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Boersma MR, Patrick RM, Jillings SL, Shaipulah NFM, Sun P, Haring MA, Dudareva N, Li Y, Schuurink RC. ODORANT1 targets multiple metabolic networks in petunia flowers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1134-1151. [PMID: 34863006 PMCID: PMC9306810 DOI: 10.1111/tpj.15618] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 05/19/2023]
Abstract
Scent bouquets produced by the flowers of Petunia spp. (petunia) are composed of a complex mixture of floral volatile benzenoid and phenylpropanoid compounds (FVBPs), which are specialized metabolites derived from phenylalanine (Phe) through an interconnected network of enzymes. The biosynthesis and emission of high levels of these volatiles requires coordinated transcriptional activation of both primary and specialized metabolic networks. The petunia R2R3-MYB transcription factor ODORANT 1 (ODO1) was identified as a master regulator of FVBP production and emission; however, our knowledge of the direct regulatory targets of ODO1 has remained limited. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq) in petunia flowers, we identify genome-wide ODO1-bound genes that are enriched not only in genes involved in the biosynthesis of the Phe precursor, as previously reported, but also genes associated with the specialized metabolic pathways involved in generating phenylpropanoid intermediates for FVBPs. ODO1-bound genes are also involved in methionine and S-adenosylmethionine metabolism, which could modulate methyl group supplies for certain FVBPs. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and RNA-seq analysis in an ODO1 RNAi knockdown line revealed that ODO1-bound targets are expressed at lower levels when ODO1 is suppressed. A cis-regulatory motif, CACCAACCCC, was identified as a potential binding site for ODO1 in the promoters of genes that are both bound and activated by ODO1, which was validated by in planta promoter reporter assays with wild-type and mutated promoters. Overall, our work presents a mechanistic model for ODO1 controlling an extensive gene regulatory network that contributes to FVBP production to give rise to floral scent.
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Affiliation(s)
- Maaike R. Boersma
- Green Life Sciences Research ClusterSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1098 XHthe Netherlands
- Green BiotechnologyInholland University of Applied SciencesAmsterdam1098 XHthe Netherlands
| | - Ryan M. Patrick
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Sonia L. Jillings
- Green Life Sciences Research ClusterSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1098 XHthe Netherlands
| | - Nur Fariza M. Shaipulah
- Green Life Sciences Research ClusterSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1098 XHthe Netherlands
- Present address:
Faculty of Science and Marine EnvironmentUniversiti Malaysia Terrengganu21030 Kuala NerusTerrenganuMalaysia
| | - Pulu Sun
- Green Life Sciences Research ClusterSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1098 XHthe Netherlands
| | - Michel A. Haring
- Green Life Sciences Research ClusterSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1098 XHthe Netherlands
| | - Natalia Dudareva
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
- Department of BiochemistryPurdue UniversityWest LafayetteIN47907USA
| | - Ying Li
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Robert C. Schuurink
- Green Life Sciences Research ClusterSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1098 XHthe Netherlands
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Meta-Analysis as a Tool to Identify Candidate Genes Involved in the Fagus sylvatica L. Abiotic Stress Response. FORESTS 2022. [DOI: 10.3390/f13020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we aimed to evaluate whether candidate genes for abiotic stresses in Fagus sylvatica L. are also candidate genes for herbaceous plants, with the purpose of better defining the abiotic stress response model of F. sylvatica. Therefore, a meta-analysis was performed on published papers related to abiotic stress. Firstly, we carried out a systematic review regarding the activity of 24 candidate genes selected for F. sylvatica under abiotic stress reported in 503 articles. After choosing the inclusion criteria, 73 articles out of 503, regarding 12 candidate genes, were included in this analysis. We performed an exploratory meta-analysis based on the random-effect model and the combined effect-size approach (Cohen’s d). The results obtained through Forest and Funnel plots indicate that the candidate genes for F. sylvatica are considered to be candidate genes in other herbaceous species. These results allowed us to set up models of plants’ response to abiotic stresses implementing the stress models in forest species. The results of this study will serve to bridge knowledge gaps regarding the pathways of response to abiotic stresses in trees based on the meta-analysis. The study approach used could be extended to observe larger gene databases and different species.
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De la Peña M, Marín-Peña AJ, Urmeneta L, Coleto I, Castillo-González J, van Liempd SM, Falcón-Pérez JM, Álvarez-Fernández A, González-Moro MB, Marino D. Ammonium nutrition interacts with iron homeostasis in Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:263-274. [PMID: 34570887 DOI: 10.1093/jxb/erab427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Most plant species develop stress symptoms when exposed to high ammonium (NH4+) concentrations. The root is the first organ in contact with high NH4+ and therefore the first barrier to cope with ammonium stress. In this work, we focused on root adaptation to ammonium nutrition in the model plant Brachypodium distachyon. Proteome analysis revealed changes associated with primary metabolism, cell wall remodelling, and redox homeostasis. In addition, it showed a strong induction of proteins related to methionine (Met) metabolism and phytosiderophore (PS) synthesis in ammonium-fed plants. In agreement with this, we show how ammonium nutrition impacts Met/S-adenosyl-Met and PS metabolic pathways together with increasing root iron content. Nevertheless, ammonium-fed plants displayed higher sensitivity to iron deficiency, suggesting that ammonium nutrition triggers impaired iron utilization and root to shoot transport, which entailed an induction in iron-related responses. Overall, this work demonstrates the importance of iron homeostasis during ammonium nutrition and paves a new way to better understand and improve ammonium use efficiency and tolerance.
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Affiliation(s)
- Marlon De la Peña
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-48940, Leioa,Spain
| | - Agustín Javier Marín-Peña
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-48940, Leioa,Spain
| | - Leyre Urmeneta
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-48940, Leioa,Spain
| | - Inmaculada Coleto
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-48940, Leioa,Spain
| | - Jorge Castillo-González
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), E-50059, Zaragoza,Spain
| | | | - Juan M Falcón-Pérez
- Metabolomics Platform, CIC bioGUNE-BRTA, Derio,Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Madrid,Spain
- Ikerbasque, Basque Foundation for Science, E-48011 Bilbao,Spain
| | - Ana Álvarez-Fernández
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), E-50059, Zaragoza,Spain
| | - María Begoña González-Moro
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-48940, Leioa,Spain
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), E-48940, Leioa,Spain
- Ikerbasque, Basque Foundation for Science, E-48011 Bilbao,Spain
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Kosteletzkya pentacarpos: A Potential Halophyte Candidate for Phytoremediation in the Meta(loid)s Polluted Saline Soils. PLANTS 2021; 10:plants10112495. [PMID: 34834857 PMCID: PMC8624882 DOI: 10.3390/plants10112495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022]
Abstract
Kosteletzkya pentacarpos (L.) Ledebour is a perennial facultative halophyte species from the Malvacea family that grows in coastal areas with high amounts of salt. The tolerance of K. pentacarpos to the high concentration of salt (0.5–1.5% salinity range of coastal saline land) has been widely studied for decades. Nowadays, with the dramatic development of the economy and urbanization, in addition to the salt, the accumulation of mate(loid)s in coastal soil is increasing, which is threatening the survival of halophyte species as well as the balance of wetland ecosystems. Recently, the capacity of K. pentacarpos to cope with either single heavy metal stress or a combination of multiple meta(loid) toxicities was studied. Hence, this review focused on summarizing the physiological and biochemical behaviors of K. pentacarpos that has been simultaneously exposed to the combination of several meta(loid) toxicities. How the salt accumulated by K. pentacarpos impacts the response to meta(loid) stress was discussed. We conclude that as a potential candidate for phytoremediation, K. pentacarpos was able to cope with various environmental constrains such as multiple meta(loid) stresses due to its relative tolerance to meta(loid) toxicity.
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Elkelish A, El-Mogy MM, Niedbała G, Piekutowska M, Atia MAM, Hamada MMA, Shahin M, Mukherjee S, El-Yazied AA, Shebl M, Jahan MS, Osman A, El-Gawad HGA, Ashour H, Farag R, Selim S, Ibrahim MFM. Roles of Exogenous α-Lipoic Acid and Cysteine in Mitigation of Drought Stress and Restoration of Grain Quality in Wheat. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112318. [PMID: 34834681 PMCID: PMC8619972 DOI: 10.3390/plants10112318] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 05/13/2023]
Abstract
Cysteine (Cys) and α-lipoic acid (ALA) are naturally occurring antioxidants (sulfur-containing compounds) that can protect plants against a wide spectrum of environmental stresses. However, up to now, there are no conclusive data on their integrative roles in mitigation of drought stress in wheat plants. Here, we studied the influence of ALA at 0.02 mM (grain dipping pre-cultivation treatment) and Cys (25 and 50 ppm as a foliar application) under well watered and deficit irrigation (100% and 70% of recommended dose). The results showed that deficit irrigation markedly caused obvious cellular oxidative damage as indicated by elevating the malondialdehyde (MDA) and hydrogen peroxide content (H2O2). Moreover, water stressed plants exhibited multiple changes in physiological metabolism, which affected the quantitative and qualitative variables of grain yield. The enzymatic antioxidants, including superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POX) were improved by Cys application. SOD and APX had the same response when treated with ALA, but CAT and POX did not. Moreover, both studied molecules stimulated chlorophyll (Chl) and osmolytes' biosynthesis. In contrast, the Chl a/b ratio was decreased, while flavonoids were not affected by either of the examined molecules. Interestingly, all above-mentioned changes were associated with an improvement in the scavenging capacity of reactive oxygen species (ROS), leaf relative water content (RWC), grain number, total grain yield, weight of 1000 kernels, gluten index, falling number, and alveographic parameters (P, W, and P/L values). Furthermore, heatmap plot analysis revealed several significant correlations between different studied parameters, which may explore the importance of applied Cys and ALA as effective compounds in wheat cultivation under water deficit conditions.
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Affiliation(s)
- Amr Elkelish
- Botany Department, Faculty of Science, Suez Canal University Ismailia, Ismailia 41522, Egypt;
| | - Mohamed M. El-Mogy
- Vegetable Crops Department, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
- Correspondence: (M.M.E.-M); (M.F.M.I.); Tel.: +20-1068027607 (M.M.E.-M); +20-1123403173 (M.F.M.I.)
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Partyzantów 27, 76-200 Słupsk, Poland;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Maha M. A. Hamada
- Department of Agronomy, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (M.M.A.H.); (M.S.)
| | - Mostafa Shahin
- Department of Agronomy, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (M.M.A.H.); (M.S.)
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, Kalyani 742213, India;
| | - Ahmed Abou El-Yazied
- Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (A.A.E.-Y.); (H.G.A.E.-G.)
| | - Mohamed Shebl
- Food Science Department, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt;
| | - Mohammad Shah Jahan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
- Department of Horticulture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Ali Osman
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt;
| | - Hany G. Abd El-Gawad
- Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (A.A.E.-Y.); (H.G.A.E.-G.)
| | - Hatem Ashour
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (H.A.); (R.F.)
| | - Reham Farag
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (H.A.); (R.F.)
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Mohamed F. M. Ibrahim
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (H.A.); (R.F.)
- Correspondence: (M.M.E.-M); (M.F.M.I.); Tel.: +20-1068027607 (M.M.E.-M); +20-1123403173 (M.F.M.I.)
