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Komatsu S, Egishi M, Ohno T. The Changes of Amino-Acid Metabolism between Wheat and Rice during Early Growth under Flooding Stress. Int J Mol Sci 2024; 25:5229. [PMID: 38791268 PMCID: PMC11121113 DOI: 10.3390/ijms25105229] [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: 04/07/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Floods induce hypoxic stress and reduce wheat growth. On the other hand, rice is a semi-aquatic plant and usually grows even when partially submerged. To clarify the dynamic differences in the cellular mechanism between rice and wheat under flooding stress, morphological and biochemical analyses were performed. Although the growth of wheat in the early stage was significantly suppressed due to flooding stress, rice was hardly affected. Amino-acid analysis revealed significant changes in amino acids involved in the gamma-aminobutyric acid (GABA) shunt and anaerobic/aerobic metabolism. Flood stress significantly increased the contents of GABA and glutamate in wheat compared with rice, though the abundances of glutamate decarboxylase and succinyl semialdehyde dehydrogenase did not change. The abundance of alcohol dehydrogenase and pyruvate carboxylase increased in wheat and rice, respectively. The contents of aspartic acid and pyruvic acid increased in rice root but remained unchanged in wheat; however, the abundance of aspartate aminotransferase increased in wheat root. These results suggest that flooding stress significantly inhibits wheat growth through upregulating amino-acid metabolism and increasing the alcohol-fermentation system compared to rice. When plant growth is inhibited by flooding stress and the aerobic-metabolic system is activated, GABA content increases.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Life and Environmental Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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2
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Meloni M, Rossi J, Fanti S, Carloni G, Tedesco D, Treffon P, Piccinini L, Falini G, Trost P, Vierling E, Licausi F, Giuntoli B, Musiani F, Fermani S, Zaffagnini M. Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1054-1070. [PMID: 38308388 DOI: 10.1111/tpj.16651] [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: 10/20/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.
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Affiliation(s)
- Maria Meloni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Giacomo Carloni
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Daniele Tedesco
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), 40129, Bologna, Italy
| | - Patrick Treffon
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Luca Piccinini
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Giuseppe Falini
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | | | - Beatrice Giuntoli
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064, Bologna, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
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Zong S, Huang G, Pan B, Zhao S, Ling C, Cheng B. A Hypoxia-Related miRNA-mRNA Signature for Predicting the Response and Prognosis of Transcatheter Arterial Chemoembolization in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:525-542. [PMID: 38496249 PMCID: PMC10944249 DOI: 10.2147/jhc.s454698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Purpose Transcatheter arterial chemoembolization (TACE) is commonly used in the treatment of hepatocellular carcinoma (HCC). However, not all patients respond to this treatment. TACE typically leads to hypoxia in the tumor microenvironment. Therefore, we aimed to construct a prognostic model based on hypoxia-related differentially expressed microRNA (miRNAs) in hepatocellular carcinoma (HCC) and to investigate the potential target mRNAs for predicting TACE response. Methods The hypoxia-related miRNAs (HRMs) were identified in liver cancer cells, then global test was performed to further select the miRNAs which were associated with recurrence and vascular invasion. A prognostic model was constructed based on multivariate Cox regression analysis; qRT-PCR analysis was used to validate the differentially expressed miRNAs in HCC cell lines under hypoxic condition. We further identified the putative target genes of the miRNAs and investigate the relationship between the target genes and TACE response, immune cells infiltration. Results We established a HRMs prognostic model for HCC patients, containing two miRNAs (miR-638, miR-501-5p), the patients with high-HRMs score showed worse survival in discovery and validation cohort; qRT-PCR analysis confirmed that these two miRNAs are up-regulated in hepatoma cells under hypoxic condition. Furthermore, four putative target genes of these two miRNAs were identified (ADH1B, CTH, FTCD, RCL1), which were significantly associated with TACE response, immune score, immunosuppressive immune cells infiltration, PDCD1 and CTLA4. Conclusion The HCC-HRMs signature may be utilized as a promising prognostic factor and may have implications for guiding TACE and immune therapy.
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Affiliation(s)
- Shaoqi Zong
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200043, People’s Republic of China
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Guokai Huang
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200043, People’s Republic of China
- Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, People’s Republic of China
| | - Bo Pan
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200043, People’s Republic of China
| | - Shasha Zhao
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, People’s Republic of China
| | - Changquan Ling
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200043, People’s Republic of China
- Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, People’s Republic of China
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200043, People’s Republic of China
- Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, People’s Republic of China
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Zhao Y, Chen Y, Gao M, Wang Y. Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis. PLANT PHYSIOLOGY 2024; 194:1674-1691. [PMID: 37831423 DOI: 10.1093/plphys/kiad553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.
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Affiliation(s)
- Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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Wang R, Du C, Gu G, Zhang B, Lin X, Chen C, Li T, Chen R, Xie X. Genome-wide identification and expression analysis of the ADH gene family under diverse stresses in tobacco (Nicotiana tabacum L.). BMC Genomics 2024; 25:13. [PMID: 38166535 PMCID: PMC10759372 DOI: 10.1186/s12864-023-09813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Alcohol dehydrogenases (ADHs) are the crucial enzymes that can convert ethanol into acetaldehyde. In tobacco, members of ADH gene family are involved in various stresses tolerance reactions, lipid metabolism and pathways related to plant development. It will be of great application significance to analyze the ADH gene family and expression profile under various stresses in tobacco. RESULTS A total of 53 ADH genes were identified in tobacco (Nicotiana tabacum L.) genome and were grouped into 6 subfamilies based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were highly conserved among the NtADH genes, especially the members within the same subfamily. A total of 5 gene pairs of tandem duplication, and 3 gene pairs of segmental duplication were identified based on the analysis of gene duplication events. Cis-regulatory elements of the NtADH promoters participated in cell development, plant hormones, environmental stress, and light responsiveness. The analysis of expression profile showed that NtADH genes were widely expressed in topping stress and leaf senescence. However, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 13 NtADH genes displayed their differential expression pattern in response to the bacterial pathogen Ralstonia solanacearum L. INFECTION Metabolomics analysis revealed that NtADH genes were primarily associated with carbohydrate metabolism, and moreover, four NtADH genes (NtADH20/24/48/51) were notably involved in the pathway of alpha-linolenic acid metabolism which related to the up-regulation of 9-hydroxy-12-oxo-10(E), 15(Z)-octadecadienoic acid and 9-hydroxy-12-oxo-15(Z)-octadecenoic acid. CONCLUSION The genome-wide identification, evolutionary analysis, expression profiling, and exploration of related metabolites and metabolic pathways associated with NtADH genes have yielded valuable insights into the roles of these genes in response to various stresses. Our results could provide a basis for functional analysis of NtADH gene family under stressful conditions.
