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Dziubek D, Poeker L, Siemitkowska B, Graf A, Marino G, Alseekh S, Arrivault S, Fernie AR, Armbruster U, Geigenberger P. NTRC and thioredoxins m1/m2 underpin the light acclimation of plants on proteome and metabolome levels. PLANT PHYSIOLOGY 2024; 194:982-1005. [PMID: 37804523 PMCID: PMC10828201 DOI: 10.1093/plphys/kiad535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
During photosynthesis, plants must manage strong fluctuations in light availability on different time scales, leading to long-term acclimation and short-term responses. However, little is known about the regulation and coordination of these processes and the modulators involved. In this study, we used proteomics, metabolomics, and reverse genetics to investigate how different light environmental factors, such as intensity or variability, affect long-term and short-term acclimation responses of Arabidopsis (Arabidopsis thaliana) and the importance of the chloroplast redox network in their regulation. In the wild type, high light, but not fluctuating light, led to large quantitative changes in the proteome and metabolome, accompanied by increased photosynthetic dynamics and plant growth. This finding supports light intensity as a stronger driver for acclimation than variability. Deficiencies in NADPH-thioredoxin reductase C (NTRC) or thioredoxins m1/m2, but not thioredoxin f1, almost completely suppressed the re-engineering of the proteome and metabolome, with both the induction of proteins involved in stress and redox responses and the repression of those involved in cytosolic and plastid protein synthesis and translation being strongly attenuated. Moreover, the correlations of protein or metabolite levels with light intensity were severely disturbed, suggesting a general defect in the light-dependent acclimation response, resulting in impaired photosynthetic dynamics. These results indicate a previously unknown role of NTRC and thioredoxins m1/m2 in modulating light acclimation at proteome and metabolome levels to control dynamic light responses. NTRC, but not thioredoxins m1/m2 or f1, also improves short-term photosynthetic responses by balancing the Calvin-Benson cycle in fluctuating light.
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Affiliation(s)
- Dejan Dziubek
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Louis Poeker
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Beata Siemitkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Giada Marino
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departments of Metabolomics and Crop Quantitative Genetics, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgari
| | - Stéphanie Arrivault
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departments of Metabolomics and Crop Quantitative Genetics, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgari
| | - Ute Armbruster
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS—Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Geigenberger
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
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Chaloupsky P, Kolackova M, Dobesova M, Pencik O, Tarbajova V, Capal P, Svec P, Ridoskova A, Bytesnikova Z, Pelcova P, Adam V, Huska D. Mechanistic transcriptome comprehension of Chlamydomonas reinhardtii subjected to black phosphorus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115823. [PMID: 38176180 DOI: 10.1016/j.ecoenv.2023.115823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024]
Abstract
Two-dimensional materials have recently gained significant awareness. A representative of such materials, black phosphorous (BP), earned attention based on its comprehensive application potential. The presented study focuses on the mode of cellular response underlying the BP interaction with Chlamydomonas reinhardtii as an algal model organism. We observed noticeable ROS formation and changes in outer cellular topology after 72 h of incubation at 5 mg/L BP. Transcriptome profiling was employed to examine C. reinhardtii response after exposure to 25 mg/L BP for a deeper understanding of the associated processes. The RNA sequencing has revealed a comprehensive response with abundant transcript downregulation. The mode of action was attributed to cell wall disruption, ROS elevation, and chloroplast disturbance. Besides many other dysregulated genes, the cell response involved the downregulation of GH9 and gametolysin within a cell wall, pointing to a shift to discrete manipulation with resources. The response also included altered expression of the PRDA1 gene associated with redox governance in chloroplasts implying ROS disharmony. Altered expression of the Cre-miR906-3p, Cre-miR910, and Cre-miR914 pointed to those as potential markers in stress response studies.
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Affiliation(s)
- Pavel Chaloupsky
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Marketa Dobesova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Ondrej Pencik
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Vladimira Tarbajova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Petr Capal
- Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Slechtitelu 241/27, 783 71 Olomouc, Czech Republic
| | - Pavel Svec
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Andrea Ridoskova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Zuzana Bytesnikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Pavlina Pelcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Dalibor Huska
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.
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Wang KW, Ling ZJ, Yuan Z, Zhang J, Yi SJ, Xiong YW, Chang W, Lin ZJ, Zhu HL, Yang L, Wang H. The Long-Term Effect of Maternal Iron Levels in the Second Trimester on Mild Thinness among Preschoolers: The Modifying Effect of Small for Gestational Age. Nutrients 2023; 15:3939. [PMID: 37764723 PMCID: PMC10535896 DOI: 10.3390/nu15183939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/23/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The supplementation of multiple micronutrients throughout pregnancy can reduce the risk of adverse birth outcomes and various diseases in children. However, the long-term effect of maternal multiple micronutrient levels in the second trimester on the overall development of preschoolers remains unknown. Therefore, 1017 singleton mother-infant pairs and 6-year-old preschoolers were recruited based on the China-Wuxi Birth Cohort Study. Meanwhile, information on the demographic characteristics of pregnant women and preschoolers, maternal copper, calcium, iron, magnesium, and zinc levels in whole blood during the second trimester, and neonatal outcomes, were collected. We aimed to investigate the long-term impact of maternal copper, calcium, iron, magnesium, and zinc levels in the second trimester on mild thinness among 6-year-old preschoolers, and the modifying effect of small for gestational age (SGA), within the Chinese population. Multiple logistic regression models revealed that high-level maternal iron in the second trimester reduced the risk of mild thinness [adjusted OR: 0.46 (95% CI: 0.26, 0.80)] among 6-year-old preschoolers. However, no significant association was found for the remaining four maternal essential metal elements. Additionally, the restricted cubic spline function showed that the risk of mild thinness decreased when maternal iron concentration exceeded 7.47 mmol/L in whole blood during the second trimester. Furthermore, subgroup analysis indicated that the long-term protective effect of high-level maternal iron on mild thinness was only observed in SGA infants. Summarily, high-level maternal iron in the second trimester distinctly lowers the risk of mild thinness among 6-year-old preschoolers, especially in preschoolers with birth outcomes of SGA. Our findings offer evidence for the implementation of iron supplementation in the second trimester as a preventive measure against mild thinness in children.
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Affiliation(s)
- Kai-Wen Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Zheng-Jia Ling
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
- Department of Medical Genetics and Prenatal Diagnosis, Wuxi Maternity and Child Health Care Hospital, Wuxi 214002, China
| | - Zhi Yuan
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Jin Zhang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Song-Jia Yi
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Yong-Wei Xiong
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Wei Chang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Zhi-Jing Lin
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Hua-Long Zhu
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
| | - Lan Yang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Department of Medical Genetics and Prenatal Diagnosis, Wuxi Maternity and Child Health Care Hospital, Wuxi 214002, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei 230032, China
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Mai HJ, Baby D, Bauer P. Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1204723. [PMID: 37554559 PMCID: PMC10406446 DOI: 10.3389/fpls.2023.1204723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/04/2023] [Indexed: 08/10/2023]
Abstract
Cellular homeostasis of the micronutrient iron is highly regulated in plants and responsive to nutrition, stress, and developmental signals. Genes for iron management encode metal and other transporters, enzymes synthesizing chelators and reducing substances, transcription factors, and several types of regulators. In transcriptome or proteome datasets, such iron homeostasis-related genes are frequently found to be differentially regulated. A common method to detect whether a specific cellular pathway is affected in the transcriptome data set is to perform Gene Ontology (GO) enrichment analysis. Hence, the GO database is a widely used resource for annotating genes and identifying enriched biological pathways in Arabidopsis thaliana. However, iron homeostasis-related GO terms do not consistently reflect gene associations and levels of evidence in iron homeostasis. Some genes in the existing iron homeostasis GO terms lack direct evidence of involvement in iron homeostasis. In other aspects, the existing GO terms for iron homeostasis are incomplete and do not reflect the known biological functions associated with iron homeostasis. This can lead to potential errors in the automatic annotation and interpretation of GO term enrichment analyses. We suggest that applicable evidence codes be used to add missing genes and their respective ortholog/paralog groups to make the iron homeostasis-related GO terms more complete and reliable. There is a high likelihood of finding new iron homeostasis-relevant members in gene groups and families like the ZIP, ZIF, ZIFL, MTP, OPT, MATE, ABCG, PDR, HMA, and HMP. Hence, we compiled comprehensive lists of genes involved in iron homeostasis that can be used for custom enrichment analysis in transcriptomic or proteomic studies, including genes with direct experimental evidence, those regulated by central transcription factors, and missing members of small gene families or ortholog/paralog groups. As we provide gene annotation and literature alongside, the gene lists can serve multiple computational approaches. In summary, these gene lists provide a valuable resource for researchers studying iron homeostasis in A. thaliana, while they also emphasize the importance of improving the accuracy and comprehensiveness of the Gene Ontology.
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Affiliation(s)
- Hans-Jörg Mai
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Dibin Baby
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
- Heinrich Heine University, Center of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
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5
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Fakih Z, Plourde MB, Germain H. Differential Participation of Plant Ribosomal Proteins from the Small Ribosomal Subunit in Protein Translation under Stress. Biomolecules 2023; 13:1160. [PMID: 37509195 PMCID: PMC10377644 DOI: 10.3390/biom13071160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Upon exposure to biotic and abiotic stress, plants have developed strategies to adapt to the challenges imposed by these unfavorable conditions. The energetically demanding translation process is one of the main elements regulated to reduce energy consumption and to selectively synthesize proteins involved in the establishment of an adequate response. Emerging data have shown that ribosomes remodel to adapt to stresses. In Arabidopsis thaliana, ribosomes consist of approximately eighty-one distinct ribosomal proteins (RPs), each of which is encoded by two to seven genes. Recent research has revealed that a mutation in a given single RP in plants can not only affect the functions of the RP itself but can also influence the properties of the ribosome, which could bring about changes in the translation to varying degrees. However, a pending question is whether some RPs enable ribosomes to preferentially translate specific mRNAs. To reveal the role of ribosomal proteins from the small subunit (RPS) in a specific translation, we developed a novel approach to visualize the effect of RPS silencing on the translation of a reporter mRNA (GFP) combined to the 5'UTR of different housekeeping and defense genes. The silencing of genes encoding for NbRPSaA, NbRPS5A, and NbRPS24A in Nicotiana benthamiana decreased the translation of defense genes. The NbRACK1A-silenced plant showed compromised translations of specific antioxidant enzymes. However, the translations of all tested genes were affected in NbRPS27D-silenced plants. These findings suggest that some RPS may be potentially involved in the control of protein translation.