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Bednarek PT, Orłowska R, Mańkowski DR, Oleszczuk S, Zebrowski J. Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley. Cells 2021; 10:2774. [PMID: 34685752 PMCID: PMC8534894 DOI: 10.3390/cells10102774] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
The process of anther culture involves numerous abiotic stresses required for cellular reprogramming, microspore developmental switch, and plant regeneration. These stresses affect DNA methylation patterns, sequence variation, and the number of green plants regenerated. Recently, in barley (Hordeum vulgare L.), mediation analysis linked DNA methylation changes, copper (Cu2+) and silver (Ag+) ion concentrations, sequence variation, β-glucans, green plants, and duration of anther culture (Time). Although several models were used to explain particular aspects of the relationships between these factors, a generalized complex model employing all these types of data was not established. In this study, we combined the previously described partial models into a single complex model using the structural equation modeling approach. Based on the evaluated model, we demonstrated that stress conditions (such as starvation and darkness) influence β-glucans employed by cells for glycolysis and the tricarboxylic acid cycle. Additionally, Cu2+ and Ag+ ions affect DNA methylation and induce sequence variation. Moreover, these ions link DNA methylation with green plants. The structural equation model also showed the role of time in relationships between parameters included in the model and influencing plant regeneration via anther culture. Utilization of structural equation modeling may have both scientific and practical implications, as it demonstrates links between biological phenomena (e.g., culture-induced variation, green plant regeneration and biochemical pathways), and provides opportunities for regulating these phenomena for particular biotechnological purposes.
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Affiliation(s)
- Piotr Tomasz Bednarek
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, 05-870 Błonie, Poland;
| | - Renata Orłowska
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, 05-870 Błonie, Poland;
| | - Dariusz Rafał Mańkowski
- Department of Seed Science and Technology, Plant Breeding and Acclimatization Institute—National Research Institute, 05-870 Błonie, Poland;
| | - Sylwia Oleszczuk
- Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute—National Research Institute, 05-870 Błonie, Poland;
| | - Jacek Zebrowski
- Institute of Biology and Biotechnology, University of Rzeszow, 35-959 Rzeszow, Poland;
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Kamiab F, Tavassolian I, Hosseinifarahi M. Biologia futura: the role of polyamine in plant science. Biol Futur 2021; 71:183-194. [PMID: 34554509 DOI: 10.1007/s42977-020-00027-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 06/10/2020] [Indexed: 12/27/2022]
Abstract
Polyamines (PAs) are positively charged amines such as putrescine, spermidine and spermine that ubiquitously exist in all organisms. They have been considered as a new type of plant biostimulants, with pivotal roles in many physiological processes. Polyamine levels are controlled by intricate regulatory feedback mechanisms. PAs are directly or indirectly regulated through interaction with signaling metabolites (H202, NO), aminobutyric acid (GABA), phytohormones (abscisic acid, gibberellins, ethylene, cytokinins, auxin, jasmonic acid and brassinosteroids) and nitrogen metabolism (maintaining the balance of C:N in plants). Exogenous applications of PAs enhance the stress resistance, flowering and fruit set, synthesis of bioactive compounds and extension of agricultural crops shelf life. Up-regulation of PAs biosynthesis by genetic manipulation can be a novel strategy to increase the productivity of agricultural crops. Recently, the role of PAs in symbiosis relationships between plants and beneficial microorganisms has been confirmed. PA metabolism has also been targeted to design new harmless fungicides.
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Affiliation(s)
- Fereshteh Kamiab
- Department of Horticulture, Faculty of Agriculture, Rafsanjan Branch, Islamic Azad University, Rafsanjan, Iran.
| | - Iraj Tavassolian
- Research and Technology Institute of Plant Production, Shahid Bahonar University of Kerman, Kerman, Iran.,Department of Horticulture, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mehdi Hosseinifarahi
- Department of Horticultural Science, Yasooj Branch, Islamic Azad University, Yasooj, Iran
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GSNOR Contributes to Demethylation and Expression of Transposable Elements and Stress-Responsive Genes. Antioxidants (Basel) 2021; 10:antiox10071128. [PMID: 34356361 PMCID: PMC8301139 DOI: 10.3390/antiox10071128] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022] Open
Abstract
In the past, reactive nitrogen species (RNS) were supposed to be stress-induced by-products of disturbed metabolism that cause oxidative damage to biomolecules. However, emerging evidence demonstrates a substantial role of RNS as endogenous signals in eukaryotes. In plants, S-nitrosoglutathione (GSNO) is the dominant RNS and serves as the •NO donor for S-nitrosation of diverse effector proteins. Remarkably, the endogenous GSNO level is tightly controlled by S-nitrosoglutathione reductase (GSNOR) that irreversibly inactivates the glutathione-bound NO to ammonium. Exogenous feeding of diverse RNS, including GSNO, affected chromatin accessibility and transcription of stress-related genes, but the triggering function of RNS on these regulatory processes remained elusive. Here, we show that GSNO reductase-deficient plants (gsnor1-3) accumulate S-adenosylmethionine (SAM), the principal methyl donor for methylation of DNA and histones. This SAM accumulation triggered a substantial increase in the methylation index (MI = [SAM]/[S-adenosylhomocysteine]), indicating the transmethylation activity and histone methylation status in higher eukaryotes. Indeed, a mass spectrometry-based global histone profiling approach demonstrated a significant global increase in H3K9me2, which was independently verified by immunological detection using a selective antibody. Since H3K9me2-modified regions tightly correlate with methylated DNA regions, we also determined the DNA methylation status of gsnor1-3 plants by whole-genome bisulfite sequencing. DNA methylation in the CG, CHG, and CHH contexts in gsnor1-3 was significantly enhanced compared to the wild type. We propose that GSNOR1 activity affects chromatin accessibility by controlling the transmethylation activity (MI) required for maintaining DNA methylation and the level of the repressive chromatin mark H3K9me2.
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Bednarek PT, Pachota KA, Dynkowska WM, Machczyńska J, Orłowska R. Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System. Int J Mol Sci 2021; 22:7546. [PMID: 34299165 PMCID: PMC8304781 DOI: 10.3390/ijms22147546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.
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Affiliation(s)
- Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.A.P.); (W.M.D.); (J.M.); (R.O.)
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Comparative transcriptome analysis of the hyperaccumulator plant Phytolacca americana in response to cadmium stress. 3 Biotech 2021; 11:327. [PMID: 34194911 DOI: 10.1007/s13205-021-02865-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
To study the molecular mechanism of the hyperaccumulator plant Phytolacca americana against cadmium (Cd) stress, the leaves of P. americana treated with 400 μM Cd for 0, 2, 12, and 24 h were harvested for comparative transcriptome analysis. In total, 110.07 Gb of clean data were obtained, and 63,957 unigenes were acquired after being assembled. Due to the lack of P. americana genome information, only 24,517 unigenes were annotated by public databases. After Cd treatment, 5054 differentially expressed genes (DEGs) were identified. KEGG pathway enrichment analysis of DEGs showed that genes involved in the flavonoid biosynthesis and antenna proteins of photosynthesis were significantly down-regulated, while genes related to the lignin biosynthesis pathway were remarkably up-regulated, indicating that P. americana could synthesize more lignin to cope with Cd stress. Moreover, genes related to heavy metal accumulation, sulfur metabolism and glutathione metabolism were also significantly up-regulated. The gene expression pattern of several key genes related to distinct metabolic pathways was verified by qRT-PCR. The results indicated that the immobilization of lignin in cell wall, chelation, vacuolar compartmentalization, as well as the increase of thiol compounds content may be the important mechanisms of Cd detoxification in hyperaccumulator plant P. americana. Accession numbers: the raw data of P. americana transcriptome presented in this study are openly available in NCBI SRA database, under the BioProject of PRJNA649785. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02865-x.
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Chronic exercise mediates epigenetic suppression of L-type Ca2+ channel and BKCa channel in mesenteric arteries of hypertensive rats. J Hypertens 2021; 38:1763-1776. [PMID: 32384389 DOI: 10.1097/hjh.0000000000002457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Regular exercise is a lifestyle intervention for controlling hypertension and has an improving effect on vascular function. Voltage-gated L-type Ca (LTCC) and large-conductance Ca-activated K (BKCa) channels are two principal mediators of vascular smooth muscle cell contractility and arterial tone. The present study tested the hypothesis that DNA methylation dynamics plays a key role in exercise-induced reprogramming and downregulation of LTCC and BKCa channel in mesenteric arteries from spontaneously hypertensive rats (SHRs). METHODS SHRs and Wistar-Kyoto (WKY) rats were subjected to exercise training or kept sedentary, and vascular molecular and functional properties were evaluated. RESULTS Exercise inhibited hypertension-induced upregulation of LTCC and BKCa channel function in mesenteric arteries by repressing LTCC α1c and BKCa β1 subunit expression. In accordance, exercise triggered hypermethylation of α1c and β1 gene in SHR, with concomitant decreasing TET1, increasing DNMT1 and DNMT3b expression in mesenteric arteries, as well as altering peripheral α-KG and S-adenosylmethionine/ S-adenosylhomocysteine ratio. Acting synergistically, these exercise-induced functional and molecular amelioration could allow for attenuating hypertension-induced elevation in arterial blood pressure. CONCLUSION Our results indicate that exercise suppresses LTCC and BKCa channel function via hypermethylation of α1c and β1 subunits, which contributes to the restoration of mesenteric arterial function and vasodilation during hypertension.
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Cartelier K, Aimé D, Ly Vu J, Combes-Soia L, Labas V, Prosperi JM, Buitink J, Gallardo K, Le Signor C. Genetic determinants of seed protein plasticity in response to the environment in Medicago truncatula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1298-1311. [PMID: 33733554 DOI: 10.1111/tpj.15236] [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: 10/26/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
As the frequency of extreme environmental events is expected to increase with climate change, identifying candidate genes for stabilizing the protein composition of legume seeds or optimizing this in a given environment is increasingly important. To elucidate the genetic determinants of seed protein plasticity, major seed proteins from 200 ecotypes of Medicago truncatula grown in four contrasting environments were quantified after one-dimensional electrophoresis. The plasticity index of these proteins was recorded for each genotype as the slope of Finlay and Wilkinson's regression and then used for genome-wide association studies (GWASs), enabling the identification of candidate genes for determining this plasticity. This list was enriched in genes related to transcription, DNA repair and signal transduction, with many of them being stress responsive. Other over-represented genes were related to sulfur and aspartate family pathways leading to the synthesis of the nutritionally essential amino acids methionine and lysine. By placing these genes in metabolic pathways, and using a M. truncatula mutant impaired in regenerating methionine from S-methylmethionine, we discovered that methionine recycling pathways are major contributors to globulin composition establishment and plasticity. These data provide a unique resource of genes that can be targeted to mitigate negative impacts of environmental stresses on seed protein composition.
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Affiliation(s)
- Kevin Cartelier
- Agroécologie, AgroSup Dijon, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Joseph Ly Vu
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Lucie Combes-Soia
- Physiologie de la Reproduction et des Comportements (PRC) UMR85, INRAE, CNRS, Université de Tours, IFCE, Nouzilly, France
| | - Valérie Labas
- Physiologie de la Reproduction et des Comportements (PRC) UMR85, INRAE, CNRS, Université de Tours, IFCE, Nouzilly, France
| | - Jean-Marie Prosperi
- Genetic Improvement and Adaptation of Mediterranean and Tropical Plants (AGAP), INRAE, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD, Montpellier SupAgro, Montpellier, France
| | - Julia Buitink
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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Watanabe M, Chiba Y, Hirai MY. Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:643403. [PMID: 34025692 PMCID: PMC8137854 DOI: 10.3389/fpls.2021.643403] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 05/19/2023]
Abstract
The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.