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Affiliation(s)
- Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Chaofan Du
- Longyan Tobacco Company, Longyan, 364000, China
| | - Gang Gu
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, 350003, China
| | - Binghui Zhang
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, 350003, China
| | - Xiaolu Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Chengliang Chen
- Jianning Branch of Sanming Tobacco Company, Sanming, 354500, China
| | - Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory of Crop Breeding By Design, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
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Yang H, Wei Z, Wu Y, Zhang C, Lyu L, Wu W, Li W. Transcriptomic and Metabolomic Profiling Reveals the Variations in Carbohydrate Metabolism between Two Blueberry Cultivars. Int J Mol Sci 2023; 25:293. [PMID: 38203463 PMCID: PMC10778917 DOI: 10.3390/ijms25010293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Blueberry is a high-quality fruit tree with significant nutritional and economic value, but the intricate mechanism of sugar accumulation in its fruit remains unclear. In this study, the ripe fruits of blueberry cultivars 'Anna' and 'Misty' were utilized as experimental materials, and physiological and multi-omics methodologies were applied to analyze the regulatory mechanisms of the difference in sugar content between them. The results demonstrated that the 'Anna' fruit was smaller and had less hardness than the 'Misty' fruit, as well as higher sugar content, antioxidant capability, and lower active substance content. A total of 7067 differentially expressed genes (DEGs) (3674 up-regulated and 3393 down-regulated) and 140 differentially abundant metabolites (DAMs) (82 up-regulated and 58 down-regulated) were identified between the fruits of the two cultivars. According to KEGG analysis, DEGs were primarily abundant in phenylpropanoid synthesis and hormone signal transduction pathways, whereas DAMs were primarily enriched in ascorbate and aldarate metabolism, phenylpropanoid biosynthesis, and the pentose phosphate pathway. A combined multi-omics study showed that 116 DEGs and 3 DAMs in starch and sucrose metabolism (48 DEGs and 1 DAM), glycolysis and gluconeogenesis (54 DEGs and 1 DAM), and the pentose phosphate pathway (14 DEGs and 1 DAM) were significantly enriched. These findings suggest that blueberries predominantly increase sugar accumulation by activating carbon metabolism network pathways. Moreover, we identified critical transcription factors linked to the sugar response. This study presents new understandings regarding the molecular mechanisms underlying blueberry sugar accumulation and will be helpful in improving blueberry fruit quality through breeding.
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Affiliation(s)
- Haiyan Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (H.Y.); (Y.W.); (C.Z.); (L.L.)
| | - Zhiwen Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China;
| | - Yaqiong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (H.Y.); (Y.W.); (C.Z.); (L.L.)
| | - Chunhong Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (H.Y.); (Y.W.); (C.Z.); (L.L.)
| | - Lianfei Lyu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (H.Y.); (Y.W.); (C.Z.); (L.L.)
| | - Wenlong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (H.Y.); (Y.W.); (C.Z.); (L.L.)
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China;
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Alcalde MA, Hidalgo-Martinez D, Bru Martínez R, Sellés-Marchart S, Bonfill M, Palazon J. Insights into enhancing Centella asiatica organ cell biofactories via hairy root protein profiling. FRONTIERS IN PLANT SCIENCE 2023; 14:1274767. [PMID: 37965024 PMCID: PMC10642384 DOI: 10.3389/fpls.2023.1274767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Recent advancements in plant biotechnology have highlighted the potential of hairy roots as a biotechnological platform, primarily due to their rapid growth and ability to produce specialized metabolites. This study aimed to delve deeper into hairy root development in C. asiatica and explore the optimization of genetic transformation for enhanced bioactive compound production. Previously established hairy root lines of C. asiatica were categorized based on their centelloside production capacity into HIGH, MID, or LOW groups. These lines were then subjected to a meticulous label-free proteomic analysis to identify and quantify proteins. Subsequent multivariate and protein network analyses were conducted to discern proteome differences and commonalities. Additionally, the quantification of rol gene copy numbers was undertaken using qPCR, followed by gene expression measurements. From the proteomic analysis, 213 proteins were identified. Distinct proteome differences, especially between the LOW line and other lines, were observed. Key proteins related to essential processes like photosynthesis and specialized metabolism were identified. Notably, potential biomarkers, such as the Tr-type G domain-containing protein and alcohol dehydrogenase, were found in the HIGH group. The presence of ornithine cyclodeaminase in the hairy roots emerged as a significant biomarker linked with centelloside production capacity lines, indicating successful Rhizobium-mediated genetic transformation. However, qPCR results showed an inconsistency with rol gene expression levels, with the HIGH line displaying notably higher expression, particularly of the rolD gene. The study unveiled the importance of ornithine cyclodeaminase as a traceable biomarker for centelloside production capacity. The strong correlation between this biomarker and the rolD gene emphasizes its potential role in optimizing genetic transformation processes in C. asiatica.
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Affiliation(s)
- Miguel Angel Alcalde
- Biotechnology, Health and Education Research Group, Posgraduate School, Cesar Vallejo University, Trujillo, Peru
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Diego Hidalgo-Martinez
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Roque Bru Martínez
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology, Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology, Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Mercedes Bonfill
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Javier Palazon
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
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Jan N, Wani UM, Wani MA, Qazi HA, John R. Comparative physiological, antioxidant and proteomic investigation reveal robust response to cold stress in Digitalis purpurea L. Mol Biol Rep 2023; 50:7319-7331. [PMID: 37439898 DOI: 10.1007/s11033-023-08635-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND OF THE STUDY Digitalis purpurea (L) is an important medicinal plant growing at Alpine region of Himalayas and withstands low temperatures and harsh climatic conditions existing at high altitude. It serves as an ideal plant system to decipher the tolerance to cold stress (CS) in plants from high altitudes. METHODS AND RESULTS To understand the complexity of plant response to CS, we performed a comparative physiological and biochemical study complemented with proteomics in one-month-old D. purpurea grown at 25 °C (control) and 4 °C (CS). We observed an enhanced accumulation of different osmo-protectants (glycine betaine, soluble sugar and proline) and higher transcription (mRNA levels) of various antioxidant enzymes with an increased antioxidant enzyme activity in D. purpurea when exposed to CS. Furthermore, higher concentrations of non-enzymatic antioxidants (flavonoids, phenolics) was also associated with the response to CS. Differential proteomic analysis revealed the role of various proteins primarily involved in redox reactions, protein stabilization, quinone and sterol metabolism involved in CS response in D. purpurea.. CONCLUSION Our results provide a framework for better understanding the physiological and molecular mechanism of CS response in D. purpurea at high altitudes.
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Affiliation(s)
- Nelofer Jan
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Umer Majeed Wani
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Mubashir Ahmad Wani
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Hilal Ahmad Qazi
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Riffat John
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India.
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Zhu Q, Han Y, Yang W, Zhu H, Li G, Xu K, Long M. Genome-wide identification and characterization of ADH gene family and the expression under different abiotic stresses in tomato ( Solanum lycopersicum L.). Front Genet 2023; 14:1186192. [PMID: 37727375 PMCID: PMC10506264 DOI: 10.3389/fgene.2023.1186192] [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: 03/14/2023] [Accepted: 08/22/2023] [Indexed: 09/21/2023] Open
Abstract
The SlADH gene plays a key role in environmental stress response. However, limited studies exist regarding the tomato SlADH gene. In this study, we identified 35 SlADH genes in tomato by genome-wide identification. Among the 12 chromosomes of tomato, SlADH gene is distributed on 10 chromosomes, among which the 7th and 10th chromosomes have no family members, while the 11th chromosome has the most members with 8 family members. Members of this gene family are characterized by long coding sequences, few amino acids, and introns that make up a large proportion of the genetic structure of most members of this family. Moreover, the molecular weight of the proteins of the family members was similar, and the basic proteins were mostly, and the overall distribution was relatively close to neutral (pI = 7). This may indicate that proteins in this family have a more conserved function. In addition, a total of four classes of cis-acting elements were detected in all 35 SlADH promoter regions, most of which were associated with biotic and abiotic stresses. The results indicate that SlADH gene had a certain response to cold stress, salt stress, ABA treatment and PEG stress. This study provides a new candidate gene for improving tomato stress resistance.