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Affiliation(s)
- Zainab Fakih
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada
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6
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Voronezhskaya V, Volkova P, Bitarishvili S, Shesterikova E, Podlutskii M, Clement G, Meyer C, Duarte GT, Kudin M, Garbaruk D, Turchin L, Kazakova E. Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone. PLANTS (BASEL, SWITZERLAND) 2023; 12:2318. [PMID: 37375943 DOI: 10.3390/plants12122318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Our understanding of the long-term consequences of chronic ionising radiation for living organisms remains scarce. Modern molecular biology techniques are helpful tools for researching pollutant effects on biota. To reveal the molecular phenotype of plants growing under chronic radiation exposure, we sampled Vicia cracca L. plants in the Chernobyl exclusion zone and areas with normal radiation backgrounds. We performed a detailed analysis of soil and gene expression patterns and conducted coordinated multi-omics analyses of plant samples, including transcriptomics, proteomics, and metabolomics. Plants growing under chronic radiation exposure showed complex and multidirectional biological effects, including significant alterations in the metabolism and gene expression patterns of irradiated plants. We revealed profound changes in carbon metabolism, nitrogen reallocation, and photosynthesis. These plants showed signs of DNA damage, redox imbalance, and stress responses. The upregulation of histones, chaperones, peroxidases, and secondary metabolism was noted.
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Affiliation(s)
| | | | | | | | | | - Gilles Clement
- Institute Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Christian Meyer
- Institute Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | | | - Maksim Kudin
- Polesye State Radiation-Ecological Reserve, 247618 Khoiniki, Belarus
| | - Dmitrii Garbaruk
- Polesye State Radiation-Ecological Reserve, 247618 Khoiniki, Belarus
| | - Larisa Turchin
- Polesye State Radiation-Ecological Reserve, 247618 Khoiniki, Belarus
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Tola AJ, Missihoun TD. Iron Availability Influences Protein Carbonylation in Arabidopsis thaliana Plants. Int J Mol Sci 2023; 24:ijms24119732. [PMID: 37298684 DOI: 10.3390/ijms24119732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Protein carbonylation is an irreversible form of post-translational modification triggered by reactive oxygen species in animal and plant cells. It occurs either through the metal-catalyzed oxidation of Lys, Arg, Pro, and Thr side chains or the addition of α, β-unsaturated aldehydes and ketones to the side chains of Cys, Lys, and His. Recent genetic studies concerning plants pointed to an implication of protein carbonylation in gene regulation through phytohormones. However, for protein carbonylation to stand out as a signal transduction mechanism, such as phosphorylation and ubiquitination, it must be controlled in time and space by a still unknown trigger. In this study, we tested the hypothesis that the profile and extent of protein carbonylation are influenced by iron homeostasis in vivo. For this, we compared the profile and the contents of the carbonylated proteins in the Arabidopsis thaliana wild-type and mutant-deficient in three ferritin genes under normal and stress conditions. Additionally, we examined the proteins specifically carbonylated in wild-type seedlings exposed to iron-deficient conditions. Our results indicated that proteins were differentially carbonylated between the wild type and the triple ferritin mutant Fer1-3-4 in the leaves, stems, and flowers under normal growth conditions. The profile of the carbonylated proteins was also different between the wild type and the ferritin triple mutant exposed to heat stress, thus pointing to the influence of iron on the carbonylation of proteins. Consistent with this, the exposure of the seedlings to iron deficiency and iron excess greatly influenced the carbonylation of certain proteins involved in intracellular signal transduction, translation, and iron deficiency response. Overall, the study underlined the importance of iron homeostasis in the occurrence of protein carbonylation in vivo.
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Affiliation(s)
- Adesola J Tola
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 Boul. des Forges, Trois-Rivières, QC G9A 5H7, Canada
| | - Tagnon D Missihoun
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 Boul. des Forges, Trois-Rivières, QC G9A 5H7, Canada
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Yu X, Wei P, Zhao S, Chen Z, Li X, Zhang W, Liu C, Yang Y, Li X, Liu X. Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau. PLANT CELL REPORTS 2023; 42:879-893. [PMID: 36973418 DOI: 10.1007/s00299-023-03005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Shuqi Zhao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinzhong Li
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Wencai Zhang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China.
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Coppa E, Vigani G, Aref R, Savatin D, Bigini V, Hell R, Astolfi S. Differential modulation of Target of Rapamycin activity under single and combined iron and sulfur deficiency in tomato plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36976541 DOI: 10.1111/tpj.16213] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Over the past few decades, a close relationship between sulfur (S) and iron (Fe) in terms of functionality and nutrition was demonstrated in the tomato. However, very little is known about the regulatory mechanisms underlying S/Fe interactions. Recently, the potential role of citrate in plant adaptation to Fe deficiency and combined S and Fe deficiency has been described. It is known that an impaired organic acid metabolism may stimulate a retrograde signal, which has been proven to be linked to the Target of Rapamycin (TOR) signaling in yeast and animal cells. Recent reports provided evidence of TOR involvement in S nutrient sensing in plants. This suggestion prompted us to investigate whether TOR may play a role in the cross-talk of signaling pathway occurring during plant adaptation to combined nutrient deficiency of Fe and S. Our results revealed that Fe deficiency elicited an increase of TOR activity associated with enhanced accumulation of citrate. In contrast, S deficiency resulted in decreased TOR activity and citrate accumulation. Interestingly, citrate accumulated in shoots of plants exposed to combined S/Fe deficiency to values between those found in Fe- and S-deficient plants, again correlated with TOR activity level. Our results suggest that citrate might be involved in establishing a link between plant response to combined S/Fe deficiency and the TOR network.
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Affiliation(s)
- Eleonora Coppa
- Department of Agriculture and Forest Sciences, University of Tuscia, via S.C. de Lellis, Viterbo, 01100, Italy
| | - Gianpiero Vigani
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Via G. Quarello 15/A, Torino, 10135, Italy
| | - Rasha Aref
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 11241, Cairo, Egypt
| | - Daniel Savatin
- Department of Agriculture and Forest Sciences, University of Tuscia, via S.C. de Lellis, Viterbo, 01100, Italy
| | - Valentina Bigini
- Department of Agriculture and Forest Sciences, University of Tuscia, via S.C. de Lellis, Viterbo, 01100, Italy
| | - Ruediger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 360, Heidelberg, 69120, Germany
| | - Stefania Astolfi
- Department of Agriculture and Forest Sciences, University of Tuscia, via S.C. de Lellis, Viterbo, 01100, Italy
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10
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Yang X, Niu X, Li L, Wang L, Liu C, Liu J, Yuan Q, Pei X. Understanding the molecular mechanism of drought resistance in Shanlan upland rice by transcriptome and phenotype analyses. Int J Biol Macromol 2023; 231:123387. [PMID: 36693603 DOI: 10.1016/j.ijbiomac.2023.123387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Rice (Oryza sativa L.) is an important grain crop worldwide, and drought has become an important factor restricting rice yield. As a unique rice germplasm in Hainan (China), Shanlan upland rice has rich genetic diversity and certain advantage for breeding water-saving and drought-resistance rice. 48 varieties, including 41 Shanlan upland rice, 3 upland rice, and 4 irrigated rice varieties was cultivated in soil pots. The drought resistance was assessed at the seedling stage using the stress coefficients of seven indicators, as the D value calculating from five principal components to rank the varieties. Five cultivars with strong, medium, and low resistance, were selected for transcriptome sequencing. The results of the GSEA analysis showed that free amino acid content increased through the redistribution of energy in Shanlan upland rice to cope with drought stress. In addition, we found that Os03g0623100 was significantly up-regulated under drought stress conditions in varieties with high drought resistance, as compared with low resistance cultivars. The Os03g0623100 was predicted to interact with LEA protein in the STRING database, which may contribute to maintaining the energy metabolisms to under stress conditions. This study provides a view of Shanlan upland rice as a drought-resistant germplasm resource, and a deeper understanding of the molecular mechanism of crop drought resistance.
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Affiliation(s)
- Xinsen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xiaoling Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Laiyi Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Liu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianing Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qianhua Yuan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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11
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Wei P, Yu X, Yang Y, Chen Z, Zhao S, Li X, Zhang W, Liu C, Li X, Liu X. Biased gene expression reveals the contribution of subgenome to altitude adaptation in allopolyploid Isoetes sinensis. Ecol Evol 2022; 12:e9677. [PMID: 36619709 PMCID: PMC9797765 DOI: 10.1002/ece3.9677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Allopolyploids are believed to inherit the genetic characteristics of its progenitors and exhibit stronger adaptability and vigor. The allotetraploid Isoetes sinensis was formed by the natural hybridization and polyploidization of two diploid progenitors, Isoetes taiwanensis and Isoetes yunguiensis, and was believed to have the potential to adapt to plateau environments. To explore the expression pattern of homoeologous genes and their contributions to altitude adaptation, we transplanted natural allotetraploid I. sinensis (TnTnYnYn) along the altitude gradient for a long-term, and harvested them in summer and winter, respectively. One year after transplanting, it still lived well, even in the extreme environment of the Qinghai-Tibet Plateau. Then, we performed high-throughput RNA sequencing to measure their gene expression level. A total of 7801 homoeologous genes were expressed, among which 5786 were identified as shared expression in different altitudes and seasons. We further found that altitude variations could change the subgenome bias trend of I. sinensis, but season could not. Moreover, the functions of uniquely expressed genes indicated that temperature might be an important restrictive factor during the adaptation process. Through the analysis of DEGs and uniquely expressed genes, we found that Y subgenome provided more contributions to high altitude adaptation than T subgenome. These adaptive traits to high altitude may be inherited from its plateau progenitor I. yunguiensis. Through weighted gene co-expression network analysis, pentatricopeptide repeats gene family and glycerophospholipid metabolism pathway were considered to play important roles in high-altitude adaptation. Totally, this study will enrich our understanding of allopolyploid in environmental adaptation.