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Affiliation(s)
- Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yukako Chiba
- Graduate School of Life Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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64
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García MJ, Lucena C, Romera FJ. Ethylene and Nitric Oxide Involvement in the Regulation of Fe and P Deficiency Responses in Dicotyledonous Plants. Int J Mol Sci 2021; 22:4904. [PMID: 34063156 PMCID: PMC8125717 DOI: 10.3390/ijms22094904] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 11/16/2022] Open
Abstract
Iron (Fe) and phosphorus (P) are two essential elements for plant growth. Both elements are abundant in soils but with poor availability for plants, which favor their acquisition by developing morphological and physiological responses in their roots. Although the regulation of the genes related to these responses is not totally known, ethylene (ET) and nitric oxide (NO) have been involved in the activation of both Fe-related and P-related genes. The common involvement of ET and NO suggests that they must act in conjunction with other specific signals, more closely related to each deficiency. Among the specific signals involved in the regulation of Fe- or P-related genes have been proposed Fe-peptides (or Fe ion itself) and microRNAs, like miR399 (P), moving through the phloem. These Fe- or P-related phloem signals could interact with ET/NO and confer specificity to the responses to each deficiency, avoiding the induction of the specific responses when ET/NO increase due to other nutrient deficiencies or stresses. Besides the specificity conferred by these signals, ET itself could confer specificity to the responses to Fe- or P-deficiency by acting through different signaling pathways in each case. Given the above considerations, there are preliminary results suggesting that ET could regulate different nutrient responses by acting both in conjunction with other signals and through different signaling pathways. Because of the close relationship among these two elements, a better knowledge of the physiological and molecular basis of their interaction is necessary to improve their nutrition and to avoid the problems associated with their misuse. As examples of this interaction, it is known that Fe chlorosis can be induced, under certain circumstances, by a P over- fertilization. On the other hand, Fe oxides can have a role in the immobilization of P in soils. Qualitative and quantitative assessment of the dynamic of known Fe- and P-related genes expression, selected ad hoc and involved in each of these deficiencies, would allow us to get a profound knowledge of the processes that regulate the responses to both deficiencies. The better knowledge of the regulation by ET of the responses to these deficiencies is necessary to properly understand the interactions between Fe and P. This will allow the obtention of more efficient varieties in the absorption of P and Fe, and the use of more rational management techniques for P and Fe fertilization. This will contribute to minimize the environmental impacts caused by the use of P and Fe fertilizers (Fe chelates) in agriculture and to adjust the costs for farmers, due to the high prices and/or scarcity of Fe and P fertilizers. This review aims to summarize the latest advances in the knowledge about Fe and P deficiency responses, analyzing the similarities and differences among them and considering the interactions among their main regulators, including some hormones (ethylene) and signaling substances (NO and GSNO) as well as other P- and Fe-related signals.
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Affiliation(s)
- María José García
- Department of Botany, Ecology and Plant Physiology, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Carlos Lucena
- Department of Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, 14071 Córdoba, Spain;
| | - Francisco Javier Romera
- Department of Agronomy, (DAUCO-María de Maeztu Unit of Excellence) Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, 14071 Córdoba, Spain;
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Zuo D, Li C, Liu T, Yue M, Zhang J, Ning G. Construction and validation of a metabolic risk model predicting prognosis of colon cancer. Sci Rep 2021; 11:6837. [PMID: 33767290 PMCID: PMC7994414 DOI: 10.1038/s41598-021-86286-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/12/2021] [Indexed: 01/31/2023] Open
Abstract
Metabolic genes have played a significant role in tumor development and prognosis. In this study, we constructed a metabolic risk model to predict the prognosis of colon cancer based on The Cancer Genome Atlas (TCGA) and validated the model by Gene Expression Omnibus (GEO). We extracted 753 metabolic genes and identified 139 differentially expressed genes (DEGs) from TCGA database. Then we conducted univariate cox regression analysis and Least Absolute Shrinkage and Selection Operator Cox regression analysis to identify prognosis-related genes and construct the metabolic risk model. An eleven-gene prognostic model was constructed after 1000 resamples. The gene signature has been proved to have an excellent ability to predict prognosis by Kaplan-Meier analysis, time-dependent receiver operating characteristic, risk score, univariate and multivariate cox regression analysis based on TCGA. Then we validated the model by Kaplan-Meier analysis and risk score based on GEO database. Finally, we performed a weighted gene co-expression network analysis and protein-protein interaction network on DEGs, and Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology enrichment analyses were conducted. The results of functional analyses showed that most significantly enriched pathways focused on metabolism, especially glucose and lipid metabolism pathways.
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Affiliation(s)
- Didi Zuo
- grid.430605.4Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin Province China
| | - Chao Li
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Tao Liu
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Meng Yue
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Jiantao Zhang
- grid.430605.4Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, Jilin China
| | - Guang Ning
- grid.430605.4Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin Province China ,grid.16821.3c0000 0004 0368 8293Key Laboratory for Endocrine and Metabolic Diseases of Ministry of Health of China, Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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66
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Orłowska R. Barley somatic embryogenesis-an attempt to modify variation induced in tissue culture. ACTA ACUST UNITED AC 2021; 28:9. [PMID: 33726856 PMCID: PMC7962293 DOI: 10.1186/s40709-021-00138-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/19/2021] [Indexed: 11/25/2022]
Abstract
Background Somatic embryogenesis is a phenomenon carried out in an environment that generates abiotic stress. Thus, regenerants may differ from the source of explants at the morphological, genetic, and epigenetic levels. The DNA changes may be the outcome of induction media ingredients (i.e., copper and silver ions) and their concentrations and time of in vitro cultures. Results This study optimised the level of copper and silver ion concentration in culture media parallel with the induction medium longevity step towards obtaining barley regenerants via somatic embryogenesis with a minimum or maximum level of tissue culture-induced differences between the donor plant and its regenerants. The optimisation process is based on tissue culture-induced variation evaluated via the metAFLP approach for regenerants derived under varying in vitro tissue culture conditions and exploited by the Taguchi method. In the optimisation and verification experiments, various copper and silver ion concentrations and the different number of days differentiated the tested trials concerning the tissue culture-induced variation level, DNA demethylation, and de novo methylation, including symmetric (CG, CHG) and asymmetric (CHH) DNA sequence contexts. Verification of optimised conditions towards obtaining regenerants with minimum and maximum variability compared to donor plants proved useful. The main changes that discriminate optimised conditions belonged to DNA demethylation events with particular stress on CHG context. Conclusions The combination of tissue culture-induced variation evaluated for eight experimental trials and implementation of the Taguchi method allowed the optimisation of the in vitro tissue culture conditions towards the minimum and maximum differences between a source of tissue explants (donor plant) and its regenerants from somatic embryos. The tissue culture-induced variation characteristic is mostly affected by demethylation with preferences towards CHG sequence context.
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Affiliation(s)
- Renata Orłowska
- Plant Breeding & Acclimatization Institute-National Research Institute, 05-870 Błonie, Radzików, Poland.
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67
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Banuelos J, Martínez-Romero E, Montaño NM, Camargo-Ricalde SL. Folates in legume root nodules. PHYSIOLOGIA PLANTARUM 2021; 171:447-452. [PMID: 32984974 DOI: 10.1111/ppl.13218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/04/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Folates are multifunctional metabolites in plants that are essential for cell division, nucleic acids and amino acid synthesis. During symbiotic nitrogen fixation in legumes, these cofactors are needed for de novo purine biosynthesis, meaning that changes in the folate pools could directly affect the flow of fixed nitrogen to the plant. Its role related to symbiotic nitrogen fixation has not been yet explored, but recent data suggest a relevant role during the first steps. Transcriptomic, metabolomic and proteomic analyses indicate that folates are accumulated in symbiotic plant tissue, as they are involved, not only in de novo purines biosynthesis, but in nitrogen translocation, endoreduplication and phytohormones biosynthesis. Understanding the possible implication of folate pools during the nitrogen fixation and assimilation, might aid for new engineering targets, in relation to the two transformylations or the production of glycine by serine hydroxymethyltransferase during the de novo purine biosynthetic pathway. In this review, we intend to deliver and discuss the available evidence that support a relevant role of folates during the symbiotic nitrogen fixation.
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Affiliation(s)
- Jacob Banuelos
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autonoma Metropolitana, Mexico City, Mexico
| | | | - Noé Manuel Montaño
- Departamento de Biología, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Sara Lucía Camargo-Ricalde
- Departamento de Biología, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
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Luo W, Gong Y, Tang Y, Pu P, Yang X, Zhou C, Lv J, Yan X. Glutathione and ethylene biosynthesis reveal that the glume and lemma have better tolerance to water deficit in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:120-129. [PMID: 33485150 DOI: 10.1016/j.plaphy.2021.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
As senescence progresses, the sensitivity of wheat organs to plant hormones during the grain-filling stages cannot be ignored. Especially under water deficit situation, non-leaf organs (spikes) have better photosynthesis and drought-tolerance traits than flag leaves. However, the mechanism of ethylene synthesis in wheat organs under water deficit remains unclear. We have studied the influence of water deficit in wheat flag leaves and spike bracts on photosynthetic parameters and on the expression of key enzymes involved in the ethylene biosynthesis pathway during the late grain-filling stages. More stable chlorophyll content (Chl), maximum PSII quantum yield (Fv/Fm), nonphotochemical quenching (NPQ) and maximal efficiency of PSII photochemistry under light adaptation (Fv'/Fm') were observed in the spike bracts than that in the flag leaves during the late grain-filling stages. In addition, the activity of glutathione reductase (GR), γ-glutamylcysteine synthetase (γ-ECS), 1-aminocyclopropane-1-carboxylic (ACC) acid synthase (ACS), and ACC oxidase (ACO) induced ethylene synthesis and influenced plant growth. Further analysis of genes encoding cysteine-ethylene related proteins (γ-ECS, GR, ACO, ACS1, and ASC2) demonstrated that ear organs and flag leaves exhibited different expression patterns. These findings will facilitate future investigations of the regulatory senescence response mechanisms of cysteine interaction with ethylene in wheat under conditions of drought stress.
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Affiliation(s)
- Wen Luo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yanzhen Gong
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Yan Tang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Peng Pu
- College of Vveterinary Mmedicine, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xiangna Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Chunju Zhou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jinyin Lv
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Xia Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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69
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Angulo M, García MJ, Alcántara E, Pérez-Vicente R, Romera FJ. Comparative Study of Several Fe Deficiency Responses in the Arabidopsis thaliana Ethylene Insensitive Mutants ein2-1 and ein2-5. PLANTS (BASEL, SWITZERLAND) 2021; 10:262. [PMID: 33573082 PMCID: PMC7912600 DOI: 10.3390/plants10020262] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/01/2023]
Abstract
Iron (Fe) is an essential micronutrient for plants since it participates in essential processes such as photosynthesis, respiration and nitrogen assimilation. Fe is an abundant element in most soils, but its availability for plants is low, especially in calcareous soils. Fe deficiency causes Fe chlorosis, which can affect the productivity of the affected crops. Plants favor Fe acquisition by developing morphological and physiological responses in their roots. Ethylene (ET) and nitric oxide (NO) have been involved in the induction of Fe deficiency responses in dicot (Strategy I) plants, such as Arabidopsis. In this work, we have conducted a comparative study on the development of subapical root hairs, of the expression of the main Fe acquisition genes FRO2 and IRT1, and of the master transcription factor FIT, in two Arabidopsis thaliana ET insensitive mutants, ein2-1 and ein2-5, affected in EIN2, a critical component of the ET transduction pathway. The results obtained show that both mutants do not induce subapical root hairs either under Fe deficiency or upon treatments with the ET precursor 1-aminocyclopropane-1-carboxylate (ACC) and the NO donor S-nitrosoglutathione (GSNO). By contrast, both of them upregulate the Fe acquisition genes FRO2 and IRT1 (and FIT) under Fe deficiency. However, the upregulation was different when the mutants were exposed to ET [ACC and cobalt (Co), an ET synthesis inhibitor] and GSNO treatments. All these results clearly support the participation of ET and NO, through EIN2, in the regulation of subapical root hairs and Fe acquisition genes. The results will be discussed, taking into account the role of both ET and NO in the regulation of Fe deficiency responses.