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Affiliation(s)
- Qingdong Zhu
- School of Biological Sciences, Jining Medical University, Rizhao, China
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10
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Wang R, Liu C, Lyu C, Sun J, Kang C, Ma Y, Wan X, Guo J, Shi L, Wang J, Huang L, Wang S, Guo L. The discovery and characterization of AeHGO in the branching route from shikonin biosynthesis to shikonofuran in Arnebia euchroma. FRONTIERS IN PLANT SCIENCE 2023; 14:1160571. [PMID: 37180378 PMCID: PMC10167036 DOI: 10.3389/fpls.2023.1160571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023]
Abstract
Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon and Arnebia euchroma. Phytochemical studies utilizing both L. erythrorhizon and A. euchroma cultured cells indicate the existence of a competing route branching out from the shikonin biosynthetic pathway to shikonofuran. A previous study has shown that the branch point is the transformation from (Z)-3''-hydroxy-geranylhydroquinone to an aldehyde intermediate (E)-3''-oxo-geranylhydroquinone. However, the gene encoding the oxidoreductase that catalyzes the branch reaction remains unidentified. In this study, we discovered a candidate gene belonging to the cinnamyl alcohol dehydrogenase family, AeHGO, through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines of A. euchroma. In biochemical assays, purified AeHGO protein reversibly oxidized (Z)-3''-hydroxy-geranylhydroquinone to produce (E)-3''-oxo-geranylhydroquinone followed by reversibly reducing (E)-3''-oxo-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters showed that the reduction of (E)-3''-oxo-geranylhydroquinone was stereoselective and efficient in presence of NADPH, which determined that the overall reaction proceeded from (Z)-3''-hydroxy-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone. Considering that there is a competition between the accumulation of shikonin and shikonofuran derivatives in cultured plant cells, AeHGO is supposed to play an important role in the metabolic regulation of the shikonin biosynthetic pathway. Characterization of AeHGO should help expedite the development of metabolic engineering and synthetic biology toward production of shikonin derivatives.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Luqi Huang
- *Correspondence: Luqi Huang, ; Sheng Wang, ; Lanping Guo,
| | - Sheng Wang
- *Correspondence: Luqi Huang, ; Sheng Wang, ; Lanping Guo,
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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11
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Satyaveanthan MV, Ng CL, Awang A, Lam KW, Hassan M. Isolation, purification and biochemical characterization of Conopomorpha cramerella farnesol dehydrogenase. INSECT MOLECULAR BIOLOGY 2023; 32:143-159. [PMID: 36454188 DOI: 10.1111/imb.12820] [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: 06/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
In Southeast Asia, Conopomorpha cramerella (Snellen) which is commonly known as the cocoa pod borer (CPB) moth has been identified as the most detrimental pest of Theobroma cacao L. Apart from the various side effects on human health and non-target organisms, heavily relying on synthetic pyrethroid insecticides to control CPB infestations also increases the environmental contamination risks. Thus, developing biorational insecticides that minimally affect the non-target organism and environment by targeting the insect growth regulation process is needed to manage the pest population. In insects, juvenile hormones (JH) regulate critical biological events, especially metamorphosis, development and reproduction. Since the physiological roles of JH III vary among different organisms, the biochemical properties, especially substrate specificity and analogue inhibition, may also be different. Therefore, studies on the JH III biosynthetic pathway enzymes in both plants and insects are beneficial to discover more effective analogues. Bioinformatic analysis and biochemical characterization of a NADP+ -dependent farnesol dehydrogenase, an intermediate enzyme of the JH III pathway, from C. cramerella (CcFolDH), were described in this study. In addition, the farnesol analogues that may act as a potent analogue inhibitor for CcFolDH ware determined using in vitro enzymatic study. The phylogenetic analysis indicated that CcFolDH shared a close phylogenetic relationship to the honeybee's short-chain dehydrogenase/reductase. The 27 kDa CcFolDH has an NADP(H) binding domain with a typical Rossmann fold and is likely a homotetrameric protein in the solution. The enzyme had a greater preference for substrate trans, trans-farnesol and coenzyme NADP+ . In terms of analogue inhibitor inhibition, hexahydroxyfarnesyl acetone showed the highest inhibition (the lowest Ki ) compared to other farnesol analogues. Thus, hexahydroxyfarnesyl acetone would serve as the most potent active ingredient for future biorational pesticide management for C. cramerella infestation. Based on the bioinformatic analyses and biochemical characterizations conducted in this research, we proposed that rCcFolDH differs slightly from other reported farnesol dehydrogenases in terms of molecular weight, substrate preference, coenzymes utilization and analogue inhibitors selection.
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Affiliation(s)
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Alias Awang
- Cocoa Research & Development Centre (Bagan Datuk), Malaysian Cocoa Board, Sg. Sumun, Malaysia
| | - Kok Wai Lam
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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12
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Gao W, She F, Sun Y, Han B, Wang X, Xu G. Transcriptome Analysis Reveals the Genes Related to Water-Melon Fruit Expansion under Low-Light Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:935. [PMID: 36840282 PMCID: PMC9958833 DOI: 10.3390/plants12040935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Watermelon is one of people's favorite fruits globally. Fruit size is one of the important characteristics of fruit quality. Low light can seriously affect fruit development, but there have been no reports concerning molecular mechanism analysis in watermelons involved in fruit expansion under low-light stress. To understand this mechanism, the comparative transcriptomic file of watermelon fruit flesh at four different developmental stages under different light levels was studied. The results showed that the fruit size and content of soluble sugar and amino acids at low-light stress significantly decreased compared to the control. In addition, 0-15 DAP was the rapid expansion period of watermelon fruit affected by shading. In total, 8837 differentially expressed genes (DEGs) were identified and 55 DEGs were found to play a role in the four different early fruit development stages. We also found that genes related to oxidation-reduction, secondary metabolites, carbohydrate and amino acid metabolism and transcriptional regulation played a key role in watermelon fruit expansion under low-light stress. This study provides a foundation to investigate the functions of low-light stress-responsive genes and the molecular mechanism of the effects of low-light stress on watermelon fruit expansion.
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Affiliation(s)
- Wenrui Gao
- Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Fuchun She
- Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yanjun Sun
- Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Bing Han
- Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xiansheng Wang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Nanjing Station for DUS Testing Center of New Varieties of Plants of MARA, Nanjing 210014, China
| | - Gang Xu
- Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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13
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Zhang R, Xuan L, Ni L, Yang Y, Zhang Y, Wang Z, Yin Y, Hua J. ADH Gene Cloning and Identification of Flooding-Responsive Genes in Taxodium distichum (L.) Rich. PLANTS (BASEL, SWITZERLAND) 2023; 12:678. [PMID: 36771761 PMCID: PMC9919530 DOI: 10.3390/plants12030678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/14/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
As a flooding-tolerant tree species, Taxodium distichum has been utilized in afforestation projects and proven to have important value in flooding areas. Alcohol dehydrogenase (ADH), which participates in ethanol fermentation, is essential for tolerance to the anaerobic conditions caused by flooding. In a comprehensive analysis of the ADH gene family in T. distichum, TdADHs were cloned on the basis of whole-genome sequencing, and then bioinformatic analysis, subcellular localization, and gene expression level analysis under flooding were conducted. The results show that the putative protein sequences of 15 cloned genes contained seven TdADHs and eight TdADH-like genes (one Class III ADH included) that were divided into five clades. All the sequences had an ADH_N domain, and except for TdADH-likeE2, all the other genes had an ADH_zinc_N domain. Moreover, the TdADHs in clades A, B, C, and D had a similar motif composition. Additionally, the number of TdADH amino acids ranged from 277 to 403, with an average of 370.13. Subcellular localization showed that, except for TdADH-likeD3, which was not expressed in the nucleus, the other genes were predominantly expressed in both the nucleus and cytosol. TdADH-likeC2 was significantly upregulated in all three organs (roots, stems, and leaves), and TdADHA3 was also highly upregulated under 24 h flooding treatment; the two genes might play key roles in ethanol fermentation and flooding tolerance. These findings offer a comprehensive understanding of TdADHs and could provide a foundation for the molecular breeding of T. distichum and current research on the molecular mechanisms driving flooding tolerance.