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Affiliation(s)
- Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina
| | - Xiao‐lei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina
| | - Yu‐jiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina
| | - Zhu‐yifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina
| | - Shu‐qi Zhao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina
| | - Xin‐zhong Li
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of SciencesTibet UniversityLhasaChina
| | - Wen‐cai Zhang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of SciencesTibet UniversityLhasaChina
| | - Chen‐lai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina
| | - Xiao‐yan Li
- Biology Experimental Teaching Center, School of Life ScienceWuhan UniversityWuhanChina
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life SciencesWuhan UniversityWuhanChina,Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of SciencesTibet UniversityLhasaChina
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12
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Ortigosa F, Lobato-Fernández C, Pérez-Claros JA, Cantón FR, Ávila C, Cánovas FM, Cañas RA. Epitranscriptome changes triggered by ammonium nutrition regulate the proteome response of maritime pine roots. FRONTIERS IN PLANT SCIENCE 2022; 13:1102044. [PMID: 36618661 PMCID: PMC9815506 DOI: 10.3389/fpls.2022.1102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Epitranscriptome constitutes a gene expression checkpoint in all living organisms. Nitrogen is an essential element for plant growth and development that influences gene expression at different levels such as epigenome, transcriptome, proteome, and metabolome. Therefore, our hypothesis is that changes in the epitranscriptome may regulate nitrogen metabolism. In this study, epitranscriptomic modifications caused by ammonium nutrition were monitored in maritime pine roots using Oxford Nanopore Technology. Transcriptomic responses mainly affected transcripts involved in nitrogen and carbon metabolism, defense, hormone synthesis/signaling, and translation. Global detection of epitranscriptomic marks was performed to evaluate this posttranscriptional mechanism in un/treated seedlings. Increased N6-methyladenosine (m6A) deposition in the 3'-UTR was observed in response to ammonium, which seems to be correlated with poly(A) lengths and changes in the relative abundance of the corresponding proteins. The results showed that m6A deposition and its dynamics seem to be important regulators of translation under ammonium nutrition. These findings suggest that protein translation is finely regulated through epitranscriptomic marks likely by changes in mRNA poly(A) length, transcript abundance and ribosome protein composition. An integration of multiomics data suggests that the epitranscriptome modulates responses to nutritional, developmental and environmental changes through buffering, filtering, and focusing the final products of gene expression.
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Affiliation(s)
- Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología de Plantas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología de Plantas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | | | | | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología de Plantas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | - Francisco M. Cánovas
- Grupo de Biología Molecular y Biotecnología de Plantas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | - Rafael A. Cañas
- Integrative Molecular Biology Lab, Universidad de Málaga, Málaga, Spain
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13
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Valencia-Lozano E, Herrera-Isidrón L, Flores-López JA, Recoder-Meléndez OS, Barraza A, Cabrera-Ponce JL. Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis. Int J Mol Sci 2022; 23:ijms232213835. [PMID: 36430314 PMCID: PMC9696990 DOI: 10.3390/ijms232213835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein-protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs-MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9-may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging.
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Affiliation(s)
- Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Lisset Herrera-Isidrón
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Jorge Abraham Flores-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Osiel Salvador Recoder-Meléndez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noreste, SC. IPN 195, Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Mexico
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
- Correspondence: ; Tel.: +52-462-6239600 (ext. 9421)
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14
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Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes. Int J Mol Sci 2022; 23:ijms231810611. [PMID: 36142529 PMCID: PMC9502317 DOI: 10.3390/ijms231810611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.
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Ahmad N, Ibrahim S, Tian Z, Kuang L, Wang X, Wang H, Dun X. Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:994666. [PMID: 36172562 PMCID: PMC9511887 DOI: 10.3389/fpls.2022.994666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Plants rely on root systems for nutrient uptake from soils. Marker-assisted selection helps breeders to select desirable root traits for effective nutrient uptake. Here, 12 root and biomass traits were investigated at the seedling stage under low nitrogen (LN), low phosphorus (LP), and low potassium (LK) conditions, respectively, in a recombinant inbred line (RIL) population, which was generated from Brassica napus L. Zhongshuang11 and 4D122 with significant differences in root traits and nutrient efficiency. Significant differences for all the investigated traits were observed among RILs, with high heritabilities (0.43-0.74) and high correlations between the different treatments. Quantitative trait loci (QTL) mapping identified 57, 27, and 36 loci, explaining 4.1-10.9, 4.6-10.8, and 4.9-17.4% phenotypic variances under LN, LP, and LK, respectively. Through QTL-meta analysis, these loci were integrated into 18 significant QTL clusters. Four major QTL clusters involved 25 QTLs that could be repeatedly detected and explained more than 10% phenotypic variances, including two NPK-common and two specific QTL clusters (K and NK-specific), indicating their critical role in cooperative nutrients uptake of N, P, and K. Moreover, 264 genes within the four major QTL clusters having high expressions in roots and SNP/InDel variations between two parents were identified as potential candidate genes. Thirty-eight of them have been reported to be associated with root growth and development and/or nutrient stress tolerance. These key loci and candidate genes lay the foundation for deeper dissection of the NPK starvation response mechanisms in B. napus.
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Affiliation(s)
- Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
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16
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Hassan SH, Sferra G, Simiele M, Scippa GS, Morabito D, Trupiano D. Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator. Funct Integr Genomics 2022; 22:1159-1172. [PMID: 36094581 DOI: 10.1007/s10142-022-00897-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/15/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022]
Abstract
Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and hyperaccumulation. In this regard, understanding of interacting genes can be a crucial aspect as these interactions regulate several biological functions at molecular level in response to multiple signals. In this current study, we applied a weighted gene co-expression network analysis (WGCNA) on root and shoot RNA-seq data of A. halleri to predict the related scale-free organ specific co-expression networks, for the first time. A total of 19,653 genes of root and 18,081 genes of shoot were grouped into 14 modules and subjected to GO and KEGG enrichment analysis. "Photosynthesis" and "photosynthesis-antenna proteins" were identified as the most enriched and common pathway to both root and shoot. Whereas "glucosinolate biosynthesis," "autophagy," and "SNARE interactions in vesicular transport" were specific to root, and "circadian rhythm" was found to be enriched only in shoot. Later, hub and bottleneck genes were identified in each module by using cytoHubba plugin based on Cytoscape and scoring the relevance of each gene to the topology of the network. The modules with the most significant differential expression pattern across control and treatment (Cd-Zn treatment) were selected and their hub and bottleneck genes were screened to validate their possible involvement in heavy metal stress. Moreover, we combined the analysis of co-expression modules together with protein-protein interactions (PPIs), confirming some genes as potential candidates in plant heavy metal stress and as biomarkers. The results from this analysis shed the light on the pivotal functions to the hyperaccumulative trait of A. halleri, giving perspective to new paths for future research on this species.
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Affiliation(s)
- Sayyeda Hira Hassan
- Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy
| | - Gabriella Sferra
- Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy.
| | - Melissa Simiele
- Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy
| | | | - Domenico Morabito
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC-EA1207), Université d'Orléans, 45067, Orléans CEDEX 2, France
| | - Dalila Trupiano
- Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy
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17
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Karssemeijer PN, de Kreek KA, Gols R, Neequaye M, Reichelt M, Gershenzon J, van Loon JJA, Dicke M. Specialist root herbivore modulates plant transcriptome and downregulates defensive secondary metabolites in a brassicaceous plant. THE NEW PHYTOLOGIST 2022; 235:2378-2392. [PMID: 35717563 PMCID: PMC9540780 DOI: 10.1111/nph.18324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Plants face attackers aboveground and belowground. Insect root herbivores can lead to severe crop losses, yet the underlying transcriptomic responses have rarely been studied. We studied the dynamics of the transcriptomic response of Brussels sprouts (Brassica oleracea var. gemmifera) primary roots to feeding damage by cabbage root fly larvae (Delia radicum), alone or in combination with aboveground herbivory by cabbage aphids (Brevicoryne brassicae) or diamondback moth caterpillars (Plutella xylostella). This was supplemented with analyses of phytohormones and the main classes of secondary metabolites; aromatic, indole and aliphatic glucosinolates. Root herbivory leads to major transcriptomic rearrangement that is modulated by aboveground feeding caterpillars, but not aphids, through priming soon after root feeding starts. The root herbivore downregulates aliphatic glucosinolates. Knocking out aliphatic glucosinolate biosynthesis with CRISPR-Cas9 results in enhanced performance of the specialist root herbivore, indicating that the herbivore downregulates an effective defence. This study advances our understanding of how plants cope with root herbivory and highlights several novel aspects of insect-plant interactions for future research. Further, our findings may help breeders develop a sustainable solution to a devastating root pest.
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Affiliation(s)
- Peter N. Karssemeijer
- Laboratory of EntomologyWageningen University and Research6708PBWageningenthe Netherlands
| | - Kris A. de Kreek
- Laboratory of EntomologyWageningen University and Research6708PBWageningenthe Netherlands
| | - Rieta Gols
- Laboratory of EntomologyWageningen University and Research6708PBWageningenthe Netherlands
| | - Mikhaela Neequaye
- John Innes CentreNorwich Research ParkNR4 7UHNorwichUK
- Quadram Institute BioscienceNorwich Research ParkNR4 7UQNorwichUK
| | - Michael Reichelt
- Department of BiochemistryMax‐Planck‐Institute for Chemical Ecology07745JenaGermany
| | - Jonathan Gershenzon
- Department of BiochemistryMax‐Planck‐Institute for Chemical Ecology07745JenaGermany
| | - Joop J. A. van Loon
- Laboratory of EntomologyWageningen University and Research6708PBWageningenthe Netherlands
| | - Marcel Dicke
- Laboratory of EntomologyWageningen University and Research6708PBWageningenthe Netherlands
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18
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Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective. PLANTS 2022; 11:plants11162097. [PMID: 36015400 PMCID: PMC9415564 DOI: 10.3390/plants11162097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes they might produce. In this perspective, we go through the literature linking ribosome heterogeneity to plants’ abiotic stress response. Once unraveled, this crosstalk may serve as the foundation of novel strategies to custom cultivars tolerant to challenging environments without the yield penalty.
