil SB. UBIQUITIN-SPECIFIC PROTEASES function in plant development and stress responses. PLANT MOLECULAR BIOLOGY 2017; 94:565-576. [PMID: 28695315 DOI: 10.1007/s11103-017-0633-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/05/2017] [Indexed: 05/08/2023]
Abstract
UBIQUITIN-SPECIFIC PROTEASES play important roles in plant development and stress responses. Protein ubiquitination and deubiquitination are reversible processes, which can modulate the stability, activity as well as subcellular localization of the substrate proteins. UBIQUITIN-SPECIFIC PROTEASE (UBP) protein family participates in protein deubiquitination. Members of UBP family are involved in a variety of physiological processes in plants, as evidenced by their functional characterization in model plant Arabidopsis and other plants. UBPs are conserved in plants and distinct UBPs function in different regulatory processes, although functional redundancies exist between some members. Here we briefly reviewed recent advances in understanding the biological functions of UBP protein family in Arabidopsis, particularly the molecular mechanisms by which UBPs regulate plant development and stress responses. We believe that elucidation of UBPs function and regulation in Arabidopsis will provide new insights about protein deubiquitination and might shed light on the understanding of the mechanistic roles of UBPs in general, which will definitely contribute to crop improvement in agriculture.
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Affiliation(s)
- Huapeng Zhou
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingqing Cai
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Suyash B Patil
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Zientara-Rytter K, Sirko A. To deliver or to degrade - an interplay of the ubiquitin-proteasome system, autophagy and vesicular transport in plants. FEBS J 2017; 283:3534-3555. [PMID: 26991113 DOI: 10.1111/febs.13712] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 02/21/2016] [Accepted: 03/14/2016] [Indexed: 12/21/2022]
Abstract
The efficient utilization and subsequent reuse of cell components is a key factor in determining the proper growth and functioning of all cells under both optimum and stress conditions. The process of intracellular and intercellular recycling is especially important for the appropriate control of cellular metabolism and nutrient management in immobile organisms, such as plants. Therefore, the accurate recycling of amino acids, lipids, carbohydrates or micro- and macronutrients available in the plant cell becomes a critical factor that ensures plant survival and growth. Plant cells possess two main degradation mechanisms: a ubiquitin-proteasome system and autophagy, which, as a part of an intracellular trafficking system, is based on vesicle transport. This review summarizes knowledge of both the ubiquitin-proteasome system and autophagy pathways, describes the cross-talk between the two and discusses the relationships between autophagy and the vesicular transport systems.
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Affiliation(s)
| | - Agnieszka Sirko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Upadhyay A, Joshi V, Amanullah A, Mishra R, Arora N, Prasad A, Mishra A. E3 Ubiquitin Ligases Neurobiological Mechanisms: Development to Degeneration. Front Mol Neurosci 2017; 10:151. [PMID: 28579943 PMCID: PMC5437216 DOI: 10.3389/fnmol.2017.00151] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/04/2017] [Indexed: 01/08/2023] Open
Abstract
Cells regularly synthesize new proteins to replace old or damaged proteins. Deposition of various aberrant proteins in specific brain regions leads to neurodegeneration and aging. The cellular protein quality control system develop various defense mechanisms against the accumulation of misfolded and aggregated proteins. The mechanisms underlying the selective recognition of specific crucial protein or misfolded proteins are majorly governed by quality control E3 ubiquitin ligases mediated through ubiquitin-proteasome system. Few known E3 ubiquitin ligases have shown prominent neurodevelopmental functions, but their interactions with different developmental proteins play critical roles in neurodevelopmental disorders. Several questions are yet to be understood properly. How E3 ubiquitin ligases determine the specificity and regulate degradation of a particular substrate involved in neuronal proliferation and differentiation is certainly the one, which needs detailed investigations. Another important question is how neurodevelopmental E3 ubiquitin ligases specifically differentiate between their versatile range of substrates and timing of their functional modulations during different phases of development. The premise of this article is to understand how few E3 ubiquitin ligases sense major molecular events, which are crucial for human brain development from its early embryonic stages to throughout adolescence period. A better understanding of these few E3 ubiquitin ligases and their interactions with other potential proteins will provide invaluable insight into disease mechanisms to approach toward therapeutic interventions.