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Affiliation(s)
- Rui Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Lei Xuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Longjie Ni
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ying Yang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ya Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
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14
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Lim JM, Jung S, In JS, Park YI, Jeong WJ. Heterologous overexpression of the cyanobacterial alcohol dehydrogenase sysr1 confers cold tolerance to the oleaginous alga Nannochloropsis salina. FRONTIERS IN PLANT SCIENCE 2023; 14:1045917. [PMID: 36760652 PMCID: PMC9905847 DOI: 10.3389/fpls.2023.1045917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Temperature is an important regulator of growth in algae and other photosynthetic organisms. Temperatures above or below the optimal growth temperature could cause oxidative stress to algae through accumulation of oxidizing compounds such as reactive oxygen species (ROS). Thus, algal temperature stress tolerance could be attained by enhancing oxidative stress resistance. In plants, alcohol dehydrogenase (ADH) has been implicated in cold stress tolerance, eliciting a signal for the synthesis of antioxidant enzymes that counteract oxidative damage associated with several abiotic stresses. Little is known whether temperature stress could be alleviated by ADH in algae. Here, we generated transgenic lines of the unicellular oleaginous alga Nannochloropsis salina that heterologously expressed sysr1, which encodes ADH in the cyanobacterium Synechocystis sp. PCC 6906. To drive sysr1 expression, the heat shock protein 70 (HSP70) promoter isolated from N. salina was used, as its transcript levels were significantly increased under either cold or heat stress growth conditions. When subjected to cold stress, transgenic N. salina cells were more cold-tolerant than wild-type cells, showing less ROS production but increased activity of antioxidant enzymes such as superoxide dismutase, ascorbate peroxidase, and catalase. Thus, we suggest that reinforcement of alcohol metabolism could be a target for genetic manipulation to endow algae with cold temperature stress tolerance.
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Affiliation(s)
- Jong-Min Lim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sokyong Jung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jae-Sun In
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Won-Joong Jeong
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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15
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Langley C, Tatsis E, Hong B, Nakamura Y, Paetz C, Stevenson CEM, Basquin J, Lawson DM, Caputi L, O'Connor SE. Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism. Angew Chem Int Ed Engl 2022; 61:e202210934. [PMID: 36198083 PMCID: PMC9828224 DOI: 10.1002/anie.202210934] [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: 07/25/2022] [Indexed: 11/19/2022]
Abstract
Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.
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Affiliation(s)
- Chloe Langley
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Evangelos Tatsis
- Chinese Academy of Sciences Centre for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and Ecology300 Feng Lin RoadShanghai200032China
| | - Benke Hong
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Yoko Nakamura
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany,Research Group Biosynthesis and NMRMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Christian Paetz
- Research Group Biosynthesis and NMRMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Clare E. M. Stevenson
- Department of Biochemistry and MetabolismJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Jerome Basquin
- Department of Structural Cell BiologyMax-Planck Institute for BiochemistryAm Klopferspitz 18, Martinsried82152PlaneggGermany
| | - David M. Lawson
- Department of Biochemistry and MetabolismJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Lorenzo Caputi
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Sarah E. O'Connor
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
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16
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Transcriptomic profiling analysis to identify genes associated with PA biosynthesis and insolubilization in the late stage of fruit development in C-PCNA persimmon. Sci Rep 2022; 12:19140. [PMID: 36352175 PMCID: PMC9646812 DOI: 10.1038/s41598-022-23742-4] [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: 04/14/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
PA-enhanced content causes astringency in persimmon fruit. PCNA persimmons can lose their astringency naturally and they become edible when still on the tree, which allows for conserves of physical and financial resources. C-PCNA persimmon originates in China. Its deastringency trait primarily depends on decreased PA biosynthesis and PA insolubilization at the late stage of fruit development. Although some genes and transcription factors that may be involved in the deastringency of C-PCNA persimmon have been reported, the expression patterns of these genes during the key deastringency stage are reported less. To investigate the variation in PA contents and the expression patterns of deastringency-related genes during typical C-PCNA persimmon 'Xiaoguo-tianshi' fruit development and ripening, PA content and transcriptional profiling were carried out at five late stages from 70 to 160 DAF. The combinational analysis phenotype, PA content, and DEG enrichment revealed that 120-140 DAF and 140-160 DAF were the critical phases for PA biosynthesis reduction and PA insolubilization, respectively. The expression of PA biosynthesis-associated genes indicated that the downregulation of the ANR gene at 140-160 DAF may be associated with PA biosynthesis and is decreased by inhibiting its precursor cis-flavan-3-ols. We also found that a decrease in acetaldehyde metabolism-associated ALDH genes and an increase in ADH and PDC genes might result in C-PCNA persimmon PA insolubilization. In addition, a few MYB-bHLH-WD40 (MBW) homologous transcription factors in persimmon might play important roles in persimmon PA accumulation. Furthermore, combined coexpression network analysis and phylogenetic analysis of MBW suggested that three putative transcription factors WD40 (evm.TU.contig1.155), MYB (evm.TU.contig8910.486) and bHLH (evm.TU.contig1398.203), might connect and co-regulate both PA biosynthesis and its insolubilization in C-PCNA persimmon. The present study elucidated transcriptional insights into PA biosynthesis and insolubilization during the late development stages based on the C-PCNA D. kaki genome (unpublished). Thus, we focused on PA content variation and the expression patterns of genes involved in PA biosynthesis and insolubilization. Our work has provided additional evidence on previous knowledge and a basis for further exploration of the natural deastringency of C-PCNA persimmon.
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17
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Xu Z, Peng B, Kang F, Zhang W, Xiao M, Li J, Hong Q, Cai Y, Liu W, Yan Y, Peng J. The Roles of Drug Metabolism-Related ADH1B in Immune Regulation and Therapeutic Response of Ovarian Cancer. Front Cell Dev Biol 2022; 10:877254. [PMID: 35756990 PMCID: PMC9218672 DOI: 10.3389/fcell.2022.877254] [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: 02/16/2022] [Accepted: 04/29/2022] [Indexed: 12/19/2022] Open
Abstract
Background: The different pharmacological effects of drugs in different people can be explained by the polymorphisms of drug metabolism-related genes. Emerging studies have realized the importance of drug metabolism-related genes in the treatment and prognosis of cancers, including ovarian cancer (OV). In this study, using comprehensive bioinformatics and western blot, we identified that the drug metabolism-related gene, ADH1B, was significantly down-regulated in OV cells and tissues. The patients with a high level of ADH1B presented a good prognosis. We also found a negative correlation between ADH1B expression and the activity of chemotherapeutic agents, such as cyclophosphamide. In addition, positive correlations were observed between ADH1B expression and multiple immune checkpoints, including LAG3 and HAVCR2. The immune infiltration analysis further indicated that aberrantly expressed ADH1B might have important roles in regulating the infiltration of macrophages and neutrophils in OV tissues. Then, the co-expression analysis was conducted and the top three enriched KEGG pathways were spliceosome, RNA transport, and DNA replication. In conclusion, the drug metabolism-related gene ADH1B and its interactive network play an essential role in the immune regulation and therapeutic response and maybe identified as promising therapeutic targets for OV patients.