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19
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Zhang X, Xue C, Wang R, Shen R, Lan P. Physiological and proteomic dissection of the rice roots in response to iron deficiency and excess. J Proteomics 2022; 267:104689. [PMID: 35914714 DOI: 10.1016/j.jprot.2022.104689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 10/16/2022]
Abstract
Iron (Fe) disorder is a pivotal factor that limits rice yields in many parts of the world. Extensive research has been devoted to studying how rice molecularly copes with the stresses of Fe deficiency or excess. However, a comprehensive dissection of the whole Fe-responsive atlas at the protein level is still lacking. Here, different concentrations of Fe (0, 40, 350, and 500 μM) were supplied to rice to demonstrate its response differences to Fe deficiency and excess via physiological and proteomic analysis. Results showed that compared with the normal condition, the seedling growth and contents of Fe and manganese were significantly disturbed under either Fe stress. Proteomic analysis revealed that differentially accumulated proteins under Fe deficiency and Fe excess were commonly enriched in localization, carbon metabolism, biosynthesis of amino acids, and antioxidant system. Notably, proteins with abundance retuned by Fe starvation were individually associated with phenylpropanoid biosynthesis, cysteine and methionine metabolism, while ribosome- and endocytosis-related proteins were specifically enriched in treatment of Fe overdose of 500 μM. Moreover, several novel proteins which may play potential roles in rice Fe homeostasis were predicted. These findings expand the understanding of rice Fe nutrition mechanisms, and provide efficient guidance for genetic breeding work. SIGNIFICANCE: Both iron (Fe) deficiency and excess significantly inhibited the growth of rice seedlings. Fe deficiency and excess disturbed processes of localization and cellular oxidant detoxification, metabolisms of carbohydrates and amino acids in different ways. The Fe-deficiency and Fe-excess-responsive proteins identified by the proteome were somewhat different from the reported transcriptional profiles, providing complementary information to the transcriptomic data.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Caiwen Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Li B, Zheng L, Wang R, Xue C, Shen R, Lan P. A proteomic analysis of Arabidopsis ribosomal phosphoprotein P1A mutant. J Proteomics 2022; 262:104594. [PMID: 35483651 DOI: 10.1016/j.jprot.2022.104594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Ribosomal proteins are involved in the regulation of plant growth and development. However, the regulatory processes of most ribosomal proteins remain unclear. In this study, Arabidopsis plants with the mutation in ribosomal phosphoprotein P1A (RPP1A) produce larger and heavier seeds than wild-type plants. A comparative quantitative label-free proteomic analysis revealed that a total of 215 proteins were differentially accumulated between the young siliques of the wild type and rpp1a mutant. Knockout of RPP1A significantly reduced the abundance of proteins involved in carboxylic acid metabolism and lipid biosynthesis. Consistent with this, a metabolic analysis showed that the organic acids in the tricarboxylic acid cycle and the carbohydrates in the pentose phosphate pathway were severely reduced in the mature rpp1a mutant seeds. In contrast, the abundance of proteins related to seed maturation, especially seed storage proteins, was markedly increased during seed development. Indeed, seed storage proteins were accumulated in the mature rpp1a mutant seeds, and the seed nitrogen and sulfur contents were also increased. These results indicate that more carbon intermediates probably enter the nitrogen flow for the enhanced synthesis of seed storage proteins, which might subsequently contribute to the enlarged seed size in the rpp1a mutant. SIGNIFICANCE: Ribosomes are responsible for protein synthesis and are generally perceived as the housekeeping components in the cells. In this study, the knockout of RPP1A leads to an increased seed size through repressing carbon metabolism and lipid biosynthesis, and increasing the synthesis of seed storage proteins. Meanwhile, the abundance of seed storage proteins and the nitrogen and sulfur concentrations were increased in the mature rpp1a mutant seeds. The results provide a novel insight into the genetic regulatory networks for the control of seed size and seed storage protein accumulation, and this knowledge may facilitate the improvement of crop seed size.
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Affiliation(s)
- Bingjuan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lu Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Caiwen Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Kumar S, Seem K, Kumar S, Mohapatra T. RNA-seq analysis reveals the genes/pathways responsible for genetic plasticity of rice to varying environmental conditions on direct-sowing and transplanting. Sci Rep 2022; 12:2241. [PMID: 35145168 PMCID: PMC8831524 DOI: 10.1038/s41598-022-06009-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/21/2022] [Indexed: 01/23/2023] Open
Abstract
Rice cultivation by transplanting requires plenty of water. It might become a challenging task in future to grow rice by transplanting due to the climatic change, water and labor scarcities. Direct-sown rice (DSR) is emerging as a resource-conserving and climate-smart alternative to transplanted rice (TPR). However, no specific variety has been bred for dry/direct-sown conditions. The present study was undertaken to decipher the molecular basis of genetic plasticity of rice under different planting methods. Comparative RNA-seq analysis revealed a number (6133) of genes exclusively up-regulated in Nagina-22 (N-22) leaf under DSR conditions, compared to that (3538) in IR64 leaf. Several genes up-regulated in N-22 were down-regulated in IR64. Genes for growth-regulation and nutrient-reservoir activities, transcription factors, translational machinery, carbohydrate metabolism, cell cycle/division, and chromatin organization/epigenetic modifications were considerably up-regulated in the leaf of N-22 under DSR conditions. Complementary effects of these factors in rendering genetic plasticity were confirmed by the agronomic/physiological performance of rice cultivar. Thus, growth-regulation/nutrient-reservoir activities, transcription factors, and translational machinery are important molecular factors responsible for the observed genetic plasticity/adaptability of Nagina-22 to different planting methods. This might help to develop molecular markers for DSR breeding, replacing TPR with DSR for better water-productivity, and minimizing greenhouse-gas emission necessary for negative emission agriculture.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Qureshi MK, Gawroński P, Munir S, Jindal S, Kerchev P. Hydrogen peroxide-induced stress acclimation in plants. Cell Mol Life Sci 2022; 79:129. [PMID: 35141765 PMCID: PMC11073338 DOI: 10.1007/s00018-022-04156-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023]
Abstract
Among all reactive oxygen species (ROS), hydrogen peroxide (H2O2) takes a central role in regulating plant development and responses to the environment. The diverse role of H2O2 is achieved through its compartmentalized synthesis, temporal control exerted by the antioxidant machinery, and ability to oxidize specific residues of target proteins. Here, we examine the role of H2O2 in stress acclimation beyond the well-studied transcriptional reprogramming, modulation of plant hormonal networks and long-distance signalling waves by highlighting its global impact on the transcriptional regulation and translational machinery.
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Affiliation(s)
- Muhammad Kamran Qureshi
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Bosan road, Multan, 60800, Pakistan
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Sana Munir
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Bosan road, Multan, 60800, Pakistan
| | - Sunita Jindal
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic.
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Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins. Int J Mol Sci 2022; 23:ijms23031537. [PMID: 35163458 PMCID: PMC8835812 DOI: 10.3390/ijms23031537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.
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Yang Z, Mu Y, Wang Y, He F, Shi L, Fang Z, Zhang J, Zhang Q, Geng G, Zhang S. Characterization of a Novel TtLEA2 Gene From Tritipyrum and Its Transformation in Wheat to Enhance Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:830848. [PMID: 35444677 PMCID: PMC9014267 DOI: 10.3389/fpls.2022.830848] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/11/2022] [Indexed: 05/12/2023]
Abstract
Late embryogenesis-abundant (LEA) proteins are critical in helping plants cope with salt stress. "Y1805" is a salt-tolerant Tritipyrum. We identified a "Y1805"-specific LEA gene that was expressed highly and sensitively under salt stress using transcriptome analysis. The novel group 2 LEA gene (TtLEA2-1) was cloned from "Y1805." TtLEA2-1 contained a 453 bp open reading frame encoding an 151-amino-acid protein that showed maximum sequence identity (77.00%) with Thinopyrum elongatum by phylogenetic analysis. It was mainly found to be expressed highly in the roots by qRT-PCR analysis and was located in the whole cell. Forty-eight candidate proteins believed to interact with TtLEA2-1 were confirmed by yeast two-hybrid analysis. These interacting proteins were mainly enriched in "environmental information processing," "glycan biosynthesis and metabolism," and "carbohydrate metabolism." Protein-protein interaction analysis indicated that the translation-related 40S ribosomal protein SA was the central node. An efficient wheat transformation system has been established. A coleoptile length of 2 cm, an Agrobacteria cell density of 0.55-0.60 OD600, and 15 KPa vacuum pressure were ideal for common wheat transformation, with an efficiency of up to 43.15%. Overexpression of TaLEA2-1 in wheat "1718" led to greater height, stronger roots, and higher catalase activity than in wild type seedlings. TaLEA2-1 conferred enhanced salt tolerance in transgenic wheat and may be a valuable gene for genetic modification in crops.
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Affiliation(s)
- Zhifen Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yuanhang Mu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yiqin Wang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Fang He
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
| | - Luxi Shi
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhongming Fang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Jun Zhang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Qingqin Zhang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Guangdong Geng
- College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Guangdong Geng,
| | - Suqin Zhang
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
- Suqin Zhang,
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25
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Preventing translational inhibition from ribosomal protein insufficiency by a herpes simplex virus-encoded ribosome-associated protein. Proc Natl Acad Sci U S A 2021; 118:2025546118. [PMID: 34725147 DOI: 10.1073/pnas.2025546118] [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] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
In addition to being required for protein synthesis, ribosomes and ribosomal proteins (RPs) also regulate messenger RNA translation in uninfected and virus-infected cells. By individually depleting 85 RPs using RNA interference, we found that overall protein synthesis in uninfected primary fibroblasts was more sensitive to RP depletion than those infected with herpes simplex virus-1 (HSV-1). Although representative RP depletion (uL3, uS4, uL5) inhibited protein synthesis in cells infected with two different DNA viruses (human cytomegalovirus, vaccinia virus), HSV-1-infected cell protein synthesis unexpectedly endured and required a single virus-encoded gene product, VP22. During individual RP insufficiency, VP22-expressing HSV-1 replicated better than a VP22-deficient variant. Furthermore, VP22 promotes polysome accumulation in virus-infected cells when uL3 or ribosome availability is limiting and cosediments with initiating and elongating ribosomes in infected and uninfected cells. This identifies VP22 as a virus-encoded, ribosome-associated protein that compensates for RP insufficiency to support viral protein synthesis and replication. Moreover, it reveals an unanticipated class of virus-encoded, ribosome-associated effectors that reduce the dependence of protein synthesis upon host RPs and broadly support translation during physiological stress such as infection.