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Affiliation(s)
- Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Vibhuti Joshi
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Ayeman Amanullah
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Ribhav Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Naina Arora
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
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Hajrah NH, Obaid AY, Atef A, Ramadan AM, Arasappan D, Nelson CA, Edris S, Mutwakil MZ, Alhebshi A, Gadalla NO, Makki RM, Al-Kordy MA, El-Domyati FM, Sabir JSM, Khiyami MA, Hall N, Bahieldin A, Jansen RK. Transcriptomic analysis of salt stress responsive genes in Rhazya stricta. PLoS One 2017; 12:e0177589. [PMID: 28520766 PMCID: PMC5433744 DOI: 10.1371/journal.pone.0177589] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022] Open
Abstract
Rhazya stricta is an evergreen shrub that is widely distributed across Western and South Asia, and like many other members of the Apocynaceae produces monoterpene indole alkaloids that have anti-cancer properties. This species is adapted to very harsh desert conditions making it an excellent system for studying tolerance to high temperatures and salinity. RNA-Seq analysis was performed on R. stricta exposed to severe salt stress (500 mM NaCl) across four time intervals (0, 2, 12 and 24 h) to examine mechanisms of salt tolerance. A large number of transcripts including genes encoding tetrapyrroles and pentatricopeptide repeat (PPR) proteins were regulated only after 12 h of stress of seedlings grown in controlled greenhouse conditions. Mechanisms of salt tolerance in R. stricta may involve the upregulation of genes encoding chaperone protein Dnaj6, UDP-glucosyl transferase 85a2, protein transparent testa 12 and respiratory burst oxidase homolog protein b. Many of the highly-expressed genes act on protecting protein folding during salt stress and the production of flavonoids, key secondary metabolites in stress tolerance. Other regulated genes encode enzymes in the porphyrin and chlorophyll metabolic pathway with important roles during plant growth, photosynthesis, hormone signaling and abiotic responses. Heme biosynthesis in R. stricta leaves might add to the level of salt stress tolerance by maintaining appropriate levels of photosynthesis and normal plant growth as well as by the participation in reactive oxygen species (ROS) production under stress. We speculate that the high expression levels of PPR genes may be dependent on expression levels of their targeted editing genes. Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged.
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Affiliation(s)
- Nahid H. Hajrah
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Abdullah Y. Obaid
- Department of Chemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed Atef
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed M. Ramadan
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Dhivya Arasappan
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Charllotte A. Nelson
- Centre of Genomic Research, Institute for Integrative Biology, Crown Street, Liverpool, United Kingdom
| | - Sherif Edris
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammed Z. Mutwakil
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Alawia Alhebshi
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O. Gadalla
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Rania M. Makki
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Madgy A. Al-Kordy
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Fotouh M. El-Domyati
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Jamal S. M. Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammad A. Khiyami
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Neil Hall
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ahmed Bahieldin
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Robert K. Jansen
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Fanello DD, Bartoli CG, Guiamet JJ. Qualitative and quantitative modifications of root mitochondria during senescence of above-ground parts of Arabidopis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:112-121. [PMID: 28330554 DOI: 10.1016/j.plantsci.2017.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/18/2017] [Accepted: 01/21/2017] [Indexed: 05/09/2023]
Abstract
This work studied modifications experienced by root mitochondria during whole plant senescence or under light deprivation, using Arabidopsis thaliana plants with YFP tagged to mitochondria. During post-bolting development, root respiratory activity started to decline after aboveground organs (i.e., rosette leaves) had senesced. This suggests that carbohydrate starvation may induce root senescence. Similarly, darkening the whole plant induced a decrease in respiration of roots. This was partially due to a decrease in the number of total mitochondria (YFP-labelled mitochondria) and most probably to a decrease in the quantity of mitochondria with a developed inner membrane potential (ΔΨm, i.e., Mitotracker red- labelled mitochondria). Also, the lower amount of mitochondria with ΔΨm compared to YFP-labelled mitochondria at 10d of whole darkened plant, suggests the presence of mitochondria in a "standby state". The experiments also suggest that small mitochondria made the main contribution to the respiratory activity that was lost during root senescence. Sugar supplementation partially restored the respiration of mitochondria after 10d of whole plant dark treatment. These results suggest that root senescence is triggered by carbohydrate starvation, with loss of ΔΨm mitochondria and changes in mitochondrial size distribution.
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Affiliation(s)
- Diego Darío Fanello
- Instituto de Fisiología Vegetal (INFIVE), Facultades de Ciencias Agrarias y Forestales y de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CCT-CONICET La Plata, cc 327, 1900, La Plata, Argentina.