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Affiliation(s)
- Zhijie Xu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Fanhua Kang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Wenqin Zhang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Muzhang Xiao
- Department of Burn and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jianbo Li
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Qianhui Hong
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Liu
- Department of Orthopedic Surgery, The Second Hospital University of South China, Hengyang, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Jinwu Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Changde Hospital, Changde, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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18
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Liu S, Guo L, Zhou Q, Jiang Z, Jin L, Zhu J, Xie H, Wei C. Identification and Functional Analysis of Two Alcohol Dehydrogenase Genes Involved in Catalyzing the Reduction of ( Z)-3-Hexenal into ( Z)-3-Hexenol in Tea Plants ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1830-1839. [PMID: 35112571 DOI: 10.1021/acs.jafc.1c06984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Alcohol dehydrogenase (ADH) is a vital enzyme in the biosynthesis pathway of six-carbon volatiles in plants. However, little is known about its functions in tea plants. Here, we identified two ADH genes (CsADH1 and CsADH2). An in vitro protein expression assay showed that both CsADH1 and CsADH2 proteins can catalyze the reduction of (Z)-3-hexenal into (Z)-3-hexenol. Subcellular localization revealed that both CsADH1 and CsADH2 proteins were predominantly localized in the nucleus and cytosol. CsADH1 had high transcripts in young stems in autumn, while CsADH2 showed extremely high expression levels in stems and roots. The expression of CsADH2 was mainly downregulated under ABA treatment, while CsADH1 and CsADH2 transcripts were significantly lower under MeJA treatment at 12 and 24 h. Under cold treatment, CsADH1 transcripts first decreased and then increased, while CsADH2 demonstrated an almost opposite expression pattern. Notably, CsADH2 was significantly upregulated under simulated Ectropis obliqua invasion. Gene suppression by antisense oligonucleotides (AsODNs) demonstrated that AsODN_ADH2 treatment significantly reduced CsADH2 transcripts and the abundance of (Z)-3-hexenol products. The results indicate that the two CsADH genes may play an important role in response to (a)biotic stresses and in the process of (Z)-3-hexenol biosynthesis.
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Affiliation(s)
- Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Lingxiao Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Qiying Zhou
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang 464000, China
| | | | - Ling Jin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jiaxin Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Hui Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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19
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Proteomic Studies of Roots in Hypoxia-Sensitive and -Tolerant Tomato Accessions Reveal Candidate Proteins Associated with Stress Priming. Cells 2022; 11:cells11030500. [PMID: 35159309 PMCID: PMC8834170 DOI: 10.3390/cells11030500] [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: 12/03/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 01/08/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) is a vegetable frequently exposed to hypoxia stress induced either by being submerged, flooded or provided with limited oxygen in hydroponic cultivation systems. The purpose of the study was to establish the metabolic mechanisms responsible for overcoming hypoxia in two tomato accessions with different tolerance to this stress, selected based on morphological and physiological parameters. For this purpose, 3-week-old plants (plants at the juvenile stage) of waterlogging-tolerant (WL-T), i.e., POL 7/15, and waterlogging-sensitive (WL-S), i.e., PZ 215, accessions were exposed to hypoxia stress (waterlogging) for 7 days, then the plants were allowed to recover for 14 days, after which another 7 days of hypoxia treatment was applied. Root samples were collected at the end of each time-point and 2D-DIGE with MALDI TOF/TOF, and expression analyses of gene and protein-encoded alcohol dehydrogenase (ADH2) and immunolabelling of ADH were conducted. After collating the obtained results, the different responses to hypoxia stress in the selected tomato accessions were observed. Both the WL-S and WL-T tomato accessions revealed a high amount of ADH2, which indicates an intensive alcohol fermentation pathway during the first exposure to hypoxia. In comparison to the tolerant one, the expression of the adh2 gene was about two times higher for the sensitive tomato. Immunohistochemical analysis confirmed the presence of ADH in the parenchyma cells of the cortex and vascular tissue. During the second hypoxia stress, the sensitive accession showed a decreased accumulation of ADH protein and similar expression of the adh2 gene in comparison to the tolerant accession. Additionally, the proteome showed a greater protein abundance of glyceraldehyde-3-phosphate dehydrogenase in primed WL-S tomato. This could suggest that the sensitive tomato overcomes the oxygen limitation and adapts by reducing alcohol fermentation, which is toxic to plants because of the production of ethanol, and by enhancing glycolysis. Proteins detected in abundance in the sensitive accession are proposed as crucial factors for hypoxia stress priming and their function in hypoxia tolerance is discussed.
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20
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Li H, Ghoto K, Wei MY, Gao CH, Liu YL, Ma DN, Zheng HL. Unraveling hydrogen sulfide-promoted lateral root development and growth in mangrove plant Kandelia obovata: insight into regulatory mechanism by TMT-based quantitative proteomic approaches. TREE PHYSIOLOGY 2021; 41:1749-1766. [PMID: 33580961 DOI: 10.1093/treephys/tpab025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 01/31/2021] [Indexed: 05/26/2023]
Abstract
Mangroves are the main intertidal ecosystems with varieties of root types along the tropical and subtropical coastlines around the world. The typical characteristics of mangrove habitats, including the abundant organic matter and nutrients, as well as the strong reductive environment, are favor for the production of hydrogen sulfide (H2S). H2S, as a pivotal signaling molecule, has been evidenced in a wide variety of plant physiological and developmental processes. However, whether H2S functions in the mangrove root system establishment is not clear yet. Here, we reported the possible role of H2S in regulation of Kandelia obovata root development and growth by tandem mass tag (TMT)-based quantitative proteomic approaches coupled with bioinformatic methods. The results showed that H2S could induce the root morphogenesis of K. obovata in a dose-dependent manner. The proteomic results successfully identified 8075 proteins, and 697 were determined as differentially expressed proteins. Based on the functional enrichment analysis, we demonstrated that H2S could promote the lateral root development and growth by predominantly regulating the proteins associated with carbohydrate metabolism, sulfur metabolism, glutathione metabolism and other antioxidant associated proteins. In addition, transcriptional regulation and brassinosteroid signal transduction associated proteins also act as important roles in lateral root development. The protein-protein interaction analysis further unravels a complicated regulation network of carbohydrate metabolism, cellular redox homeostasis, protein metabolism, secondary metabolism, and amino acid metabolism in H2S-promoted root development and growth of K. obovata. Overall, our results revealed that H2S could contribute to the morphogenesis of the unique root system of mangrove plant K. obovata, and play a positive role in the adaption of mangrove plants to intertidal habitats.
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Affiliation(s)
- Huan Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
| | - Kabir Ghoto
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
| | - Ming-Yue Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
| | - Chang-Hao Gao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
| | - Yi-Ling Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
| | - Dong-Na Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, P.R. China
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21
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Jiang Z, Xu C, Wang L, Hong K, Ma C, Lv C. Potential enzymes involved in beer monoterpenoids transformation: structures, functions and challenges. Crit Rev Food Sci Nutr 2021; 63:2082-2092. [PMID: 34459289 DOI: 10.1080/10408398.2021.1970510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Monoterpenes are important flavor and fragrance compounds in food. In beer, the monoterpenes mainly come from hops added during boiling process. Biotransformations of monoterpene which occurred during fermentation conferred beer with various kinds of aroma profiles, which can be mainly attributed to the contribution of enzymes in yeast. However, there are few reports on the identification and characterization of these enzymes in yeast. Illustrating the structure and functions of key enzymes related to transformations will broaden their potential applications in beer or other foodstuffs. Monoterpenoids including terpene hydrocarbons (limonene, myrcene, and pinene) and terpene alcohol (linalool, geraniol, nerol, and citronellol) gave the beer flower-like or fruit-like aroma. The biotransformation of monoterpenes and monoterpene alcohols in bacteria and yeast, and potential enzymes related to the transformation of them are reviewed here. Enzymes primarily are dehydrogenases including linalool dehydrogenase/isomerase, geraniol/geranial dehydrogenase, nerol dehydrogenase and citronellol dehydrogenase. Most of them are substrate-specific or substrate-specific after modifications by biotechnology methods, and part of them have been expressed in E. coli, while the purification and catalytic rate is very low. Efforts should be made to acquire abundant enzymes, and to fabricate enzyme-expressing yeast, which can be further applied in beer fermentation system.highlightsMonoterpenoids contributed to the flavor of food, especially beer.Transformation of monoterpenoids occurred during fermentation.Various kinds of enzymes are involved in the transformation of monoterpenoids in bacteria, yeast, etc.Crystal structures of these enzymes have been partially resolved.Few enzymes are further applied in food system to obtain abundant flavor.