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Affiliation(s)
- Macarena Angulo
- Department of Agronomy, Campus de Excelencia Internacional Agroalimentario CeiA3 de Rabanales, Universidad de Córdoba, Edificio Celestino Mutis, 14071 Córdoba, Spain; (M.A.); (E.A.); (F.J.R.)
| | - María José García
- Department of Botany, Ecology and Plant Physiology, Campus de Excelencia Internacional Agroalimentario CeiA3 de Rabanales, Universidad de Córdoba, Edificio Celestino Mutis, 14071 Córdoba, Spain;
| | - Esteban Alcántara
- Department of Agronomy, Campus de Excelencia Internacional Agroalimentario CeiA3 de Rabanales, Universidad de Córdoba, Edificio Celestino Mutis, 14071 Córdoba, Spain; (M.A.); (E.A.); (F.J.R.)
| | - Rafael Pérez-Vicente
- Department of Botany, Ecology and Plant Physiology, Campus de Excelencia Internacional Agroalimentario CeiA3 de Rabanales, Universidad de Córdoba, Edificio Celestino Mutis, 14071 Córdoba, Spain;
| | - Francisco Javier Romera
- Department of Agronomy, Campus de Excelencia Internacional Agroalimentario CeiA3 de Rabanales, Universidad de Córdoba, Edificio Celestino Mutis, 14071 Córdoba, Spain; (M.A.); (E.A.); (F.J.R.)
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Fatma M, Iqbal N, Gautam H, Sehar Z, Sofo A, D’Ippolito I, Khan NA. Ethylene and Sulfur Coordinately Modulate the Antioxidant System and ABA Accumulation in Mustard Plants under Salt Stress. PLANTS 2021; 10:plants10010180. [PMID: 33478097 PMCID: PMC7835815 DOI: 10.3390/plants10010180] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 02/01/2023]
Abstract
This study explored the interactive effect of ethephon (2-chloroethyl phosphonic acid; an ethylene source) and sulfur (S) in regulating the antioxidant system and ABA content and in maintaining stomatal responses, chloroplast structure, and photosynthetic performance of mustard plants (Brassica juncea L. Czern.) grown under 100 mM NaCl stress. The treatment of ethephon (200 µL L−1) and S (200 mg S kg−1 soil) together markedly improved the activity of enzymatic and non-enzymatic components of the ascorbate-glutathione (AsA-GSH) cycle, resulting in declined oxidative stress through lesser content of sodium (Na+) ion and hydrogen peroxide (H2O2) in salt-stressed plants. These changes promoted the development of chloroplast thylakoids and photosynthetic performance under salt stress. Ethephon + S also reduced abscisic acid (ABA) accumulation in guard cell, leading to maximal stomatal conductance under salt stress. The inhibition of ethylene action by norbornadiene (NBD) in salt- plus non-stressed treated plants increased ABA and H2O2 contents, and reduced stomatal opening, suggesting the involvement of ethephon and S in regulating stomatal conductance. These findings suggest that ethephon and S modulate antioxidant system and ABA accumulation in guard cells, controlling stomatal conductance, and the structure and efficiency of the photosynthetic apparatus in plants under salt stress.
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Affiliation(s)
- Mehar Fatma
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (M.F.); (H.G.); (Z.S.)
| | - Noushina Iqbal
- Department of Botany, Jamia Hamdard, New Delhi 110062, India;
| | - Harsha Gautam
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (M.F.); (H.G.); (Z.S.)
| | - Zebus Sehar
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (M.F.); (H.G.); (Z.S.)
| | - Adriano Sofo
- Department of European and Mediterranean Cultures: Architecture, Environment and Cultural Heritage (DiCEM), University of Basilicata, Via Lanera, 20, 75100 Matera, Italy;
- Correspondence: (A.S.); (N.A.K.)
| | - Ilaria D’Ippolito
- Department of European and Mediterranean Cultures: Architecture, Environment and Cultural Heritage (DiCEM), University of Basilicata, Via Lanera, 20, 75100 Matera, Italy;
| | - Nafees A. Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (M.F.); (H.G.); (Z.S.)
- Correspondence: (A.S.); (N.A.K.)
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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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Pattyn J, Vaughan‐Hirsch J, Van de Poel B. The regulation of ethylene biosynthesis: a complex multilevel control circuitry. THE NEW PHYTOLOGIST 2021; 229:770-782. [PMID: 32790878 PMCID: PMC7820975 DOI: 10.1111/nph.16873] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/04/2020] [Indexed: 05/06/2023]
Abstract
The gaseous plant hormone ethylene is produced by a fairly simple two-step biosynthesis route. Despite this pathway's simplicity, recent molecular and genetic studies have revealed that the regulation of ethylene biosynthesis is far more complex and occurs at different layers. Ethylene production is intimately linked with the homeostasis of its general precursor S-adenosyl-l-methionine (SAM), which experiences transcriptional and posttranslational control of its synthesising enzymes (SAM synthetase), as well as the metabolic flux through the adjacent Yang cycle. Ethylene biosynthesis continues from SAM by two dedicated enzymes: 1-aminocyclopropane-1-carboxylic (ACC) synthase (ACS) and ACC oxidase (ACO). Although the transcriptional dynamics of ACS and ACO have been well documented, the first transcription factors that control ACS and ACO expression have only recently been discovered. Both ACS and ACO display a type-specific posttranslational regulation that controls protein stability and activity. The nonproteinogenic amino acid ACC also shows a tight level of control through conjugation and translocation. Different players in ACC conjugation and transport have been identified over the years, however their molecular regulation and biological significance is unclear, yet relevant, as ACC can also signal independently of ethylene. In this review, we bring together historical reports and the latest findings on the complex regulation of the ethylene biosynthesis pathway in plants.
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Affiliation(s)
- Jolien Pattyn
- Molecular Plant Hormone Physiology LaboratoryDivision of Crop BiotechnicsDepartment of BiosystemsUniversity of LeuvenWillem de Croylaan 42Leuven3001Belgium
| | - John Vaughan‐Hirsch
- Molecular Plant Hormone Physiology LaboratoryDivision of Crop BiotechnicsDepartment of BiosystemsUniversity of LeuvenWillem de Croylaan 42Leuven3001Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology LaboratoryDivision of Crop BiotechnicsDepartment of BiosystemsUniversity of LeuvenWillem de Croylaan 42Leuven3001Belgium
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73
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Xiao C, Huang M, Gao J, Wang Z, Zhang D, Zhang Y, Yan L, Yu X, Li B, Shen Y. Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease. BMC Genomics 2020; 21:880. [PMID: 33297944 PMCID: PMC7727141 DOI: 10.1186/s12864-020-07286-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022] Open
Abstract
Background Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emerging and appearing in new areas at a very high intensity. A better understanding of the natural defense mechanisms against PI in different potato cultivars especially at the protein level is still lacking. Therefore, to elucidate potato proteome response to PI, we investigated changes in the proteome and leaf morphology of three potato cultivars, namely; Favorita (FA), Mira (MA), and E-malingshu N0.14 (E14) infected with PI by using the iTRAQ-based quantitative proteomics analysis. Results A total of 3306 proteins were found in the three potato genotypes, and 2044 proteins were quantified. Cluster analysis revealed MA and E14 clustered together separately from FA. The protein profile and related functions revealed that the cultivars shared a typical hypersensitive response to PI, including induction of elicitors, oxidative burst, and suppression of photosynthesis in the potato leaves. Meanwhile, MA and E14 deployed additional specific response mechanism different from FA, involving high induction of protease inhibitors, serine/threonine kinases, terpenoid, hormone signaling, and transport, which contributed to MA tolerance of LBD. Furthermore, inductions of pathogenesis-related proteins, LRR receptor-like kinases, mitogen-activated protein kinase, WRKY transcription factors, jasmonic acid, and phenolic compounds mediate E14 resistance against LBD. These proteins were confirmed at the transcription level by a quantitative polymerase chain reaction and at the translation level by western-blot. Conclusions We found several proteins that were differentially abundant among the cultivars, that includes common and cultivar specific proteins which highlighted similarities and significant differences between FA, MA, and E14 in terms of their defense response to PI. Here the specific accumulation of mitogen-activated protein kinase, Serine/threonine kinases, WRKY transcription played a positive role in E14 immunity against PI. The candidate proteins identified reported in this study will form the basis of future studies and may improve our understanding of the molecular mechanisms of late blight disease resistance in potato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07286-3.
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Affiliation(s)
- Chunfang Xiao
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianhua Gao
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Zhen Wang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Denghong Zhang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Yuanxue Zhang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Lei Yan
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Yanfen Shen
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China. .,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China.
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74
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The Versatile Roles of Sulfur-Containing Biomolecules in Plant Defense-A Road to Disease Resistance. PLANTS 2020; 9:plants9121705. [PMID: 33287437 PMCID: PMC7761819 DOI: 10.3390/plants9121705] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023]
Abstract
Sulfur (S) is an essential plant macronutrient and the pivotal role of sulfur compounds in plant disease resistance has become obvious in recent decades. This review attempts to recapitulate results on the various functions of sulfur-containing defense compounds (SDCs) in plant defense responses to pathogens. These compounds include sulfur containing amino acids such as cysteine and methionine, the tripeptide glutathione, thionins and defensins, glucosinolates and phytoalexins and, last but not least, reactive sulfur species and hydrogen sulfide. SDCs play versatile roles both in pathogen perception and initiating signal transduction pathways that are interconnected with various defense processes regulated by plant hormones (salicylic acid, jasmonic acid and ethylene) and reactive oxygen species (ROS). Importantly, ROS-mediated reversible oxidation of cysteine residues on plant proteins have profound effects on protein functions like signal transduction of plant defense responses during pathogen infections. Indeed, the multifaceted plant defense responses initiated by SDCs should provide novel tools for plant breeding to endow crops with efficient defense responses to invading pathogens.
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75
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Zaini PA, Feinberg NG, Grilo FS, Saxe HJ, Salemi MR, Phinney BS, Crisosto CH, Dandekar AM. Comparative Proteomic Analysis of Walnut ( Juglans regia L.) Pellicle Tissues Reveals the Regulation of Nut Quality Attributes. Life (Basel) 2020; 10:E314. [PMID: 33261033 PMCID: PMC7760677 DOI: 10.3390/life10120314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022] Open
Abstract
Walnuts (Juglans regia L.) are a valuable dietary source of polyphenols and lipids, with increasing worldwide consumption. California is a major producer, with 'Chandler' and 'Tulare' among the cultivars more widely grown. 'Chandler' produces kernels with extra light color at a higher frequency than other cultivars, gaining preference by growers and consumers. Here we performed a deep comparative proteome analysis of kernel pellicle tissue from these two valued genotypes at three harvest maturities, detecting a total of 4937 J. regia proteins. Late and early maturity stages were compared for each cultivar, revealing many developmental responses common or specific for each cultivar. Top protein biomarkers for each developmental stage were also selected based on larger fold-change differences and lower variance among replicates, including proteins for biosynthesis of lipids and phenols, defense-related proteins and desiccation stress-related proteins. Comparison between the genotypes also revealed the common and specific protein repertoires, totaling 321 pellicle proteins with differential abundance at harvest stage. The proteomics data provides clues on antioxidant, secondary, and hormonal metabolism that could be involved in the loss of quality in the pellicles during processing for commercialization.