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Ríos-Meléndez S, Valadez-Hernández E, Delgadillo C, Luna-Guevara ML, Martínez-Núñez MA, Sánchez-Pérez M, Martínez-Y-Pérez JL, Arroyo-Becerra A, Cárdenas L, Bibbins-Martínez M, Maldonado-Mendoza IE, Villalobos-López MA. Pseudocrossidium replicatum (Taylor) R.H. Zander is a fully desiccation-tolerant moss that expresses an inducible molecular mechanism in response to severe abiotic stress. PLANT MOLECULAR BIOLOGY 2021; 107:387-404. [PMID: 34189708 PMCID: PMC8648698 DOI: 10.1007/s11103-021-01167-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 06/10/2021] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE The moss Pseudocrossidium replicatum is a desiccation-tolerant species that uses an inducible system to withstand severe abiotic stress in both protonemal and gametophore tissues. Desiccation tolerance (DT) is the ability of cells to recover from an air-dried state. Here, the moss Pseudocrossidium replicatum was identified as a fully desiccation-tolerant (FDT) species. Its gametophores rapidly lost more than 90% of their water content when exposed to a low-humidity atmosphere [23% relative humidity (RH)], but abscisic acid (ABA) pretreatment diminished the final water loss after equilibrium was reached. P. replicatum gametophores maintained good maximum photosystem II (PSII) efficiency (Fv/Fm) for up to two hours during slow dehydration; however, ABA pretreatment induced a faster decrease in the Fv/Fm. ABA also induced a faster recovery of the Fv/Fm after rehydration. Protein synthesis inhibitor treatment before dehydration hampered the recovery of the Fv/Fm when the gametophores were rehydrated after desiccation, suggesting the presence of an inducible protective mechanism that is activated in response to abiotic stress. This observation was also supported by accumulation of soluble sugars in gametophores exposed to ABA or NaCl. Exogenous ABA treatment delayed the germination of P. replicatum spores and induced morphological changes in protonemal cells that resembled brachycytes. Transcriptome analyses revealed the presence of an inducible molecular mechanism in P. replicatum protonemata that was activated in response to dehydration. This study is the first RNA-Seq study of the protonemal tissues of an FDT moss. Our results suggest that P. replicatum is an FDT moss equipped with an inducible molecular response that prepares this species for severe abiotic stress and that ABA plays an important role in this response.
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Affiliation(s)
- Selma Ríos-Meléndez
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Emmanuel Valadez-Hernández
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Claudio Delgadillo
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria L Luna-Guevara
- Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, C.P. 72000, Puebla, Puebla, México
| | - Mario A Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, C.P. 97302, Mérida, Yucatán, México
| | - Mishael Sánchez-Pérez
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, México
| | - José L Martínez-Y-Pérez
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, C.P. 90210, Ixtacuixtla, Tlaxcala, México
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Luis Cárdenas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, México
| | - Martha Bibbins-Martínez
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México
| | - Ignacio E Maldonado-Mendoza
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, C.P. 81049, Guasave, Sinaloa, México
| | - Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, México.
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Li D, Liu J, Zong J, Guo H, Li J, Wang J, Wang H, Li L, Chen J. Integration of the metabolome and transcriptome reveals the mechanism of resistance to low nitrogen supply in wild bermudagrass (Cynodon dactylon (L.) Pers.) roots. BMC PLANT BIOLOGY 2021; 21:480. [PMID: 34674655 PMCID: PMC8532362 DOI: 10.1186/s12870-021-03259-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Nitrogen (N) is an essential macronutrient that significantly affects turf quality. Commercial cultivars of bermudagrass (Cynodon dactylon (L.) Pers.) require large amounts of nitrogenous fertilizer. Wild bermudagrass germplasm from natural habitats with poor nutrition and diverse N distributions is an important source for low-N-tolerant cultivated bermudagrass breeding. However, the mechanisms underlying the differences in N utilization among wild germplasm resources of bermudagrass are not clear. RESULTS To clarify the low N tolerance mechanism in wild bermudagrass germplasm, the growth, physiology, metabolome and transcriptome of two wild accessions, C291 (low-N-tolerant) and C716 (low-N-sensitive), were investigated. The results showed that root growth was less inhibited in low-N-tolerant C291 than in low-N-sensitive C716 under low N conditions; the root dry weight, soluble protein content and free amino acid content of C291 did not differ from those of the control, while those of C716 were significantly decreased. Down-regulation of N acquisition, primary N assimilation and amino acid biosynthesis was less pronounced in C291 than in C716 under low N conditions; glycolysis and the tricarboxylic acid (TCA) cycle pathway were also down-regulated, accompanied by a decrease in the biosynthesis of amino acids; strikingly, processes such as translation, biosynthesis of the structural constituent of ribosome, and the expression of individual aminoacyl-tRNA synthetase genes, most of genes associated with ribosomes related to protein synthesis were all up-regulated in C291, but down-regulated in C716. CONCLUSIONS Overall, low-N-tolerant wild bermudagrass tolerated low N nutrition by reducing N primary assimilation and amino acid biosynthesis, while promoting the root protein synthesis process and thereby maintaining root N status and normal growth.
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Affiliation(s)
- Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China.
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Alafari HA, Abd-Elgawad ME. Differential expression gene/protein contribute to heat stress-responsive in Tetraena propinqua in Saudi Arabia. Saudi J Biol Sci 2021; 28:5017-5027. [PMID: 34466077 PMCID: PMC8380999 DOI: 10.1016/j.sjbs.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/27/2022] Open
Abstract
Within their natural habitat, plants are subjected to abiotic stresses that include heat stress. In the current study, the effect of 4 h, 24 h, and 48 h of heat stress on Tetraena propinqua ssp. migahidii seedling's protein profile and proteomic analyses were investigated. Total soluble protein SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis) profile showed 18-protein bands, the newly synthesized protein band (with molecular weights 86.5, 30.2 and 31.4 KD) at 24 h of heat stress and 48 of normal conditions. Proteomic analysis showed that 81 and 930 targets are involved in gene and protein expression respectively. At 4 h, 57 genes and 110 proteins in C4 reached 56 genes and 173 proteins in T4. At 24 h, 63 genes and 180 proteins in C24 decreased to 54 genes and 151 protein in T24. After 48 h, 56 genes and 136 proteins in C48 increased to 64 genes and 180 proteins in T48. The genes and proteins involved in transcription, translation, photosynthesis, transport, and other unknown metabolic processes, were differentially expressed under treatments of heat stress. These findings provide insights into the molecular mechanisms related to heat stress, in addition to its influence on the physiological traits of T. propinqua seedlings. Heat stress-mediated differential regulation genes indicate a role in the development and stress response of T. propinqua. The candidate dual-specificity genes and proteins identified in this study paves way for more molecular analysis of up-and-down-regulation.
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Affiliation(s)
- Hayat Ali Alafari
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Magda Elsayed Abd-Elgawad
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Botany Department, Faculty of Science, Fayoum University, Fayoum, Egypt
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Hixson KK, Marques JV, Wendler JP, McDermott JE, Weitz KK, Clauss TR, Monroe ME, Moore RJ, Brown J, Lipton MS, Bell CJ, Paša-Tolić L, Davin LB, Lewis NG. New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:664250. [PMID: 34113365 PMCID: PMC8185232 DOI: 10.3389/fpls.2021.664250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, α-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.
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Affiliation(s)
- Kim K. Hixson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joaquim V. Marques
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Jason P. Wendler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jason E. McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Karl K. Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Therese R. Clauss
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Matthew E. Monroe
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J. Moore
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joseph Brown
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Mary S. Lipton
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Callum J. Bell
- National Center for Genome Resources, Santa Fe, NM, United States
| | - Ljiljana Paša-Tolić
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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Moin M, Saha A, Bakshi A, Madhav MS, Kirti PB. Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene 2021; 789:145670. [PMID: 33892070 DOI: 10.1016/j.gene.2021.145670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/14/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Abstract
We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - M S Madhav
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India; Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad 500030, India
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31
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Hsu PJ, Tan MC, Shen HL, Chen YH, Wang YY, Hwang SG, Chiang MH, Le QV, Kuo WS, Chou YC, Lin SY, Jauh GY, Cheng WH. The nucleolar protein SAHY1 is involved in pre-rRNA processing and normal plant growth. PLANT PHYSIOLOGY 2021; 185:1039-1058. [PMID: 33793900 PMCID: PMC8133687 DOI: 10.1093/plphys/kiaa085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/01/2020] [Indexed: 05/29/2023]
Abstract
Although the nucleolus is involved in ribosome biogenesis, the functions of numerous nucleolus-localized proteins remain unclear. In this study, we genetically isolated Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, pointed leaves, and sterility. SAHY1 encodes an uncharacterized protein that is predominantly expressed in root tips, early developing seeds, and mature pollen grains and is mainly restricted to the nucleolus. Dysfunction of SAHY1 primarily causes the accumulation of 32S, 18S-A3, and 27SB pre-rRNA intermediates. Coimmunoprecipitation experiments further revealed the interaction of SAHY1 with ribosome proteins and ribosome biogenesis factors. Moreover, sahy1 mutants are less sensitive to protein translation inhibitors and show altered expression of structural constituents of ribosomal genes and ribosome subunit profiles, reflecting the involvement of SAHY1 in ribosome composition and ribosome biogenesis. Analyses of ploidy, S-phase cell cycle progression, and auxin transport and signaling indicated the impairment of mitotic activity, translation of auxin transport carrier proteins, and expression of the auxin-responsive marker DR5::GFP in the root tips or embryos of sahy1 plants. Collectively, these data demonstrate that SAHY1, a nucleolar protein involved in ribosome biogenesis, plays critical roles in normal plant growth in association with auxin transport and signaling.