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Affiliation(s)
- Zhenghui Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Chen Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Limin Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Kai Hong
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Changwei Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
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Shen C, Yuan J, Ou X, Ren X, Li X. Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat ( Triticum aestivum). PeerJ 2021; 9:e11861. [PMID: 34386306 PMCID: PMC8312495 DOI: 10.7717/peerj.11861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear. Methods A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication. Results The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingqi Ou
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiujuan Ren
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xinhua Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
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23
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Hayashi S, Kuramata M, Abe T, Yamaguchi N, Takagi H, Tanikawa H, Iino M, Sugimoto K, Ishikawa S. Deficiency in alcohol dehydrogenase 2 reduces arsenic in rice grains by suppressing silicate transporters. PLANT PHYSIOLOGY 2021; 186:611-623. [PMID: 33620496 PMCID: PMC8154085 DOI: 10.1093/plphys/kiab086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 05/14/2023]
Abstract
Paddy fields are anaerobic and facilitate arsenite (As(III)) elution from the soil. Paddy-field rice accumulates arsenic (As) in its grains because silicate transporters actively assimilate As(III) during the reproductive stage. Reducing the As level in rice grains is an important challenge for agriculture. Using a forward genetic approach, we isolated a rice (Oryza sativa) mutant, low arsenic line 3 (las3), whose As levels were decreased in aerial tissues, including grains. The low-As phenotype was not observed in young plants before heading (emergence of the panicle). Genetic analyses revealed that a deficiency in alcohol dehydrogenase (ADH) 2 by mutation is responsible for the phenotype. Among the three rice ADH paralogues, ADH2 was the most efficiently produced in root tissue under anaerobic conditions. In wild-type (WT), silicon and As concentrations in aerial tissues increased with growth. However, the increase was suppressed in las3 during the reproductive stage. Accordingly, the gene expression of two silicate transporters, Lsi1 and Lsi2, was increased in WT around the time of heading, whereas the increase was suppressed in las3. These results indicate that the low-As phenotype in las3 is due to silicate transporter suppression. Measurement of intracellular pH by 31P-nuclear magnetic resonance revealed intracellular acidification of las3 roots under hypoxia, suggesting that silicate transporter suppression in las3 might arise from an intracellular pH decrease, which is known to be facilitated by a deficiency in ADH activity under anaerobic conditions. This study provides valuable insight into reducing As levels in rice grains.
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Affiliation(s)
- Shimpei Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Tadashi Abe
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Noriko Yamaguchi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Hiroki Takagi
- Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Manaka Iino
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
- Author for communication:
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24
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Xuan L, Hua J, Zhang F, Wang Z, Pei X, Yang Y, Yin Y, Creech DL. Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium hybrid 'Zhongshanshan 406'. Genes (Basel) 2021; 12:genes12020225. [PMID: 33557242 PMCID: PMC7913975 DOI: 10.3390/genes12020225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 01/23/2023] Open
Abstract
The Taxodium hybrid 'Zhongshanshan 406' (T. hybrid 'Zhongshanshan 406') [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized-ThADH1 and ThADH4 (GenBank ID: AWL83216 and AWL83217-basing on the transcriptome data of T. hybrid 'Zhongshanshan 406' grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid 'Zhongshanshan 406'.
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Affiliation(s)
- Lei Xuan
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
| | - Jianfeng Hua
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
- Correspondence: ; Tel.: +86-25-8434-7069
| | - Fan Zhang
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
| | - Zhiquan Wang
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
| | - Xiaoxiao Pei
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
| | - Ying Yang
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
| | - Yunlong Yin
- Jiangsu Province Engineering Research Center of Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing 210037, China; (L.X.); (F.Z.); (Z.W.); (X.P.); (Y.Y.); (Y.Y.)
| | - David L. Creech
- Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA;
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Das RR, Pradhan S, Parida A. De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense. Sci Rep 2020; 10:21251. [PMID: 33277539 PMCID: PMC7718891 DOI: 10.1038/s41598-020-78118-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Screening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.
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Affiliation(s)
- Rasmita Rani Das
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India
| | - Seema Pradhan
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India.
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26
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Ma L, Wang Q, Mu J, Fu A, Wen C, Zhao X, Gao L, Li J, Shi K, Wang Y, Zhang X, Zhang X, Fei Z, Grierson D, Zuo J. The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. HORTICULTURE RESEARCH 2020; 7:199. [PMID: 33328440 PMCID: PMC7704671 DOI: 10.1038/s41438-020-00423-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 05/03/2023]
Abstract
Snake gourd (Trichosanthes anguina L.), which belongs to the Cucurbitaceae family, is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world. Although progress has been made in its genetic improvement, the organization, composition, and evolution of the snake gourd genome remain largely unknown. Here, we report a high-quality genome assembly for snake gourd, comprising 202 contigs, with a total size of 919.8 Mb and an N50 size of 20.1 Mb. These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date. The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0% of the genome consists of repetitive sequences. Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor ~33-47 million years ago. The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species. In addition, fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jianlou Mu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Yunxiang Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xuechuan Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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27
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De la Rosa C, Lozano L, Castillo-Ramírez S, Covarrubias AA, Reyes JL. Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes. Genome Biol Evol 2020; 12:2355-2369. [PMID: 33045056 PMCID: PMC7846098 DOI: 10.1093/gbe/evaa205] [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] [Accepted: 09/29/2020] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs are important regulators of gene expression in eukaryotes. Previously, we reported that in Phaseolus vulgaris, the precursor for miR2119 is located in the same gene as miR398a, conceiving a dicistronic MIR gene. Both miRNA precursors are transcribed and processed from a single transcript resulting in two mature microRNAs that regulate the mRNAs encoding ALCOHOL DEHYDROGENASE 1 (ADH1) and COPPER-ZINC SUPEROXIDE DISMUTASE 1 (CSD1). Genes for miR398 are distributed throughout the spermatophytes; however, miR2119 is only found in Leguminosae species, indicating its recent emergence. Here, we used public databases to explore the presence of the miR2119 sequence in several plant species. We found that miR2119 is present only in specific clades within the Papilionoideae subfamily, including important crops used for human consumption and forage. Within this subfamily, MIR2119 and MIR398a are found together as a single gene in the genomes of the Millettioids and Hologalegina. In contrast, in the Dalbergioids MIR2119 is located in a different locus from MIR398a, suggesting this as the ancestral genomic organization. To our knowledge, this is a unique example where two separate MIRNA genes have merged to generate a single polycistronic gene. Phylogenetic analysis of ADH1 gene sequences in the Papilionoideae subfamily revealed duplication events resulting in up to four ADH1 genes in certain species. Notably, the presence of MIR2119 correlates with the conservation of target sites in particular ADH1 genes in each clade. Our results suggest that post-transcriptional regulation of ADH1 genes by miR2119 has contributed to shaping the expansion and divergence of this gene family in the Papilionoideae. Future experimental work on ADH1 regulation by miR2119 in more legume species will help to further understand the evolutionary history of the ADH1 gene family and the relevance of miRNA regulation in this process.