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Affiliation(s)
- Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Noah G. Feinberg
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Filipa S. Grilo
- Department of Food Sciences and Technology, University of California, Davis, CA 95616, USA;
| | - Houston J. Saxe
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Michelle R. Salemi
- Proteomics Core Facility, University of California, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Carlos H. Crisosto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
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76
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Sooklal SA, Mpangase PT, Tomescu MS, Aron S, Hazelhurst S, Archer RH, Rumbold K. Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. Sci Rep 2020; 10:20539. [PMID: 33239700 PMCID: PMC7688953 DOI: 10.1038/s41598-020-77598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022] Open
Abstract
Dichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly, there is a severe lack in knowledge on a genetic level for fluorometabolite-producing plants, impeding research on the subject. Here, we report on the first transcriptome for D. cymosum and investigate the wound response for insights into fluorometabolite production. Mechanical wounding studies were performed and libraries of the unwounded (control) and wounded (30 and 60 min post wounding) plant were sequenced using the Illumina HiSeq platform. A combined reference assembly generated 77,845 transcripts. Using the SwissProt, TrEMBL, GO, eggNOG, KEGG, Pfam, EC and PlantTFDB databases, a 69% annotation rate was achieved. Differential expression analysis revealed the regulation of 364 genes in response to wounding. The wound responses in D. cymosum included key mechanisms relating to signalling cascades, phytohormone regulation, transcription factors and defence-related secondary metabolites. However, the role of fluoroacetate in inducible wound responses remains unclear. Bacterial fluorinases were searched against the D. cymosum transcriptome but transcripts with homology were not detected suggesting the presence of a potentially different fluorinating enzyme in plants. Nevertheless, the transcriptome produced in this study significantly increases genetic resources available for D. cymosum and will assist with future research into fluorometabolite-producing plants.
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Affiliation(s)
- Selisha A Sooklal
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Phelelani T Mpangase
- Sydney Brenner Institute for Molecular Biosciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Mihai-Silviu Tomescu
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Biosciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Biosciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Robert H Archer
- National Herbarium, South African National Biodiversity Institute, Pretoria, 0186, South Africa
| | - Karl Rumbold
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2000, South Africa.
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77
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Edwards H, Yang Z, Xu P. Characterization of Met25 as a color associated genetic marker in Yarrowia lipolytica. Metab Eng Commun 2020; 11:e00147. [PMID: 33083227 PMCID: PMC7554020 DOI: 10.1016/j.mec.2020.e00147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Yarrowia lipolytica offers an ideal host for biosynthesis of high value natural products and oleochemicals through metabolic engineering despite being restricted to a limited number of selective markers, and counter-selection achieved primarily with URA3. In this work, we investigate MET25, a locus encoding sulfide housekeeping gene within the cell, to be exploited as a standard genetic marker. Divalent lead supplemented in media induces lead sulfide (PbS) aggregation in MET25-deficient cells such that deficient cells grow brown/black, and cells with functional copies of MET25 grow white. Loss of MET25 did not induce strict auxotrophic requirements for methionine in Y. lipolytica, indicating MET25 deficiency could be rescued by alternative pathways. Plasmid and chromosomal-based complementation of MET25 in the met25 deficient cells on a double layer agar plate with nutrient gradients demonstrates delayed phenotype (white morphology) restoration, indicating post-transcriptional feedback regulation of methionine biosynthesis in this yeast. MET25 deficient Y. lipolytica could be used as an efficient whole-cell lead sensor with detection limit as low as 10 ppm of lead in drinking water. We further tested whether MET25 deficiency can be exploited to confer resistance to methyl-mercury through chemical neutralization and detoxification. Kinetic growth curves of wild type and MET25-deficient cells were obtained under varying concentrations of methylmercury and cellular toxicity to methyl mercury was calculated from the Hill equation. Our results indicate that methylmecury may not be used as the counter-selectable marker due to insignificant changes of growth fitness. This work demonstrates the utility of using MET25 as a sensitive lead sensor and the challenges of using MET25 as a counter-selectable genetic marker, as well as the complex regulation of methionine biosynthesis in Y. lipolyitca, which may shed lights for us to develop valuable biotechnological applications centering around the sulfur house-keeping metabolism of the nonconventional yeast. Sulfur house-keeping gene MET25 was characterized as a standard genetic marker in Y. lipolytica. MET25 deficiency leads to visual phenotypic change of yeast colony with brown/black pigmentation. Delayed phenotype restoration indicates post-transcriptional feedback regulation of methionine biosynthesis. MET25 deficiency was exploited as a sensitive whole-cell sensor to detect lead in drinking water. MET25 may not be used as the counter-selectable marker due to insignificant changes of growth fitness when the cell is challenged with methylmercury.
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Affiliation(s)
- Harley Edwards
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Zhiliang Yang
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
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Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%. Sci Rep 2020; 10:17219. [PMID: 33057137 PMCID: PMC7560729 DOI: 10.1038/s41598-020-73709-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.
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79
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Kadam SB, Pable AA, Barvkar VT. Mycorrhiza induced resistance (MIR): a defence developed through synergistic engagement of phytohormones, metabolites and rhizosphere. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:880-890. [PMID: 32586416 DOI: 10.1071/fp20035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Plants get phosphorus, water and other soil nutrients at the cost of sugar through mycorrhizal symbiotic association. A common mycorrhizal network (CMN) - a dense network of mycorrhizal hyphae - provides a passage for exchange of chemicals and signals between the plants sharing CMN. Mycorrhisation impact plants at hormonal, physiological and metabolic level and successful symbiosis also regulates ecology of the plant rhizosphere. Apart from nutritional benefits, mycorrhisation provides an induced resistance to the plants known as mycorrhiza induced resistance (MIR). MIR is effective against soil as well as foliar pathogens and pest insects. In this review, molecular mechanisms underlying MIR such as role of phytohormones, their cross talk and priming effect are discussed. Evidence of MIR against economically important pathogens and pest insects in different plants is summarised. Mycorrhiza induces many plant secondary metabolites, many of which have a role in plant defence. Involvement of these secondary metabolites in mycorrhisation and their putative role in MIR are further reviewed. Controversies about MIR are also briefly discussed in order to provide insights on the scope for research about MIR. We have further extended our review with an open ended discussion about the possibilities for transgenerational MIR.
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Affiliation(s)
- Swapnil B Kadam
- Department of Botany, Savitribai Phule Pune University, Pune-411007, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune-411007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune-411007, India; and Corresponding authors. ;
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Li Z, Hou J, Zhang Y, Zeng W, Cheng B, Hassan MJ, Zhang Y, Pu Q, Peng Y. Spermine Regulates Water Balance Associated with Ca2+-Dependent Aquaporin (TrTIP2-1, TrTIP2-2 and TrPIP2-7) Expression in Plants under Water Stress. PLANT & CELL PHYSIOLOGY 2020; 61:1576-1589. [PMID: 32544243 DOI: 10.1093/pcp/pcaa080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/09/2020] [Indexed: 05/20/2023]
Abstract
Spermine (Spm) regulates water balance involved in water channel proteins, aquaporins (AQPs), in plants. An increase in endogenous Spm content via exogenous Spm application significantly improved cell membrane stability, photosynthesis, osmotic adjustment (OA) and water use efficiency (WUE) contributing to enhanced tolerance to water stress in white clover. Spm upregulated TrTIP2-1, TrTIP2-2 and TrPIP2-7 expressions and also increased the abundance of TIP2 and PIP2-7 proteins in white clover under water stress. Spm quickly activated intracellular Ca2+ signaling and Spm-induced TrTIP2-2 and TrPIP2-7 expressions could be blocked by Ca2+ channel blockers and the inhibitor of Ca2+-dependent protein kinase in leaves of white clover. TrSAMS in relation to Spm biosynthesis was first cloned from white clover and the TrSAMS was located in the nucleus. Transgenic Arabidopsis overexpressing the TrSAMS had significantly higher endogenous Spm content and improved cell membrane stability, photosynthesis, OA, WUE and transcript levels of AtSIP1-1, AtSIP1-2, AtTIP2-1, AtTIP2-2, AtPIP1-2, AtPIP2-1 and AtNIP2-1 than wild type in response to water stress. Current findings indicate that Spm regulates water balance via an enhancement in OA, WUE and water transport related to Ca2+-dependent AQP expression in plants under water stress.
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Affiliation(s)
- Zhou Li
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jieru Hou
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Weihang Zeng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bizhen Cheng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Jawad Hassan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Youzhi Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Pu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Peng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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81
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Oliveira TDR, Aragão VPM, Moharana KC, Fedosejevs E, do Amaral FP, Sousa KR, Thelen JJ, Venâncio TM, Silveira V, Santa-Catarina C. Light spectra affect the in vitro shoot development of Cedrela fissilis Vell. (Meliaceae) by changing the protein profile and polyamine contents. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140529. [PMID: 32853775 DOI: 10.1016/j.bbapap.2020.140529] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022]
Abstract
The light spectrum quality is an important signal for plant growth and development. We evaluated the effects of different light spectra on the in vitro shoot development of Cedrela fissilis and its proteomic and polyamine (PA) profiles. Cotyledonary and apical nodal segments were grown under different light emitting diodes (LED) and fluorescent lamps. Shoots from cotyledonary nodal segments cultured with 6-benzyladenine (BA) that were grown under WmBdR LED showed increased length and higher fresh and dry matter compared to shoots grown under fluorescent lamps. A nonredundant protein databank generated by transcriptome sequencing and the de novo assembly of C. fissilis improved, and almost doubled, the protein identification compared to a Citrus sinensis databank. A total of 616 proteins were identified, with 23 up- and 103 down-accumulated in the shoots under WmBdR LEDs compared to fluorescent lamps. Most differentially accumulated proteins in shoots grown under the WmBdR LED lamp treatment compared to the fluorescent lamp treatment are involved in responding to metabolic processes, stress, biosynthetic and cellular protein modifications, and light stimulus processes. Among the proteins, the up-accumulation of argininosuccinate synthase was associated with an increase in the free putrescine content and, consequently, with higher shoot elongation under WmBdR LED. The down-accumulation of calreticulin, heat shock proteins, plastid-lipid-associated protein, ubiquitin-conjugating enzymes, and ultraviolet-B receptor UVR8 isoform X1 could be related to the longer shoot length noted under LED treatment. This study provides important data related to the effects of the light spectrum quality on in vitro morphogenesis through the modulation of specific proteins and free putrescine biosynthesis in C. fissilis, an endangered wood species from the Brazilian Atlantic Forest of economic and ecological relevance. The nonredundant protein databank of C. fissilis is available via ProteomeXchange under identifier PXD018020.