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Affiliation(s)
- Pei-jung Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Chen Tan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hwei-Ling Shen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ya-Huei Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Ying Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - San-Gwang Hwang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hau Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Quang-Vuong Le
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Shuo Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ying-Chan Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung County,Taiwan
| | - Shih-Yun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Moin M, Saha A, Bakshi A, D. D, M.S. M, P.B. K. Study on Transcriptional Responses and Identification of Ribosomal Protein Genes for Potential Resistance against Brown Planthopper and Gall Midge Pests in Rice. Curr Genomics 2021; 22:98-110. [PMID: 34220297 PMCID: PMC8188583 DOI: 10.2174/1389202922666210219113220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 01/02/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Our previous studies have revealed the roles of ribosomal protein (RP) genes in the abiotic stress responses of rice. METHODS In the current investigation, we examine the possible involvement of these genes in insect stress responses. We have characterized the RP genes that included both Ribosomal Protein Large (RPL) and Ribosomal Protein Small (RPS) subunit genes in response to infestation by two economically important insect pests, the brown planthopper (BPH) and the Asian rice gall midge (GM) in rice. Differential transcript patterns of seventy selected RP genes were studied in a susceptible and a resistant genotype of indica rice: BPT5204 and RPNF05, respectively. An in silico analyses of the upstream regions of these genes also revealed the presence of cis-elements that are associated with wound signaling. RESULTS We identified the genes that were up or downregulated in either one of the genotypes, or both of them after pest infestation. The transcript patterns of a majority of the genes were found to be temporally-regulated by both the pests. In the resistant RPNF05, BPH infestation activated RPL15, L51 and RPS5a genes while GM infestation induced RPL15, L18a, L22, L36.2, L38, RPS5, S9.2 and S25a at a certain point of time. These genes that were particularly upregulated in the resistant genotype, RPNF05, but not in BPT5204 suggest their potential involvement in plant resistance against either of the two pests studied. CONCLUSION Taken together, RPL15, L51, L18a, RPS5, S5a, S9.2, and S25a appear to be the genes with possible roles in insect resistance in rice.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Divya D.
- Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad-500030, India
| | - Madhav M.S.
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Kirti P.B.
- Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
- Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad-500030, India
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33
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Mehta D, Ghahremani M, Pérez-Fernández M, Tan M, Schläpfer P, Plaxton WC, Uhrig RG. Phosphate and phosphite have a differential impact on the proteome and phosphoproteome of Arabidopsis suspension cell cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:924-941. [PMID: 33184936 DOI: 10.1111/tpj.15078] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/01/2020] [Accepted: 10/19/2020] [Indexed: 05/21/2023]
Abstract
Phosphorus absorbed in the form of phosphate (H2 PO4- ) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding of how plants respond to phosphate starvation is essential for the development of more phosphate-efficient crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses to 48 h of phosphate versus phosphite (H2 PO3- ) resupply to phosphate-deprived Arabidopsis thaliana suspension cells. Phosphite is similarly sensed, taken up and transported by plant cells as phosphate, but cannot be metabolized or used as a nutrient. Phosphite is thus a useful tool for differentiating between non-specific processes related to phosphate sensing and transport and specific responses to phosphorus nutrition. We found that responses to phosphate versus phosphite resupply occurred mainly at the level of protein phosphorylation, complemented by limited changes in protein abundance, primarily in protein translation, phosphate transport and scavenging, and central metabolism proteins. Altered phosphorylation of proteins involved in core processes such as translation, RNA splicing and kinase signaling was especially important. We also found differential phosphorylation in response to phosphate and phosphite in 69 proteins, including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 histone acetyltransferase - potential phospho-switches signaling changes in phosphorus nutrition. Our study illuminates several new aspects of the phosphate starvation response and identifies important targets for further investigation and potential crop improvement.
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Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada
| | - Mina Ghahremani
- Department of Biology, Queen's University, 116 Barrie St., Kingston, ON, K7L 3N6, Canada
| | - Maria Pérez-Fernández
- Departamento de Sistemas Físicos Químicos y Naturales, Universidad Pablo de Olavide, Ecology Area. Faculty os Experimental Sciences. Carretera de Utrera Km 1, Sevilla, 41013, Spain
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada
| | - Pascal Schläpfer
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - William C Plaxton
- Department of Biology, Queen's University, 116 Barrie St., Kingston, ON, K7L 3N6, Canada
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada
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Sun M, Shen B, Li W, Samir P, Browne CM, Link AJ, Frank J. A Time-Resolved Cryo-EM Study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source. Proteomics 2020; 21:e2000125. [PMID: 33007145 DOI: 10.1002/pmic.202000125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/31/2020] [Indexed: 12/28/2022]
Abstract
The role of the ribosome in the regulation of gene expression has come into increased focus. It is proposed that ribosomes are catalytic engines capable of changing their protein composition in response to environmental stimuli. Time-resolved cryo-electron microscopy (cryo-EM) techniques are employed to identify quantitative changes in the protein composition and structure of the Saccharomyces cerevisiae 80S ribosomes after shifting the carbon source from glucose to glycerol. Using cryo-EM combined with the computational classification approach, it is found that a fraction of the yeast cells' 80S ribosomes lack ribosomal proteins at the entrance and exit sites for tRNAs, including uL16(RPL10), eS1(RPS1), uS11(RPS14A/B), and eS26(RPS26A/B). This fraction increased after a change from glucose to glycerol medium. The quantitative structural analysis supports the hypothesis that ribosomes are dynamic complexes that alter their composition in response to changes in growth or environmental conditions.
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Affiliation(s)
- Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Bingxin Shen
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Parimal Samir
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Christopher M Browne
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Andrew J Link
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
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Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11101124. [PMID: 32987927 PMCID: PMC7650634 DOI: 10.3390/genes11101124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.
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36
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Garcia-Molina A, Marino G, Lehmann M, Leister D. Systems biology of responses to simultaneous copper and iron deficiency in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2119-2138. [PMID: 32578228 DOI: 10.1111/tpj.14887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/09/2020] [Indexed: 05/29/2023]
Abstract
Plant responses to coincident nutrient deficiencies cannot be predicted from the responses to individual deficiencies. Although copper (Cu) and iron (Fe) are essential micronutrients for plant growth that are often and concurrently limited in soils, the combinatorial response to Cu-Fe deficiency remains elusive. In the present study, we characterised the responses of Arabidopsis thaliana plants deprived of Cu, Fe or both (-Cu-Fe) at the level of plant development, mineral composition, and reconfiguration of transcriptomes, proteomes and metabolomes. Compared to single deficiencies, simultaneous -Cu-Fe leads to a distinct pattern in leaf physiology and microelement concentration characterised by lowered protein content and enhanced manganese and zinc levels. Conditional networking analysis of molecular changes indicates that biological processes also display different co-expression patterns among single and double deficiencies. Indeed, the interaction between Cu and Fe deficiencies causes distinct expression profiles for 15% of all biomolecules, leading to specific enhancement of general stress responses and protein homeostasis mechanisms, at the same time as severely arresting photosynthesis. Accordingly, central carbon metabolites, in particular photosynthates, decrease especially under -Cu-Fe conditions, whereas the pool of free amino acids increases. Further meta-analysis of transcriptomes and proteomes corroborated that protein biosynthesis and folding capacity were readjusted during the combinatorial response and unveiled important rearrangements in the metabolism of organic acids. Consequently, our results demonstrate that the response to -Cu-Fe imposes a distinct reconfiguration of large sets of molecules, not triggered by single deficiencies, resulting into a switch from autotrophy to heterotrophy and involving organic acids such as fumaric acid as central mediators of the response.
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Affiliation(s)
- Antoni Garcia-Molina
- Faculty of Biology, Plant Molecular Biology (Botany), Ludwig-Maximilians Universität München, Großhadernerstr. 2-4, Planegg-Martinsried, D-82152, Germany
| | - Giada Marino
- Faculty of Biology, Plant Molecular Biology (Botany), Ludwig-Maximilians Universität München, Großhadernerstr. 2-4, Planegg-Martinsried, D-82152, Germany
| | - Martin Lehmann
- Faculty of Biology, Plant Molecular Biology (Botany), Ludwig-Maximilians Universität München, Großhadernerstr. 2-4, Planegg-Martinsried, D-82152, Germany
| | - Dario Leister
- Faculty of Biology, Plant Molecular Biology (Botany), Ludwig-Maximilians Universität München, Großhadernerstr. 2-4, Planegg-Martinsried, D-82152, Germany
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37
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Salih KJ, Duncan O, Li L, O'Leary B, Fenske R, Trösch J, Millar AH. Impact of oxidative stress on the function, abundance, and turnover of the Arabidopsis 80S cytosolic ribosome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:128-139. [PMID: 32027433 DOI: 10.1111/tpj.14713] [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: 10/06/2019] [Revised: 01/05/2020] [Accepted: 01/23/2020] [Indexed: 05/22/2023]
Abstract
Abiotic stress in plants causes accumulation of reactive oxygen species (ROS) leading to the need for new protein synthesis to defend against ROS and to replace existing proteins that are damaged by oxidation. Functional plant ribosomes are critical for these activities, however we know little about the impact of oxidative stress on plant ribosome abundance, turnover, and function. Using Arabidopsis cell culture as a model system, we induced oxidative stress using 1 µm of H2 O2 or 5 µm menadione to more than halve cell growth rate and limit total protein content. We show that ribosome content on a total cell protein basis decreased in oxidatively stressed cells. However, overall protein synthesis rates on a ribosome abundance basis showed the resident ribosomes retained their function in oxidatively stressed cells. 15 N progressive labelling was used to calculate the rate of ribosome synthesis and degradation to track the fate of 62 r-proteins. The degradation rates and the synthesis rates of most r-proteins slowed following oxidative stress leading to an ageing population of ribosomes in stressed cells. However, there were exceptions to this trend; r-protein RPS14C doubled its degradation rate in both oxidative treatments. Overall, we show that ribosome abundance decreases and their age increases with oxidative stress in line with loss of cell growth rate and total cellular protein amount, but ribosome function of the ageing ribosomes appeared to be maintained concomittently with differences in the turnover rate and abundance of specific ribosomal proteins. Data are available via ProteomeXchange with identifier PXD012840.