| | - Carlos Guillermo Bartoli
- Instituto de Fisiología Vegetal (INFIVE), Facultades de Ciencias Agrarias y Forestales y de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CCT-CONICET La Plata, cc 327, 1900, La Plata, Argentina
| | - Juan José Guiamet
- Instituto de Fisiología Vegetal (INFIVE), Facultades de Ciencias Agrarias y Forestales y de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CCT-CONICET La Plata, cc 327, 1900, La Plata, Argentina
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Kumaravel M, Uma S, Backiyarani S, Saraswathi MS, Vaganan MM, Muthusamy M, Sajith KP. Differential proteome analysis during early somatic embryogenesis in Musa spp. AAA cv. Grand Naine. PLANT CELL REPORTS 2017; 36:163-178. [PMID: 27807644 DOI: 10.1007/s00299-016-2067-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/20/2016] [Indexed: 05/22/2023]
Abstract
Endogenous hormone secretion proteins along with stress and defense proteins play predominant role in banana embryogenesis. This study reveals the underlying molecular mechanism during transition from vegetative to embryogenic state. Banana (Musa spp.) is well known globally as a food fruit crop for millions. The requirement of quality planting material of banana is enormous. Although mass multiplication through tissue culture is in vogue, high-throughput techniques like somatic embryogenesis (SE) as a mass multiplication tool needs to be improved. Apart from clonal propagation, SE has extensive applications in genetic improvement and mutation. SE in banana is completely genome-dependent and most of the commercial cultivars exhibit recalcitrance. Thus, understanding the molecular basis of embryogenesis in Musa will help to develop strategies for mass production of quality planting material. In this study, differentially expressed proteins between embryogenic calli (EC) and non-embryogenic calli (NEC) with respect to the explant, immature male flower buds (IMFB), of cv. Grand Naine (AAA) were determined using two-dimensional gel electrophoresis (2DE). The 2DE results were validated through qRT-PCR. In total, 65 proteins were identified: 42 were highly expressed and 23 were less expressed in EC compared to NEC and IMFB. qRT-PCR analysis of five candidate proteins, upregulated in EC, were well correlated with expression at transcript level. Further analysis of proteins showed that embryogenesis in banana is associated with the control of oxidative stress. The regulation of ROS scavenging system and protection of protein structure occurred in the presence of heat shock proteins. Alongside, high accumulation of stress-related cationic peroxidase and plant growth hormone-related proteins like indole-3-pyruvate monooxygenase and adenylate isopentenyltransferase in EC revealed the association with the induction of SE.
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Affiliation(s)
- Marimuthu Kumaravel
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India
| | - Subbaraya Uma
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India.
| | - Suthanthiram Backiyarani
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India
| | - Marimuthu Somasundaram Saraswathi
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India
| | - Muthu Mayil Vaganan
- Crop Protection Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India
| | - Muthusamy Muthusamy
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India
| | - Kallu Purayil Sajith
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Main Road, Thayanoor Post, Tiruchirappalli, 102, Tamil Nadu, India
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Diaz-Mendoza M, Velasco-Arroyo B, Santamaria ME, González-Melendi P, Martinez M, Diaz I. Plant senescence and proteolysis: two processes with one destiny. Genet Mol Biol 2016; 39:329-38. [PMID: 27505308 PMCID: PMC5004835 DOI: 10.1590/1678-4685-gmb-2016-0015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/10/2016] [Indexed: 01/03/2023] Open
Abstract
Senescence-associated proteolysis in plants is a complex and controlled process,
essential for mobilization of nutrients from old or stressed tissues, mainly leaves,
to growing or sink organs. Protein breakdown in senescing leaves involves many
plastidial and nuclear proteases, regulators, different subcellular locations and
dynamic protein traffic to ensure the complete transformation of proteins of high
molecular weight into transportable and useful hydrolysed products. Protease
activities are strictly regulated by specific inhibitors and through the activation
of zymogens to develop their proteolytic activity at the right place and at the
proper time. All these events associated with senescence have deep effects on the
relocation of nutrients and as a consequence, on grain quality and crop yield. Thus,
it can be considered that nutrient recycling is the common destiny of two processes,
plant senescence and, proteolysis. This review article covers the most recent
findings about leaf senescence features mediated by abiotic and biotic stresses as
well as the participants and steps required in this physiological process, paying
special attention to C1A cysteine proteases, their specific inhibitors, known as
cystatins, and their potential targets, particularly the chloroplastic proteins as
source for nitrogen recycling.