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Affiliation(s)
- Tadeu Dos Reis Oliveira
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Biociências e Biotecnologia (CBB), Laboratório de Biologia Celular e Tecidual (LBCT), Av. Alberto Lamego 2000, 28013-602, Campos Dos Goytacazes, RJ, Brazil
| | - Victor Paulo Mesquita Aragão
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Biociências e Biotecnologia (CBB), Laboratório de Biologia Celular e Tecidual (LBCT), Av. Alberto Lamego 2000, 28013-602, Campos Dos Goytacazes, RJ, Brazil
| | - Kanhu Charan Moharana
- UENF, CBB, Laboratório de Química e Função de Proteínas e Peptídeos, Campos dos Goytacazes, RJ, Brazil
| | - Eric Fedosejevs
- University of Missouri, Department of Biochemistry, Christopher S. Bond Life Sciences Center, 65211, Columbia, MO, USA
| | - Fernanda Plucani do Amaral
- University of Missouri, Department of Biochemistry, Christopher S. Bond Life Sciences Center, 65211, Columbia, MO, USA
| | - Kariane Rodrigues Sousa
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Biociências e Biotecnologia (CBB), Laboratório de Biologia Celular e Tecidual (LBCT), Av. Alberto Lamego 2000, 28013-602, Campos Dos Goytacazes, RJ, Brazil
| | - Jay J Thelen
- University of Missouri, Department of Biochemistry, Christopher S. Bond Life Sciences Center, 65211, Columbia, MO, USA
| | - Thiago Motta Venâncio
- UENF, CBB, Laboratório de Química e Função de Proteínas e Peptídeos, Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- UENF, CBB, Laboratório de Biotecnologia (LBT), Campos dos Goytacazes, RJ, Brazil; UENF, Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Campos dos Goytacazes, RJ, Brazil
| | - Claudete Santa-Catarina
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Biociências e Biotecnologia (CBB), Laboratório de Biologia Celular e Tecidual (LBCT), Av. Alberto Lamego 2000, 28013-602, Campos Dos Goytacazes, RJ, Brazil.
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82
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Bednarek PT, Zebrowski J, Orłowska R. Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture. Int J Mol Sci 2020; 21:E5770. [PMID: 32796744 PMCID: PMC7461140 DOI: 10.3390/ijms21165770] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Tissue culture is an essential tool for the regeneration of uniform plant material. However, tissue culture conditions can be a source of abiotic stress for plants, leading to changes in the DNA sequence and methylation patterns. Despite the growing evidence on biochemical processes affected by abiotic stresses, how these altered biochemical processes affect DNA sequence and methylation patterns remains largely unknown. In this study, the methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach was used to investigate de novo methylation, demethylation, and sequence variation in barley regenerants derived by anther culture. Additionally, we used Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy to identify the spectral features of regenerants, which were then analyzed by mediation analysis. The infrared spectrum ranges (710-690 and 1010-940 cm-1) identified as significant in the mediation analysis were most likely related to β-glucans, cellulose, and S-adenosyl-L-methionine (SAM). Additionally, the identified compounds participated as predictors in moderated mediation analysis, explaining the role of demethylation of CHG sites (CHG_DMV) in in vitro tissue culture-induced sequence variation, depending on the duration of tissue culture. The data demonstrate that ATR-FTIR spectroscopy is a useful tool for studying the biochemical compounds that may affect DNA methylation patterns and sequence variation, if combined with quantitative characteristics determined using metAFLP molecular markers and mediation analysis. The role of β-glucans, cellulose, and SAM in DNA methylation, and in cell wall, mitochondria, and signaling, are discussed to highlight the putative cellular mechanisms involved in sequence variation.
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Affiliation(s)
- Piotr T. Bednarek
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland;
| | - Jacek Zebrowski
- Institute of Biology and Biotechnology, University of Rzeszow, Al. Rejtana 16c A, 35-959 Rzeszow, Poland;
| | - Renata Orłowska
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland;
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83
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Wang B, Xu X, Liu X, Wang D, Zhuang H, He X, Han T, Hong J. Enolase-phosphatase 1 acts as an oncogenic driver in glioma. J Cell Physiol 2020; 236:1184-1194. [PMID: 32654229 DOI: 10.1002/jcp.29926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/01/2020] [Indexed: 12/15/2022]
Abstract
Enolase-phosphatase 1 (ENOPH1), a newly identified enzyme involved in l-methionine biosynthesis, is associated with anxiety and depression. In this study, ENOPH1 was found to play a crucial role in promoting the proliferation and migration of glioma cells. Among high-grade glioma patients, the overall survival of the group showing high ENOPH1 expression was shorter than that of the group showing low ENOPH1 expression. ENOPH1 knockdown inhibited glioma cell proliferation and migration. In parallel, ENOPH1 knockdown suppressed tumor growth capacity and prolonged survival in an orthotopic glioma model. Mechanistically, we found that ENOPH1 activates the PI3K/AKT/mTOR signaling pathway by regulating THEM4. In conclusion, ENOPH1 is an important mediator that promotes glioma cell proliferation and migration.
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Affiliation(s)
- Bo Wang
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative diseases, Tianjin Neurosurgical Institute, Tianjin, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Xin Xu
- Department of Neurosurgery, Xuanwu Hospital, International Neuroscience Institute, Capital Medical University, Beijing, China
| | - Xi Liu
- Department of Gastroenterology, Tianjin Nankai Hospital, Tianjin, China
| | - Dong Wang
- Department of Neurosurgery, Tianjin Medical University, General Hospital, Tianjin Key Laboratory of Injuries, Variations, and Regeneration of Nervous System, Tianjin Neurological Institute, Tianjin, China
| | - Hao Zhuang
- Department of Hepatic Biliary Pancreatic Surgery, Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xin He
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia.,Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - Tong Han
- Department of Medical Imaging, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative diseases, Tianjin Neurosurgical Institute, Tianjin, China
| | - Jian Hong
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative diseases, Tianjin Neurosurgical Institute, Tianjin, China
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84
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Minimal cobalt metabolism in the marine cyanobacterium Prochlorococcus. Proc Natl Acad Sci U S A 2020; 117:15740-15747. [PMID: 32576688 DOI: 10.1073/pnas.2001393117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.
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85
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Insights into the SAM Synthetase Gene Family and Its Roles in Tomato Seedlings under Abiotic Stresses and Hormone Treatments. PLANTS 2020; 9:plants9050586. [PMID: 32375329 PMCID: PMC7284622 DOI: 10.3390/plants9050586] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 11/26/2022]
Abstract
S-Adenosyl-L-methionine (SAM) is a key enzyme involved in many important biological processes, such as ethylene and polyamine biosynthesis, transmethylation, and transsulfuration. Here, the SAM synthetase (SAMS) gene family was studied in ten different plants (Arabidopsis, tomato, eggplant, sunflower, Medicago truncatula, soybean, rice, barley, Triticum urartu and sorghum) with respect to its physical structure, physicochemical characteristics, and post-transcriptional and post-translational modifications. Additionally, the expression patterns of SAMS genes in tomato were analyzed based on a real-time quantitative PCR assay and an analysis of a public expression dataset. SAMS genes of monocots were more conserved according to the results of a phylogenetic analysis and the prediction of phosphorylation and glycosylation patterns. SAMS genes showed differential expression in response to abiotic stresses and exogenous hormone treatments. Solyc01g101060 was especially expressed in fruit and root tissues, while Solyc09g008280 was expressed in leaves. Additionally, our results revealed that exogenous BR and ABA treatments strongly reduced the expression of tomato SAMS genes. Our research provides new insights and clues about the role of SAMS genes. In particular, these results can inform future functional analyses aimed at revealing the molecular mechanisms underlying the functions of SAMS genes in plants.
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86
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Zeng W, Niu L, Wang Z, Wang X, Wang Y, Pan L, Lu Z, Cui G, Weng W, Wang M, Meng X, Wang Z. Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model. HORTICULTURE RESEARCH 2020; 7:31. [PMID: 32194967 PMCID: PMC7072073 DOI: 10.1038/s41438-020-0249-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/27/2019] [Accepted: 01/07/2020] [Indexed: 05/21/2023]
Abstract
Peach (Prunus persica) is a typical climacteric fruit that produces ethylene rapidly during ripening, and its fruit softens quickly. Stony hard peach cultivars, however, do not produce large amounts of ethylene, and the fruit remains firm until fully ripe, thus differing from melting flesh peach cultivars. To identify the key proteins involved in peach fruit ripening, an antibody-based proteomic analysis was conducted. A mega-monoclonal antibody (mAb) library was generated and arrayed on a chip (mAbArray) at a high density, covering ~4950 different proteins of peach. Through the screening of peach fruit proteins with the mAbArray chip, differentially expressed proteins recognized by 1587 mAbs were identified, and 33 corresponding antigens were ultimately identified by immunoprecipitation and mass spectrometry. These proteins included not only important enzymes involved in ethylene biosynthesis, such as ACO1, SAHH, SAMS, and MetE, but also novel factors such as NUDT2. Furthermore, protein-protein interaction analysis identified a metabolon containing SAHH and MetE. By combining the antibody-based proteomic data with the transcriptomic and metabolic data, a mathematical model of ethylene biosynthesis in peach was constructed. Simulation results showed that MetE is an important regulator during peach ripening, partially through interaction with SAHH.
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Affiliation(s)
- Wenfang Zeng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | - Liang Niu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | | | - Xiaobei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | - Yan Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | - Lei Pan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | - Guochao Cui
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
| | | | | | - Xun Meng
- Abmart, 200233 Shanghai, China
- Northwest University, 710127 Xi’an, China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 450009 Zhengzhou, China
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87
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Silva F, Guirgis A, von Aderkas P, Borchers CH, Thornburg R. LC-MS/MS based comparative proteomics of floral nectars reveal different mechanisms involved in floral defense of Nicotiana spp., Petunia hybrida and Datura stramonium. J Proteomics 2020; 213:103618. [PMID: 31846763 DOI: 10.1016/j.jprot.2019.103618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/01/2019] [Accepted: 12/13/2019] [Indexed: 11/19/2022]
Abstract
Tobacco floral nectar (FN) is a biological fluid produced by nectaries composed of sugars, amino acids and proteins called nectarins, involved in the floral defense. FN provides an ideal source of nutrients for microorganisms. Understanding the role of nectar proteins is essential to predict impacts in microbial growth, composition and plants-pollinators interactions. Using LC-MS/MS-based comparative proteomic analysis we identified 22 proteins from P. hybrida, 35 proteins from D. stramonium, and 144 proteins from 23 species of Nicotiana. The data are available at ProteomeXchance (PXD014760). GO analysis and secretory signal prediction demonstrated that defense/stress was the largest group of proteins in the genus Nicotiana. The Nicotiana spp. proteome consisted of 105 exclusive proteins such as lipid transfer proteins (LTPs), Nectar Redox Cycle proteins, proteases inhibitors, and PR-proteins. Analysis by taxonomic sections demonstrated that LTPs were most abundant in Undulatae and Noctiflora, while nectarins were more abundant in Rusticae, Suaveolens, Polydicliae, and Alata sections. Peroxidases (Pox) and chitinases (Chit) were exclusive to P. hybrida, while D. stramonium had only seven unique proteins. Biochemical analysis confirmed these differences. These findings support the hypothesis that, although conserved, there is differential abundance of proteins related to defense/stress which may impact the mechanisms of floral defense. SIGNIFICANCE: This study represents a comparative proteomic analysis of floral nectars of the Nicotiana spp. with two correlated Solanaceous species. Significant differences were identified between the proteome of taxonomic sections providing relevant insights into the group of proteins related to defense/stress associated with Nectar Redox Cycle, antimicrobial proteins and signaling pathways. The activity of FNs proteins is suggested impact the microbial growth. The knowledge about these proteomes provides significant insights into the diversity of proteins secreted in the nectars and the array of mechanisms used by Nicotiana spp. in its floral defense.