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Affiliation(s)
- Karzan J Salih
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
- Pharmaceutical Chemistry Department, Medical and Applied Science College, Charmo University, 46023, Chamchamal-Sulaimani, Kurdistan Region, Iraq
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
- College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Brendan O'Leary
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
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38
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Garcia-Molina A, Kleine T, Schneider K, Mühlhaus T, Lehmann M, Leister D. Translational Components Contribute to Acclimation Responses to High Light, Heat, and Cold in Arabidopsis. iScience 2020; 23:101331. [PMID: 32679545 PMCID: PMC7364123 DOI: 10.1016/j.isci.2020.101331] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/26/2020] [Accepted: 06/28/2020] [Indexed: 12/27/2022] Open
Abstract
Plant metabolism is broadly reprogrammed during acclimation to abiotic changes. Most previous studies have focused on transitions from standard to single stressful conditions. Here, we systematically analyze acclimation processes to levels of light, heat, and cold stress that subtly alter physiological parameters and assess their reversibility during de-acclimation. Metabolome and transcriptome changes were monitored at 11 different time points. Unlike transcriptome changes, most alterations in metabolite levels did not readily return to baseline values, except in the case of cold acclimation. Similar regulatory networks operate during (de-)acclimation to high light and cold, whereas heat and high-light responses exhibit similar dynamics, as determined by surprisal and conditional network analyses. In all acclimation models tested here, super-hubs in conditional transcriptome networks are enriched for components involved in translation, particularly ribosomes. Hence, we suggest that the ribosome serves as a common central hub for the control of three different (de-)acclimation responses.
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Affiliation(s)
- Antoni Garcia-Molina
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany
| | - Kevin Schneider
- Computational Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany.
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39
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Kopka J. Systematic Review of Plant Ribosome Heterogeneity and Specialization. FRONTIERS IN PLANT SCIENCE 2020; 11:948. [PMID: 32670337 PMCID: PMC7332886 DOI: 10.3389/fpls.2020.00948] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/10/2020] [Indexed: 05/25/2023]
Abstract
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Yin-Chen Hsieh
- Bioinformatics Subdivision, Wageningen University, Wageningen, Netherlands
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
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40
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Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype. Sci Rep 2020; 10:4580. [PMID: 32165659 PMCID: PMC7067865 DOI: 10.1038/s41598-020-61305-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/25/2020] [Indexed: 11/24/2022] Open
Abstract
Aluminium (Al) toxicity is the single most important contributing factor constraining crop productivity in acidic soils. Hydroponics based screening of three rice genotypes, a tolerant (ARR09, AR), a susceptible (IR 1552, IR) and an acid soil adapted landrace (Theruvii, TH) revealed that AR accumulates less Al and shows minimum decrease in shoot and root biomass under Al toxicity conditions when compared with IR. Transcriptome data generated on roots (grown in presence or absence of Al) led to identification of ~1500 transcripts per genotype with percentage annotation ranging from 21.94% (AR) to 29.94% (TH). A total of 511, 804 and 912 DEGs were identified in genotypes AR, IR and TH, respectively. IR showed upregulation of transcripts involved in exergonic processes. AR appears to conserve energy by downregulating key genes of glycolysis pathway and maintaining transcript levels of key exergonic step enzymes under Al stress. The tolerance in AR appears to be as a result of novel mechanism as none of the reported Al toxicity genes or QTLs overlap with significant DEGs. Components of signal transduction and regulatory machinery like transcripts encoding zinc finger protein, calcieurin binding protein and cell wall associated transcripts are among the highly upregulated DEGs in AR, suggesting increased and better signal transduction in response to Al stress in tolerant rice. Sequencing of NRAT1 and glycine-rich protein A3 revealed distinct haplotype for indica type AR. The newly identified components of Al tolerance will help in designing molecular breeding tools to enhance rice productivity in acidic soils.
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Tarnowski L, Collados Rodriguez M, Brzywczy J, Cysewski D, Wawrzynska A, Sirko A. Overexpression of the Selective Autophagy Cargo Receptor NBR1 Modifies Plant Response to Sulfur Deficit. Cells 2020; 9:E669. [PMID: 32164165 PMCID: PMC7140714 DOI: 10.3390/cells9030669] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
Plants exposed to sulfur deficit elevate the transcription of NBR1 what might reflect an increased demand for NBR1 in such conditions. Therefore, we investigated the role of this selective autophagy cargo receptor in plant response to sulfur deficit (-S). Transcriptome analysis of the wild type and NBR1 overexpressing plants pointed out differences in gene expression in response to -S. Our attention focused particularly on the genes upregulated by -S in roots of both lines because of significant overrepresentation of cytoplasmic ribosomal gene family. Moreover, we noticed overrepresentation of the same family in the set of proteins co-purifying with NBR1 in -S. One of these ribosomal proteins, RPS6 was chosen for verification of its direct interaction with NBR1 and proven to bind outside the NBR1 ubiquitin binding domains. The biological significance of this novel interaction and the postulated role of NBR1 in ribosomes remodeling in response to starvation remain to be further investigated. Interestingly, NBR1 overexpressing seedlings have significantly shorter roots than wild type when grown in nutrient deficient conditions in the presence of TOR kinase inhibitors. This phenotype probably results from excessive autophagy induction by the additive effect of NBR1 overexpression, starvation, and TOR inhibition.
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Affiliation(s)
- Leszek Tarnowski
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A St, 02-106 Warsaw, Poland
| | - Milagros Collados Rodriguez
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A St, 02-106 Warsaw, Poland
| | - Jerzy Brzywczy
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A St, 02-106 Warsaw, Poland
| | - Dominik Cysewski
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A St, 02-106 Warsaw, Poland
| | - Anna Wawrzynska
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A St, 02-106 Warsaw, Poland
| | - Agnieszka Sirko
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A St, 02-106 Warsaw, Poland
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Tang D, Shi X, Guo H, Bai Y, Shen C, Zhang Y, Wang Z. Comparative transcriptome analysis of the gills of Procambarus clarkii provides novel insights into the immune-related mechanism of copper stress tolerance. FISH & SHELLFISH IMMUNOLOGY 2020; 96:32-40. [PMID: 31786343 DOI: 10.1016/j.fsi.2019.11.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/19/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
The red-swamp crayfish (Procambarus clarkii) is the most important economic shrimp species in China, and is an important model crustacean organism in many fields of research. In crustaceans, gills interface directly with the ambient environment and thus play a vital role in the toxicology. In the context of increasing environmental heavy metal pollution, the relationship between copper (Cu2+) stress and the immune response of P. clarkii has recently received considerable attention. However, impact of Cu2+ on the crayfish immune system is still not fully understood. In this study, we used Illumina sequencing technology to perform a transcriptome analysis of the gills of P. clarkii after 24 h of Cu2+ treatment. A total of 37,226,812 unigenes were assembled, and 1943 unigenes were significantly differentially expressed between the control and Cu2+ treatment groups. Functional categorization of differentially expressed genes (DEGs) revealed that genes related to antioxidant activity, detoxication, metabolic processes, biosynthetic processes, and immune system processes were differentially regulated during Cu2+ stress. In addition, DEGs in the immune system were classified as being related to the MAPK signaling pathway, purine metabolism, Toll and Imd signaling pathway, PI3K-Akt signaling pathway and Hippo signaling pathway. Five genes (CuZnSOD, CAT, IDH1, PHYH and DECR2) were significantly up-regulated in the peroxisome pathway, which plays an important role in reacting to oxidative stress. Importantly, qRT-PCR validation of the results for seven genes chosen at random (NDK, ATP6L, ATP5C1, RPS14, RPL22e, CTSF and HSP90A) confirmed the Illumina sequencing results. This study provides a valuable starting point for further studies to elucidate the molecular basis of the immune system's response to Cu2+ stress in crayfish.
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Affiliation(s)
- Dan Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Xueling Shi
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Huayun Guo
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Yuze Bai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Chenchen Shen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Yiping Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China.
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Ding H, Wu Y, Yuan G, Mo S, Chen Q, Xu X, Wu X, Ge C. In-depth proteome analysis reveals multiple pathways involved in tomato SlMPK1-mediated high-temperature responses. PROTOPLASMA 2020; 257:43-59. [PMID: 31359223 DOI: 10.1007/s00709-019-01419-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
High temperature (HT) is one of the major environmental factors which limits plant growth and yield. The mitogen-activated protein kinase (MAPK) plays vital roles in environmental stress responses. However, the mechanisms triggered by MAPKs in plants in response to HT are still extremely limited. In this study, the proteomic data of differences between SlMPK1 RNA-interference mutant (SlMPK1i) and wild type and of tomato (Solanum lycopersicum) plants under HT stress using isobaric tags for relative and absolute quantitation (iTRAQ) was re-analyzed in depth. In total, 168 differently expressed proteins (DEPs) were identified in response to HT stress, including 38 DEPs only found in wild type, and 84 DEPs specifically observed in SlMPK1i after HT treatment. The majority of higher expression of 84 DEPs were annotated into photosynthesis, oxidation-reduction process, protein folding, translation, proteolysis, stress response, and amino acid biosynthetic process. More importantly, SlMPK1-mediated photosynthesis was confirmed by the physiological characterization of SlMPK1i with a higher level of photosynthetic capacity under HT stress. Overall, the results reveal a set of potential candidate proteins helping to further understand the intricate regulatory network regulated by SlMPK1 in response to HT.
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Affiliation(s)
- Haidong Ding
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.
| | - Yuan Wu
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Guibo Yuan
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Shuangrong Mo
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Qi Chen
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoying Xu
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Xiaoxia Wu
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Cailin Ge
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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Solano-De la Cruz MT, Adame-García J, Gregorio-Jorge J, Jiménez-Jacinto V, Vega-Alvarado L, Iglesias-Andreu LG, Escobar-Hernández EE, Luna-Rodríguez M. Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae. BMC Genomics 2019; 20:826. [PMID: 31703622 PMCID: PMC6839141 DOI: 10.1186/s12864-019-6229-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. RESULTS Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi. CONCLUSIONS The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.