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Affiliation(s)
- Mercedes Diaz-Mendoza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Blanca Velasco-Arroyo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
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Shen Q, Hu T, Bao M, Cao L, Zhang H, Song F, Xie Q, Zhou X. Tobacco RING E3 Ligase NtRFP1 Mediates Ubiquitination and Proteasomal Degradation of a Geminivirus-Encoded βC1. MOLECULAR PLANT 2016; 9:911-25. [PMID: 27018391 DOI: 10.1016/j.molp.2016.03.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 02/17/2016] [Accepted: 03/03/2016] [Indexed: 05/19/2023]
Abstract
The βC1 protein encoded by the Tomato yellow leaf curl China virus-associated betasatellite functions as a pathogenicity determinant. To better understand the molecular basis whereby βC1 functions in pathogenicity, a yeast two-hybrid screen of a tobacco cDNA library was carried out using βC1 as the bait. The screen revealed that βC1 interacts with a tobacco RING-finger protein designated NtRFP1, which was further confirmed by the bimolecular fluorescence complementation and co-immunoprecipitation assays in Nicotiana benthamiana cells. Expression of NtRFP1 was induced by βC1, and in vitro ubiquitination assays showed that NtRFP1 is a functional E3 ubiquitin ligase that mediates βC1 ubiquitination. In addition, βC1 was shown to be ubiquitinated in vivo and degraded by the plant 26S proteasome. After viral infection, plants overexpressing NtRFP1 developed attenuated symptoms, whereas plants with silenced expression of NtRFP1 showed severe symptoms. Other lines of evidence showed that NtRFP1 attenuates βC1-induced symptoms through promoting its degradation by the 26S proteasome. Taken together, our results suggest that tobacco RING E3 ligase NtRFP1 attenuates disease symptoms by interacting with βC1 to mediate its ubiquitination and degradation via the ubiquitin/26S proteasome system.
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Affiliation(s)
- Qingtang Shen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Min Bao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Linge Cao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Huawei Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengmin Song
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Bündig C, Jozefowicz AM, Mock HP, Winkelmann T. Proteomic analysis of two divergently responding potato genotypes ( Solanum tuberosum L.) following osmotic stress treatment in vitro. J Proteomics 2016; 143:227-241. [DOI: 10.1016/j.jprot.2016.04.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/20/2016] [Accepted: 04/28/2016] [Indexed: 11/17/2022]
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Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF. The transcriptomics of an experimentally evolved plant-virus interaction. Sci Rep 2016; 6:24901. [PMID: 27113435 PMCID: PMC4845063 DOI: 10.1038/srep24901] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/07/2016] [Indexed: 01/14/2023] Open
Abstract
Models of plant-virus interaction assume that the ability of a virus to infect a host genotype depends on the matching between virulence and resistance genes. Recently, we evolved tobacco etch potyvirus (TEV) lineages on different ecotypes of Arabidopsis thaliana, and found that some ecotypes selected for specialist viruses whereas others selected for generalists. Here we sought to evaluate the transcriptomic basis of such relationships. We have characterized the transcriptomic responses of five ecotypes infected with the ancestral and evolved viruses. Genes and functional categories differentially expressed by plants infected with local TEV isolates were identified, showing heterogeneous responses among ecotypes, although significant parallelism existed among lineages evolved in the same ecotype. Although genes involved in immune responses were altered upon infection, other functional groups were also pervasively over-represented, suggesting that plant resistance genes were not the only drivers of viral adaptation. Finally, the transcriptomic consequences of infection with the generalist and specialist lineages were compared. Whilst the generalist induced very similar perturbations in the transcriptomes of the different ecotypes, the perturbations induced by the specialist were divergent. Plant defense mechanisms were activated when the infecting virus was specialist but they were down-regulated when infecting with generalist.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Francisco García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012 València, Spain
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012 València, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), 46012 València, Spain
- Functional Genomics Node, INB at CIPF, 46012 València, Spain
| | - José M. Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA
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50
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Dong C, Hu H, Jue D, Zhao Q, Chen H, Xie J, Jia L. The banana E2 gene family: Genomic identification, characterization, expression profiling analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:11-24. [PMID: 26940488 DOI: 10.1016/j.plantsci.2016.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/23/2015] [Accepted: 01/13/2016] [Indexed: 05/06/2023]
Abstract
The E2 is at the center of a cascade of Ub1 transfers, and it links activation of the Ub1 by E1 to its eventual E3-catalyzed attachment to substrate. Although the genome-wide analysis of this family has been performed in some species, little is known about analysis of E2 genes in banana. In this study, 74 E2 genes of banana were identified and phylogenetically clustered into thirteen subgroups. The predicted banana E2 genes were distributed across all 11 chromosomes at different densities. Additionally, the E2 domain, gene structure and motif compositions were analyzed. The expression of all of the banana E2 genes was analyzed in the root, stem, leaf, flower organs, five stages of fruit development and under abiotic stresses. All of the banana E2 genes, with the exception of few genes in each group, were expressed in at least one of the organs and fruit developments, which indicated that the E2 genes might involve in various aspects of the physiological and developmental processes of the banana. Quantitative RT-PCR (qRT-PCR) analysis identified that 45 E2s under drought and 33 E2s under salt were induced. To the best of our knowledge, this report describes the first genome-wide analysis of the banana E2 gene family, and the results should provide valuable information for understanding the classification, cloning and putative functions of this family.
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Affiliation(s)
- Chen Dong
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Huigang Hu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Dengwei Jue
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Qiufang Zhao
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Hongliang Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Jianghui Xie
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Liqiang Jia
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China.
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