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Affiliation(s)
- FredyA Silva
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Adel Guirgis
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA; Institute of Genetic Engineering and Biotechnology, Menofiya University, Sadat City, Egypt
| | - Patrick von Aderkas
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Christoph H Borchers
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, BC V8P 5C2, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Robert Thornburg
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.
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88
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Differential regulation of genes co-involved in aroma production and stress amelioration during salt acclimation in indica rice cultivars. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00418-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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89
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Lindermayr C, Rudolf EE, Durner J, Groth M. Interactions between metabolism and chromatin in plant models. Mol Metab 2020; 38:100951. [PMID: 32199818 PMCID: PMC7300381 DOI: 10.1016/j.molmet.2020.01.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND One of the fascinating aspects of epigenetic regulation is that it provides means to rapidly adapt to environmental change. This is particularly relevant in the plant kingdom, where most species are sessile and exposed to increasing habitat fluctuations due to global warming. Although the inheritance of epigenetically controlled traits acquired through environmental impact is a matter of debate, it is well documented that environmental cues lead to epigenetic changes, including chromatin modifications, that affect cell differentiation or are associated with plant acclimation and defense priming. Still, in most cases, the mechanisms involved are poorly understood. An emerging topic that promises to reveal new insights is the interaction between epigenetics and metabolism. SCOPE OF REVIEW This study reviews the links between metabolism and chromatin modification, in particular histone acetylation, histone methylation, and DNA methylation, in plants and compares them to examples from the mammalian field, where the relationship to human diseases has already generated a larger body of literature. This study particularly focuses on the role of reactive oxygen species (ROS) and nitric oxide (NO) in modulating metabolic pathways and gene activities that are involved in these chromatin modifications. As ROS and NO are hallmarks of stress responses, we predict that they are also pivotal in mediating chromatin dynamics during environmental responses. MAJOR CONCLUSIONS Due to conservation of chromatin-modifying mechanisms, mammals and plants share a common dependence on metabolic intermediates that serve as cofactors for chromatin modifications. In addition, plant-specific non-CG methylation pathways are particularly sensitive to changes in folate-mediated one-carbon metabolism. Finally, reactive oxygen and nitrogen species may fine-tune epigenetic processes and include similar signaling mechanisms involved in environmental stress responses in plants as well as animals.
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Affiliation(s)
- Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany.
| | - Eva Esther Rudolf
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany
| | - Martin Groth
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany.
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90
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Sekula B, Ruszkowski M, Dauter Z. S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int J Biol Macromol 2020; 151:554-565. [PMID: 32057875 DOI: 10.1016/j.ijbiomac.2020.02.100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
S-adenosylmethionine synthases (MATs) are responsible for production of S-adenosylmethionine, the cofactor essential for various methylation reactions, production of polyamines and phytohormone ethylene, etc. Plants have two distinct MAT types (I and II). This work presents the structural analysis of MATs from Arabidopsis thaliana (AtMAT1 and AtMAT2, both type I) and Medicago truncatula (MtMAT3a, type II), which, unlike most MATs from other domains of life, are dimers where three-domain subunits are sandwiched flat with one another. Although MAT types are very similar, their subunits are differently oriented within the dimer. Structural snapshots along the enzymatic reaction reveal the exact conformation of precatalytic methionine in the active site and show a binding niche, characteristic only for plant MATs, that may serve as a lock of the gate loop. Nevertheless, plants, in contrary to mammals, lack the MAT regulatory subunit, and the regulation of plant MAT activity is still puzzling. Our structures open a possibility of an allosteric activity regulation of type I plant MATs by linear compounds, like polyamines, which would tighten the relationship between S-adenosylmethionine and polyamine biosynthesis.
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Affiliation(s)
- Bartosz Sekula
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, USA.
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, USA
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91
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Minici C, Mosca L, Ilisso CP, Cacciapuoti G, Porcelli M, Degano M. Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues. J Struct Biol 2020; 210:107462. [PMID: 31962159 DOI: 10.1016/j.jsb.2020.107462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/21/2023]
Abstract
Methionine adenosyltransferases catalyse the biosynthesis of S-adenosylmethionine, the primary methyl group donor in biochemical reactions, through the condensation of methionine and ATP. Here, we report the structural analysis of the Pyrococcus furiosus methionine adenosyltransferase (PfMAT) captured in the unliganded, substrate- and product-bound states. The conformational changes taking place during the enzymatic catalytic cycle are allosterically propagated by amino acid residues conserved in the archaeal orthologues to induce an asymmetric dimer structure. The distinct occupancy of the active sites within a PfMAT dimer is consistent with a half-site reactivity that is mediated by a product-induced negative cooperativity. The structures of intermediate states of PfMAT reported here suggest a distinct molecular mechanism for S-adenosylmethionine synthesis in Archaea, likely consequence of the evolutionary pressure to achieve protein stability under extreme conditions.
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Affiliation(s)
- Claudia Minici
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132 Milan, Italy
| | - Laura Mosca
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Concetta Paola Ilisso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanna Cacciapuoti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marina Porcelli
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132 Milan, Italy.
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92
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Matamoros MA, Cutrona MC, Wienkoop S, Begara-Morales JC, Sandal N, Orera I, Barroso JB, Stougaard J, Becana M. Altered Plant and Nodule Development and Protein S-Nitrosylation in Lotus japonicus Mutants Deficient in S-Nitrosoglutathione Reductases. PLANT & CELL PHYSIOLOGY 2020; 61:105-117. [PMID: 31529085 DOI: 10.1093/pcp/pcz182] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/08/2019] [Indexed: 05/11/2023]
Abstract
Nitric oxide (NO) is a crucial signaling molecule that conveys its bioactivity mainly through protein S-nitrosylation. This is a reversible post-translational modification (PTM) that may affect protein function. S-nitrosoglutathione (GSNO) is a cellular NO reservoir and NO donor in protein S-nitrosylation. The enzyme S-nitrosoglutathione reductase (GSNOR) degrades GSNO, thereby regulating indirectly signaling cascades associated with this PTM. Here, the two GSNORs of the legume Lotus japonicus, LjGSNOR1 and LjGSNOR2, have been functionally characterized. The LjGSNOR1 gene is very active in leaves and roots, whereas LjGSNOR2 is highly expressed in nodules. The enzyme activities are regulated in vitro by redox-based PTMs. Reducing conditions and hydrogen sulfide-mediated cysteine persulfidation induced both activities, whereas cysteine oxidation or glutathionylation inhibited them. Ljgsnor1 knockout mutants contained higher levels of S-nitrosothiols. Affinity chromatography and subsequent shotgun proteomics allowed us to identify 19 proteins that are differentially S-nitrosylated in the mutant and the wild-type. These include proteins involved in biotic stress, protein degradation, antioxidant protection and photosynthesis. We propose that, in the mutant plants, deregulated protein S-nitrosylation contributes to developmental alterations, such as growth inhibition, impaired nodulation and delayed flowering and fruiting. Our results highlight the importance of GSNOR function in legume biology.
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Affiliation(s)
- Manuel A Matamoros
- Departamento de Nutrici�n Vegetal, Estaci�n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient�ficas, Apartado 13034, 50080 Zaragoza, Spain
| | - Maria C Cutrona
- Departamento de Nutrici�n Vegetal, Estaci�n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient�ficas, Apartado 13034, 50080 Zaragoza, Spain
| | - Stefanie Wienkoop
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna 1090, Austria
| | - Juan C Begara-Morales
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Faculty of Experimental Sciences, Center for Advanced Studies in Olive Grove and Olive Oils, Campus Universitario "Las Lagunillas", University of Ja�n, 23071 Ja�n, Spain
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Irene Orera
- Proteomics Unit, Centro Investigaciones Biom�dicas de Arag�n, Instituto Aragon�s de Ciencias de la Salud, 50059 Zaragoza, Spain
| | - Juan B Barroso
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Faculty of Experimental Sciences, Center for Advanced Studies in Olive Grove and Olive Oils, Campus Universitario "Las Lagunillas", University of Ja�n, 23071 Ja�n, Spain
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Manuel Becana
- Departamento de Nutrici�n Vegetal, Estaci�n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient�ficas, Apartado 13034, 50080 Zaragoza, Spain
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93
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Yang Q, Zhao D, Liu Q. Connections Between Amino Acid Metabolisms in Plants: Lysine as an Example. FRONTIERS IN PLANT SCIENCE 2020; 11:928. [PMID: 32636870 PMCID: PMC7317030 DOI: 10.3389/fpls.2020.00928] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/08/2020] [Indexed: 05/19/2023]
Abstract
Extensive efforts have been made to fortify essential amino acids and boost nutrition in plants, but unintended effects on growth and physiology are also observed. Understanding how different amino acid metabolisms are connected with other biological pathways is therefore important. In addition to protein synthesis, amino acid metabolism is also tightly linked to energy and carbohydrate metabolism, the carbon-nitrogen budget, hormone and secondary metabolism, stress responses, and so on. Here, we update the currently available information on the connections between amino acid metabolisms, which tend to be overlooked in higher plants. Particular emphasis was placed on the connections between lysine metabolism and other pathways, such as tryptophan metabolism, the tricarboxylic acid cycle, abiotic and biotic stress responses, starch metabolism, and the unfolded protein response. Interestingly, regulation of lysine metabolism was found to differ between plant species, as is the case between dicots and monocots. Determining the metabolic connection between amino acid metabolisms will help improve our understanding of the metabolic flux, supporting studies on crop nutrition.
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Affiliation(s)
- Qingqing Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Dongsheng Zhao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- *Correspondence: Qiaoquan Liu,
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94
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Jiang J, Ren X, Li L, Hou R, Sun W, Jiao C, Yang N, Dong Y. H 2S Regulation of Metabolism in Cucumber in Response to Salt-Stress Through Transcriptome and Proteome Analysis. FRONTIERS IN PLANT SCIENCE 2020; 11:1283. [PMID: 32973842 PMCID: PMC7466724 DOI: 10.3389/fpls.2020.01283] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/06/2020] [Indexed: 05/02/2023]
Abstract
In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11,761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense, and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase, and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.
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Affiliation(s)
- Jinglong Jiang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
- *Correspondence: Jinglong Jiang,
| | - Xuming Ren
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Li Li
- School of Chemical and Environmental Sciences, Shaanxi University of Technology, Hanzhong, China
| | - Ruping Hou
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Wang Sun
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Chengjin Jiao
- School of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Ni Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Yanxin Dong
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
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95
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Osorio S, Carneiro RT, Lytovchenko A, McQuinn R, Sørensen I, Vallarino JG, Giovannoni JJ, Fernie AR, Rose JKC. Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:106-118. [PMID: 31131540 PMCID: PMC6920187 DOI: 10.1111/pbi.13176] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/26/2019] [Accepted: 05/20/2019] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) fruit ripening is regulated co-operatively by the action of ethylene and a hierarchy of transcription factors, including RIPENING INHIBITOR (RIN) and NON-RIPENING (NOR). Mutations in these two genes have been adopted commercially to delay ripening, and accompanying textural deterioration, as a means to prolong shelf life. However, these mutations also affect desirable traits associated with colour and nutritional value, although the extent of this trade-off has not been assessed in detail. Here, we evaluated changes in tomato fruit pericarp primary metabolite and carotenoid pigment profiles, as well as the dynamics of specific associated transcripts, in the rin and nor mutants during late development and postharvest storage, as well of those of the partially ripening delayed fruit ripening (dfd) tomato genotype. These profiles were compared with those of the wild-type tomato cultivars Ailsa Craig (AC) and M82. We also evaluated the metabolic composition of M82 fruit ripened on or off the vine over a similar period. In general, the dfd mutation resulted in prolonged firmness and maintenance of quality traits without compromising key metabolites (sucrose, glucose/fructose and glucose) and sectors of intermediary metabolism, including tricarboxylic acid cycle intermediates. Our analysis also provided insights into the regulation of carotenoid formation and highlighted the importance of the polyamine, putrescine, in extending fruit shelf life. Finally, the metabolic composition analysis of M82 fruit ripened on or off the vine provided insights into the import into fruit of compounds, such as sucrose, during ripening.