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Affiliation(s)
- Carlos De la Rosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis D. Colosio S/N entre Reforma y Sahuaripa, Col Centro, Hermosillo, Mexico
| | - Luis Lozano
- Luis Lozano Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, México.,Santiago Castillo Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Luis Lozano Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, México.,Santiago Castillo Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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28
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The Anaerobic Product Ethanol Promotes Autophagy-Dependent Submergence Tolerance in Arabidopsis. Int J Mol Sci 2020; 21:ijms21197361. [PMID: 33028029 PMCID: PMC7583018 DOI: 10.3390/ijms21197361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
In response to hypoxia under submergence, plants switch from aerobic respiration to anaerobic fermentation, which leads to the accumulation of the end product, ethanol. We previously reported that Arabidopsis thaliana autophagy-deficient mutants show increased sensitivity to ethanol treatment, indicating that ethanol is likely involved in regulating the autophagy-mediated hypoxia response. Here, using a transcriptomic analysis, we identified 3909 genes in Arabidopsis seedlings that were differentially expressed in response to ethanol treatment, including 2487 upregulated and 1422 downregulated genes. Ethanol treatment significantly upregulated genes involved in autophagy and the detoxification of reactive oxygen species. Using transgenic lines expressing AUTOPHAGY-RELATED PROTEIN 8e fused to green fluorescent protein (GFP-ATG8e), we confirmed that exogenous ethanol treatment promotes autophagosome formation in vivo. Phenotypic analysis showed that deletions in the alcohol dehydrogenase gene in adh1 mutants result in attenuated submergence tolerance, decreased accumulation of ATG proteins, and diminished submergence-induced autophagosome formation. Compared to the submergence-tolerant Arabidopsis accession Columbia (Col-0), the submergence-intolerant accession Landsberg erecta (Ler) displayed hypersensitivity to ethanol treatment; we linked these phenotypes to differences in the functions of ADH1 and the autophagy machinery between these accessions. Thus, ethanol promotes autophagy-mediated submergence tolerance in Arabidopsis.
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29
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Su W, Ren Y, Wang D, Su Y, Feng J, Zhang C, Tang H, Xu L, Muhammad K, Que Y. The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation. BMC Genomics 2020; 21:521. [PMID: 32727370 PMCID: PMC7392720 DOI: 10.1186/s12864-020-06929-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenases (ADHs) in plants are encoded by a multigene family. ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in sugarcane is still unclear. RESULTS In the present study, 151 ADH genes from 17 species including 32 ADH genes in Saccharum spontaneum and 6 ADH genes in modern sugarcane cultivar R570 were identified. Phylogenetic analysis demonstrated two groups of ADH genes and suggested that these genes underwent duplication during angiosperm evolution. Whole-genome duplication (WGD)/segmental and dispersed duplications played critical roles in the expansion of ADH family in S. spontaneum and R570, respectively. ScADH3 was cloned and preferentially expressed in response to cold stress. ScADH3 conferred improved cold tolerance in E. coli cells. Ectopic expression showed that ScADH3 can also enhance cold tolerance in transgenic tobacco. The accumulation of reactive oxygen species (ROS) in leaves of transgenic tobacco was significantly lower than in wild-type tobacco. The transcript levels of ROS-related genes in transgenic tobacco increased significantly. ScADH3 seems to affect cold tolerance by regulating the ROS-related genes to maintain the ROS homeostasis. CONCLUSIONS This study depicted the size and composition of the ADH gene family in 17 species, and investigated their evolution pattern. Comparative genomics analysis among the ADH gene families of S. bicolor, R570 and S. spontaneum revealed their close evolutionary relationship. Functional analysis suggested that ScADH3, which maintained the steady state of ROS by regulating ROS-related genes, was related to cold tolerance. These findings will facilitate research on evolutionary and functional aspects of the ADH genes in sugarcane, especially for the understanding of ScADH3 under cold stress.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingfang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hanchen Tang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Khushi Muhammad
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Zeng W, Qiao X, Li Q, Liu C, Wu J, Yin H, Zhang S. Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species. Genomics 2020; 112:3484-3496. [PMID: 32585175 DOI: 10.1016/j.ygeno.2020.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 01/26/2023]
Abstract
Alcohol dehydrogenase (ADH) is essential to the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Rosaceae fruit species. In this study, 464 ADH genes were identified in eight Rosaceae fruit species, 68 of the genes were from pear and which were classified into four subgroups. Frequent single gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those derived from other types of duplication. RNA-Seq and qRT-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds detected during fruit development.
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Affiliation(s)
- Weiwei Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chunxin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hao Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
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31
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Zhou Z, Wu Q, Yao Z, Deng H, Liu B, Yue C, Deng T, Lai Z, Sun Y. Dynamics of ADH and related genes responsible for the transformation of C 6-aldehydes to C 6-alcohols during the postharvest process of oolong tea. Food Sci Nutr 2020; 8:104-113. [PMID: 31993137 PMCID: PMC6977495 DOI: 10.1002/fsn3.1272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 01/15/2023] Open
Abstract
Aroma is an important index of tea quality. The volatile C6-compounds formed from linoleic and linolenic acids in tea leaf lipids are essential components of tea. C6-compounds are formed and transformed during the postharvest process of tea leaves. However, the metabolic flux of these C6-compounds, the activities of related enzymes, and the transcription of related genes during the postharvest process of oolong tea remain unclear. In this study, the chemical profiles of C6-aldehydes and C6-alcohols, the pattern of ADH enzyme activity, and the level of CsADH gene expression during the postharvest process of oolong tea were investigated. We found that the turnover process had a positive effect on the accumulation of C6-alcohols and simultaneously induced ADH activity, especially during the withering stage. The expression of CsADH peaked during the turnover stage. The relative expression level of CSA019598 typically increased during the postharvest process. Correlation analysis demonstrated that CSA019598 expression increased as ADH activity increased. This finding suggests that CSA019598 may play a prominent role in regulating ADH. These results advance our understanding of C6-compound formation during the postharvest process of oolong tea. We aim to evaluate how green leaf volatiles affect the enzymatic formation and genetic transcription of aromatic compounds in oolong tea in future studies.