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Affiliation(s)
- Marco Tulio Solano-De la Cruz
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de las Culturas Veracruzanas s/n, Xalapa, Veracruz, Mexico
- Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N anexo, Jardín Botánico exterior, Ciudad Universitaria, Ciudad de México, Mexico
| | - Jacel Adame-García
- Tecnológico Nacional de México, Instituto Tecnológico de Úrsulo Galván, Úrsulo Galván, Veracruz, Mexico
| | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología - Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional (CIBA-IPN), Av. Insurgentes Sur 1582, Col. Crédito Constructor, Del. Benito Juárez, 03940, Ciudad de México, Mexico
| | - Verónica Jiménez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Lourdes Georgina Iglesias-Andreu
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de las Culturas Veracruzanas s/n, Xalapa, Veracruz, Mexico
| | | | - Mauricio Luna-Rodríguez
- Laboratorio de Genética e Interacciones Planta Microorganismos, Facultad de Ciencias Agrícolas, Universidad Veracruzana. Circuito Gonzalo Aguirre Beltrán s/n, Zona Universitaria, Xalapa, Veracruz, Mexico.
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Gava SG, Tavares NC, Falcone FH, Oliveira G, Mourão MM. Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase. Front Genet 2019; 10:1036. [PMID: 31681440 PMCID: PMC6813216 DOI: 10.3389/fgene.2019.01036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) play a regulatory role and influence various biological activities, such as cell proliferation, differentiation, and survival. Our group has demonstrated through functional studies that Schistosoma mansoni c-Jun N-terminal kinase (SmJNK) MAPK is involved in the parasite's development, reproduction, and survival. SmJNK can, therefore, be considered a potential target for the development of new drugs. Considering the importance of SmJNK in S. mansoni maturation, we aimed at understanding of SmJNK regulated signaling pathways in the parasite, correlating expression data with S. mansoni development. To better understand the role of SmJNK in S. mansoni intravertebrate host life stages, RNA interference knockdown was performed in adult worms and in schistosomula larval stage. SmJNK knocked-down in adult worms showed a decrease in oviposition and no significant alteration in their movement. RNASeq libraries of SmJNK knockdown schistosomula were sequenced. A total of 495 differentially expressed genes were observed in the SmJNK knockdown parasites, of which 373 were down-regulated and 122 up-regulated. Among the down-regulated genes, we found transcripts related to protein folding, purine nucleotide metabolism, the structural composition of ribosomes and cytoskeleton. Genes coding for proteins that bind to nucleic acids and proteins involved in the phagosome and spliceosome pathways were enriched. Additionally, we found that SmJNK and Smp38 MAPK signaling pathways converge regulating the expression of a large set of genes. C. elegans orthologous genes were enriched for genes related to sterility and oocyte maturation, corroborating the observed phenotype alteration. This work allowed an in-depth analysis of the SmJNK signaling pathway, elucidating gene targets of regulation and functional roles of this critical kinase for parasite maturation.
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Affiliation(s)
- Sandra Grossi Gava
- Laboratório de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Naiara Clemente Tavares
- Laboratório de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Franco Harald Falcone
- Allergy and Infectious Diseases Laboratory, Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- Institute of Parasitology, BFS, Justus Liebig University, Giessen, Germany
| | | | - Marina Moraes Mourão
- Laboratório de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
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Téllez-Robledo B, Manzano C, Saez A, Navarro-Neila S, Silva-Navas J, de Lorenzo L, González-García MP, Toribio R, Hunt AG, Baigorri R, Casimiro I, Brady SM, Castellano MM, Del Pozo JC. The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1203-1219. [PMID: 31111599 DOI: 10.1111/tpj.14416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 05/28/2023]
Abstract
Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5' untranslated regions (5'-UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.
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Affiliation(s)
- Barbara Téllez-Robledo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Concepcion Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- DTD, Timac Agro Spain, Lodosa, 31580, Navarra, Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Javier Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Mary-Paz González-García
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | | | - Ilda Casimiro
- Facultad de Ciencias, Department de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - J Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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Zhao Y, Wei X, Ji X, Ma W. Endogenous NO-mediated transcripts involved in photosynthesis and carbohydrate metabolism in alfalfa (Medicago sativa L.) seedlings under drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:456-465. [PMID: 31247428 DOI: 10.1016/j.plaphy.2019.06.023] [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: 05/07/2019] [Revised: 06/15/2019] [Accepted: 06/16/2019] [Indexed: 06/09/2023]
Abstract
Alfalfa (Medicago sativa L.) is an important perennial legume and used as a forage crop worldwide, and has extensive resistance to various abiotic stresses. Nitric oxide (NO) plays a critical role in response to external and internal cues to regulate plant growth and development. However, endogenous NO-mediated molecular mechanisms of drought tolerance in alfalfa is poorly understood. To get a deeper insight into the regulate pathway of NO, RNA-Seq was used to profile transcriptome changes of alfalfa seedlings, which were treated with NO scavenger under normal and drought conditions. A total of 1,025 and 3,461 differently-expressed genes (FDR < 0.0001; fold change ≥ 2) were observed while NO absence under normal and drought conditions, respectively. Based on GO enrich and KEGG pathway analysis, we found NO absence induced photosynthesis, carbon fixation in photosynthetic organisms and primary metabolism were significantly up-enriched. Most oxidoreductase, dehydrogenase, reductase and transferase genes were down-regulated in the above processes. Moreover, NO absence restrained chlorophyll biosynthesis and decreased different sugar content. Therefore, this work provides insights into the mechanism that NO-mediated enhanced photosynthesis and carbohydrate metabolism in alfalfa under drought stress.
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Affiliation(s)
- Ying Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, PR China.
| | - Xiangzhuo Ji
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Wenjing Ma
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, PR China
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You J, Zhang Y, Liu A, Li D, Wang X, Dossa K, Zhou R, Yu J, Zhang Y, Wang L, Zhang X. Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress. BMC PLANT BIOLOGY 2019; 19:267. [PMID: 31221078 PMCID: PMC6585049 DOI: 10.1186/s12870-019-1880-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/10/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes. RESULTS Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame. CONCLUSION The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.
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Affiliation(s)
- Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Special Economic Crop Research Center of Shandon Academy of Agricultural Sciences, Shandong Cotton Research Center, Jinan, 250100 China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiao Wang
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan, 430062 China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, 3320 Sénégal
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
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Eskelin K, Varjosalo M, Ravantti J, Mäkinen K. Ribosome profiles and riboproteomes of healthy and Potato virus A- and Agrobacterium-infected Nicotiana benthamiana plants. MOLECULAR PLANT PATHOLOGY 2019; 20:392-409. [PMID: 30375150 PMCID: PMC6637900 DOI: 10.1111/mpp.12764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Nicotiana benthamiana is an important model plant for plant-microbe interaction studies. Here, we compared ribosome profiles and riboproteomes of healthy and infected N. benthamiana plants. We affinity purified ribosomes from transgenic leaves expressing a FLAG-tagged ribosomal large subunit protein RPL18B of Arabidopsis thaliana. Purifications were prepared from healthy plants and plants that had been infiltrated with Agrobacterium tumefaciens carrying infectious cDNA of Potato virus A (PVA) or firefly luciferase gene, referred to here as PVA- or Agrobacterium-infected plants, respectively. Plants encode a number of paralogous ribosomal proteins (r-proteins). The N. benthamiana riboproteome revealed approximately 6600 r-protein hits representing 424 distinct r-proteins that were members of 71 of the expected 81 r-protein families. Data are available via ProteomeXchange with identifier PXD011602. The data indicated that N. benthamiana ribosomes are heterogeneous in their r-protein composition. In PVA-infected plants, the number of identified r-protein paralogues was lower than in Agrobacterium-infected or healthy plants. A. tumefaciens proteins did not associate with ribosomes, whereas ribosomes from PVA-infected plants co-purified with viral cylindrical inclusion protein and helper component proteinase, reinforcing their possible role in protein synthesis during virus infection. In addition, viral NIa protease-VPg, RNA polymerase NIb and coat protein were occasionally detected. Infection did not affect the proportions of ribosomal subunits or the monosome to polysome ratio, suggesting that no overall alteration in translational activity took place on infection with these pathogens. The riboproteomic data of healthy and pathogen-infected N. benthamiana will be useful for studies on the specific use of r-protein paralogues to control translation in infected plants.
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Affiliation(s)
- Katri Eskelin
- Department of Microbiology, Faculty of Agriculture and ForestryUniversity of HelsinkiPO Box 56FI‐00014Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiPO Box 56FI‐00014Finland
| | - Markku Varjosalo
- Institute of BiotechnologyUniversity of HelsinkiPO Box 65FI‐00014Finland
| | - Janne Ravantti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiPO Box 56FI‐00014Finland
| | - Kristiina Mäkinen
- Department of Microbiology, Faculty of Agriculture and ForestryUniversity of HelsinkiPO Box 56FI‐00014Finland
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Wang X, Li M, Liu X, Zhang L, Duan Q, Zhang J. Quantitative Proteomic Analysis of Castor ( Ricinus communis L.) Seeds During Early Imbibition Provided Novel Insights into Cold Stress Response. Int J Mol Sci 2019; 20:E355. [PMID: 30654474 PMCID: PMC6359183 DOI: 10.3390/ijms20020355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 12/23/2022] Open
Abstract
Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the differential abundance protein species (DAPS) between cold stress (4 °C) and control conditions (30 °C) imbibed seeds. As a result, 127 DAPS were identified according to isobaric tag for relative and absolute quantification (iTRAQ) strategy. These DAPS were mainly involved in carbohydrate and energy metabolism, translation and posttranslational modification, stress response, lipid transport and metabolism, and signal transduction. Enzyme-linked immunosorbent assays (ELISA) demonstrated that the quantitative proteomics data collected here were reliable. This study provided some invaluable insights into the cold stress responses of early imbibed castor seeds: (1) up-accumulation of all DAPS involved in translation might confer cold tolerance by promoting protein synthesis; (2) stress-related proteins probably protect the cell against damage caused by cold stress; (3) up-accumulation of key DAPS associated with fatty acid biosynthesis might facilitate resistance or adaptation of imbibed castor seeds to cold stress by the increased content of unsaturated fatty acid (UFA). The data has been deposited to the ProteomeXchange with identifier PXD010043.
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Affiliation(s)
- Xiaoyu Wang
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Min Li
- College of Agriculture, Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Xuming Liu
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Lixue Zhang
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Qiong Duan
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Jixing Zhang
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
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