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Affiliation(s)
- Sonia Osorio
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”University of Malaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - Raphael T. Carneiro
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Anna Lytovchenko
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Ryan McQuinn
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterIthacaNYUSA
| | - Iben Sørensen
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - José G. Vallarino
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”University of Malaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - James J. Giovannoni
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterIthacaNYUSA
| | - Alisdair R. Fernie
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jocelyn K. C. Rose
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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96
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Traynor AM, Sheridan KJ, Jones GW, Calera JA, Doyle S. Involvement of Sulfur in the Biosynthesis of Essential Metabolites in Pathogenic Fungi of Animals, Particularly Aspergillus spp.: Molecular and Therapeutic Implications. Front Microbiol 2019; 10:2859. [PMID: 31921039 PMCID: PMC6923255 DOI: 10.3389/fmicb.2019.02859] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Fungal sulfur uptake is required for incorporation into the sidechains of the amino acids cysteine and methionine, and is also essential for the biosynthesis of the antioxidant glutathione (GSH), S-adenosylmethionine (SAM), the key source of methyl groups in cellular transmethylation reactions, and S-adenosylhomocysteine (SAH). Biosynthesis of redox-active gliotoxin in the opportunistic fungal pathogen Aspergillus fumigatus has been elucidated over the past 10 years. Some fungi which produce gliotoxin-like molecular species have undergone unexpected molecular rewiring to accommodate this high-risk biosynthetic process. Specific disruption of gliotoxin biosynthesis, via deletion of gliK, which encodes a γ-glutamyl cyclotransferase, leads to elevated intracellular antioxidant, ergothioneine (EGT), levels, and confirms crosstalk between the biosynthesis of both sulfur-containing moieties. Gliotoxin is ultimately formed by gliotoxin oxidoreductase GliT-mediated oxidation of dithiol gliotoxin (DTG). In fact, DTG is a substrate for both GliT and a bis-thiomethyltransferase, GtmA. GtmA converts DTG to bisdethiobis(methylthio)gliotoxin (BmGT), using 2 mol SAM and resultant SAH must be re-converted to SAM via the action of the Methyl/Met cycle. In the absence of GliT, DTG fluxes via GtmA to BmGT, which results in both SAM depletion and SAH overproduction. Thus, the negative regulation of gliotoxin biosynthesis via GtmA must be counter-balanced by GliT activity to avoid Methyl/Met cycle dysregulation, SAM depletion and trans consequences on global cellular biochemistry in A. fumigatus. DTG also possesses potent Zn2+ chelation properties which positions this sulfur-containing metabolite as a putative component of the Zn2+ homeostasis system within fungi. EGT plays an essential role in high-level redox homeostasis and its presence requires significant consideration in future oxidative stress studies in pathogenic filamentous fungi. In certain filamentous fungi, sulfur is additionally indirectly required for the formation of EGT and the disulfide-bridge containing non-ribosomal peptide, gliotoxin, and related epipolythiodioxopiperazines. Ultimately, interference with emerging sulfur metabolite functionality may represent a new strategy for antifungal drug development.
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Affiliation(s)
- Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Ireland
| | | | - Gary W Jones
- Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, United Kingdom
| | - José A Calera
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Salamanca, Spain.,Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Ireland
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97
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Zhao JH, He YY, Guo SS, Yan Y, Wang Z, Ye J, Zhang JL, Wang Y, Pang XB, Xie XM, Lin JH, Jing ZC, Han ZY. Circulating Plasma Metabolomic Profiles Differentiate Rodent Models of Pulmonary Hypertension and Idiopathic Pulmonary Arterial Hypertension Patients. Am J Hypertens 2019; 32:1109-1117. [PMID: 31350549 DOI: 10.1093/ajh/hpz121] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/14/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a severe progressive disease with systemic metabolic dysregulation. Monocrotaline (MCT)-induced and hypoxia-induced pulmonary hypertension (PH) rodent models are the most widely used preclinical models, however, whether or not these preclinical models recapitulate metabolomic profiles of PAH patients remain unclear. METHODS In this study, a targeted metabolomics panel of 126 small molecule metabolites was conducted. We applied it to the plasma of the 2 preclinical rodent models of PH and 30 idiopathic pulmonary arterial hypertension (IPAH) patients as well as 30 healthy controls to comparatively assess the metabolomic profiles of PAH patients and rodent models. RESULTS Significantly different metabolomics profiling and pathways were shown among the 2 classical rodent models and IPAH patients. Pathway analysis demonstrated that methionine metabolism and urea cycle metabolism were the most significant pathway involved in the pathogenesis of hypoxia-induced PH model and MCT-induced model, respectively, and both of them were also observed in the dysregulated pathways in IPAH patients. CONCLUSIONS These 2 models may develop PAH through different metabolomic pathways and each of the 2 classical PH model resembles IPAH patients in certain aspects.
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Affiliation(s)
- Jun-Han Zhao
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang-Yang He
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shan-Shan Guo
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Biochemistry, Pharmaceutical College, Henan University, Kaifeng, Henan, China
| | - Yi Yan
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhe Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jue Ye
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Wang
- Department of Respiration, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xiao-Bin Pang
- Department of Biochemistry, Pharmaceutical College, Henan University, Kaifeng, Henan, China
| | - Xin-Mei Xie
- Department of Biochemistry, Pharmaceutical College, Henan University, Kaifeng, Henan, China
| | - Jian-Hui Lin
- Department of Infection, Immunity, and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Zhi-Cheng Jing
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhi-Yan Han
- Department of Anesthesiology, FuWai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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98
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Huang XY, Li M, Luo R, Zhao FJ, Salt DE. Epigenetic regulation of sulfur homeostasis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4171-4182. [PMID: 31087073 DOI: 10.1093/jxb/erz218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
Plants have evolved sophisticated mechanisms for adaptation to fluctuating availability of nutrients in soil. Such mechanisms are of importance for plants to maintain homeostasis of nutrient elements for their development and growth. The molecular mechanisms controlling the homeostasis of nutrient elements at the genetic level have been gradually revealed, including the identification of regulatory factors and transporters responding to nutrient stresses. Recent studies have suggested that such responses are controlled not only by genetic regulation but also by epigenetic regulation. In this review, we present recent studies on the involvement of DNA methylation, histone modifications, and non-coding RNA-mediated gene silencing in the regulation of sulfur homeostasis and the response to sulfur deficiency. We also discuss the potential effect of sulfur-containing metabolites such as S-adenosylmethionine on the maintenance of DNA and histone methylation.
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Affiliation(s)
- Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengzhen Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Rongjian Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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99
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Matityahu I, Godo I, Hacham Y, Amir R. The level of threonine in tobacco seeds is limited by substrate availability, while the level of methionine is limited also by the activity of cystathionine γ-synthase. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:195-201. [PMID: 31128689 DOI: 10.1016/j.plantsci.2019.02.020] [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: 12/04/2018] [Revised: 01/25/2019] [Accepted: 02/28/2019] [Indexed: 06/09/2023]
Abstract
Methionine and threonine are two essential amino acids whose low levels limit the nutritional quality of seeds. The current objective was to define factors that regulate and might increase their levels in seeds. Feeding experiments carried out on receptacles of developing tobacco (Nicotiana tabacum) capsules showed that 1 mM of S-methylmethionine increased the level of methionine to contents similar to 2.5 mM of homoserine, an intermediate metabolite of the aspartate family of amino acids. The latter also increased the level of threonine. Based on these findings, we generated tobacco seeds that expressed a combination of bacterial feedback-insensitive aspartate kinase (bAK), which was previously reported to have a high level of threonine/methionine, and feedback-insensitive cystathionine γ-synthase (CGS), the regulatory enzyme of the methionine biosynthesis pathway. Plants expressing this latter gene previously showed having higher levels of methionine. The results of total amino acids analysis showed that the level of threonine was highest in the bAK line, which has moderate levels of methionine and lysine, while the highest level of methionine was found in seeds expressing both heterologous genes. The results suggest that the level of threonine in tobacco seeds is limited by the substrate, while that of methionine is limited also by the activity of CGS.
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Affiliation(s)
- I Matityahu
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - I Godo
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Y Hacham
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel; Tel-Hai College, Upper Galilee 11016, Israel
| | - R Amir
- Laboratory of Plant Science, Migal - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel; Tel-Hai College, Upper Galilee 11016, Israel.
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100
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Klimenko O, Pernis M, Danchenko M, Skultéty L, Klubicová K, Shevchenko G. Natural ecotype of Arabidopsis thaliana (L.) Heynh (Chernobyl-07) respond to cadmium stress more intensively than the sensitive ecotypes Oasis and Columbia. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 173:86-95. [PMID: 30769207 DOI: 10.1016/j.ecoenv.2019.02.012] [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: 10/11/2018] [Revised: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 05/19/2023]
Abstract
Large areas polluted with toxic heavy metals or radionuclides were formed as a side product of rapid industrial development of human society. Plants, due to their sessile nature, should adapt to these challenging genotoxic environmental conditions and develop resistance. Herein, we evaluated the response of three natural ecotypes of Arabidopsis thaliana (L.) Heynh (Oasis, Columbia-0, and Chernobyl-07) to cadmium, using discovery gel-based proteomics. These accessions are differing by level of tolerance to heavy metal probably achieved by various exposure to chronic ionizing radiation. Based on the pairwise comparison (control versus cadmium-treated) we recognized 5.8-13.4% of identified proteins as significantly altered at the presence of cadmium. Although the majority of photosynthesis-related proteins were found to be less abundant in all ecotypes it was noted that in contrast to the sensitive variants (Col and Oas), the tolerant Che accession may activate the mechanism preserving photosynthesis and energy production. Also, proteins modulating energy budget through alternative route and mediating higher resistance to heavy metals were upregulated in this ecotype. Although we suggest that regulation of enzymes acting in peptide and protein synthesis, protection of the plants against various abiotic stresses, or those neutralizing the effects of reactive oxygen species are rather associated with general response to cadmium, they were found to be altered more intensively in the Che accession. Thus, the identified affected proteins may represent good candidate molecules for molecular breeding to improve tolerance of crops to heavy metal stress.
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Affiliation(s)
- Olena Klimenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07 Nitra, Slovakia; Mykola Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Tereshchenkivska 2, 01004 Kyiv, Ukraine
| | - Miroslav Pernis
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07 Nitra, Slovakia
| | - Maksym Danchenko
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - Ludovít Skultéty
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia; Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Katarína Klubicová
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07 Nitra, Slovakia.
| | - Galina Shevchenko
- Mykola Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Tereshchenkivska 2, 01004 Kyiv, Ukraine
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