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Affiliation(s)
- Zi‐Wei Zhou
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
- Institute of Horticultural BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qing‐Yang Wu
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
- Institute of Horticultural BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhi‐Ling Yao
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Hui‐Li Deng
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
- Institute of Horticultural BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Bin‐Bin Liu
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
- Institute of Horticultural BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chuan Yue
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Ting‐Ting Deng
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhong‐Xiong Lai
- Institute of Horticultural BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yun Sun
- Key Laboratory of Tea Science in Fujian ProvinceCollege of Horticulture Fujian Agriculture and Forestry UniversityFuzhouChina
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Guan C, Wang M, Zhang Y, Ruan X, Zhang Q, Luo Z, Yang Y. DkWRKY interacts with pyruvate kinase gene DkPK1 and promotes natural deastringency in C-PCNA persimmon. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110285. [PMID: 31779905 DOI: 10.1016/j.plantsci.2019.110285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/04/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
PAs, also known as condensed tannins, cause the astringency sensation in the persimmon fruit. The astringency of Chinese pollination-constant non-astringent (C-PCNA) persimmon (Diospyros kaki Thunb.) can be naturally removed on the tree, but the regulatory mechanisms of deastringency remain to be elucidated. In our previous research, DkPK1 was shown to be involved in the natural loss of astringency of C-PCNA persimmon fruit. In the present study, yeast one-hybrid (Y1H) library screening using the DkPK1 promoter as baits identified two DkWRKY transcription factor genes (DkWRKY3 and -15). The transcript levels of both DkWRKY3 and -15 exhibited a positive correlation with the decrease in soluble proanthocyanidin (PA) content during the last developmental stage in C-PCNA persimmon. Multiple sequence analysis and subcellular localization confirmed that DkWRKY3 and -15 belonging to the group II and I families, respectively, were both located in the nucleus. Dual-luciferase and Y1H assays demonstrated that DkWRKY3 and -15 can transactivate the DkPK1 promoters. The combination of DkWRKY3 and -15 most likely produced an additive activation effect compared to a single activator on DkPK1, although the two transcriptional activators were not capable of interacting. Notably, DkWRKY3 and -15 showed ubiquitous expression in various organs and abundant upregulation in seeds. Furthermore, transient overexpression of both DkWRKY3 and -15 in persimmon leaves led to a significant decrease in the content of soluble PAs but a significant increase in the expression levels of the acetaldehyde metabolism-related DkPK, DkPDC and DkADH genes. Thus, we suggest that DkWRKY3 and -15 are the upstream regulators of DkPK1 and positively regulate the natural deastringency in C-PCNA persimmon.
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Affiliation(s)
- Changfei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mengke Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yangfan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofeng Ruan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qinglin Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yong Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
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Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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Almeida FA, Vale EM, Reis RS, Santa-Catarina C, Silveira V. LED lamps enhance somatic embryo maturation in association with the differential accumulation of proteins in the Carica papaya L. 'Golden' embryogenic callus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:109-118. [PMID: 31491701 DOI: 10.1016/j.plaphy.2019.08.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
The use of light-emitting diode (LED) lamps has been shown to be a promising approach for improving somatic embryo maturation during somatic embryogenesis. The aim of this work was to study the influence of the light source on somatic embryo differentiation and its relationship with the differential abundance of proteins in the Carica papaya L. 'Golden' embryogenic callus at 14 days of maturation. The white plus medium-blue (WmB) LED and fluorescent lamp treatments produced an average of 82.4 and 47.6 cotyledonary somatic embryos per callus, respectively. A shotgun proteomics analysis revealed 28 upaccumulated and 7 downaccumulated proteins. The proteins upaccumulated in the embryogenic callus matured under the WmB LED lamp compared with that matured under the fluorescent lamp included indole-3-acetic acid-amido synthetase (GH3) and actin-depolymerizing factor 2 (ADF2), which are involved in the regulation of auxin levels by auxin conjugation and transport. Additionally, proteins related to energy production (aconitate, ADH1, GAPCp, PKp and TPI), cell wall remodeling (PG and GLPs), and intracellular trafficking (NUP50A, IST1, small GTPases and H+-PPase) showed significantly higher abundance in the embryogenic callus incubated under the WmB LED lamp than in that incubated under the fluorescent lamp. The results showed that the WmB LED lamp improved somatic embryo maturation in association with the differential accumulation of proteins in the C. papaya 'Golden' embryogenic callus.
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Affiliation(s)
- Felipe Astolpho Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ, 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ, 28013-602, Brazil
| | - Ellen Moura Vale
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ, 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ, 28013-602, Brazil
| | - Ricardo Souza Reis
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ, 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ, 28013-602, Brazil
| | | | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ, 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ, 28013-602, Brazil.
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35
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Cheng L, Zhang S, Yang L, Wang Y, Yu B, Zhang F. Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro. PLANTA 2019; 250:199-217. [PMID: 30976909 DOI: 10.1007/s00425-019-03163-w] [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: 10/17/2018] [Accepted: 04/05/2019] [Indexed: 05/05/2023]
Abstract
The present study is the first to integrate physiological and proteomic data providing information on Fe, Mn and Zn deficiency-responsive mechanisms of potato plants in vitro. Micronutrient deficiency is an important limiting factor for potato production that causes substantial tuber yield and quality losses. To under the underlying molecular mechanisms of potato in response to Fe, Mn and Zn deficiency, a comparative proteomic approach was applied. Leaf proteome change of in vitro-propagated potato plantlets subjected to a range of Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA), Mn-deficiency treatments (1 and 0 μM MnCl2·4H2O) and Zn-deficiency treatment (0 μM ZnCl2) using two-dimensional gel electrophoresis was analyzed. Quantitative image analysis showed a total of 146, 55 and 42 protein spots under Fe, Mn and Zn deficiency with their abundance significantly altered (P < 0.05) more than twofold, respectively. By MALDI-TOF/TOF MS analyses, the differentially abundant proteins were found mainly involved in bioenergy and metabolism, photosynthesis, defence, redox homeostasis and protein biosynthesis/degradation under the metal deficiencies. Signaling, transport, cellular structure and transcription-related proteins were also identified. The hierarchical clustering results revealed that these proteins were involved in a dynamic network in response to Fe, Mn and Zn deficiency. All these metal deficiencies caused cellular metabolic remodeling to improve metal acquisition and distribution in potato plants. The reduced photosynthetic efficiency occurred under each metal deficiency, yet Fe-deficient plants showed a more severe damage of photosynthesis. More defence mechanisms were induced by Fe deficiency than Mn and Zn deficiency, and the antioxidant systems showed different responses to each metal deficiency. Reprogramming of protein biosynthesis/degradation and assembly was more strongly required for acclimation to Fe deficiency. The signaling cascades involving auxin and NDPKs might also play roles in micronutrient stress signaling and pinpoint interesting candidates for future studies. Our results first provide an insight into the complex functional and regulatory networks in potato plants under Fe, Mn and Zn deficiency.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shaomei Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lili Yang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Bin Yu
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China.
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36
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Song Y, Liu L, Ma X. CbADH1 improves plant cold tolerance. PLANT SIGNALING & BEHAVIOR 2019; 14:1612680. [PMID: 31056000 PMCID: PMC6620001 DOI: 10.1080/15592324.2019.1612680] [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: 03/07/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 05/21/2023]
Abstract
ADH1 (alcohol dehydrogenase 1) was involved in plant growth and development and responded to various stresses. We published a cold-induced alcohol dehydrogenase 1 gene from C. bungeana, CbADH1, which exists 43 unique amino acids. Here, we confirmed that overexpression of CbADH1 in Arabidopsis and tobacco significantly improved cold shock tolerance through electrolyte leakage, semi-lethal temperature, phenotypic and survival analysis. These results indicate that CbADH1 is the candidate gene to improve the ability of plant freezing resistance, and it has great application value.
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Affiliation(s)
- Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lijun Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiang Ma
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
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37
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Bui LT, Novi G, Lombardi L, Iannuzzi C, Rossi J, Santaniello A, Mensuali A, Corbineau F, Giuntoli B, Perata P, Zaffagnini M, Licausi F. Conservation of ethanol fermentation and its regulation in land plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1815-1827. [PMID: 30861072 PMCID: PMC6436157 DOI: 10.1093/jxb/erz052] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/24/2019] [Indexed: 05/18/2023]
Abstract
Ethanol fermentation is considered as one of the main metabolic adaptations to ensure energy production in higher plants under anaerobic conditions. Following this pathway, pyruvate is decarboxylated and reduced to ethanol with the concomitant oxidation of NADH to NAD+. Despite its acknowledgement as an essential metabolic strategy, the conservation of this pathway and its regulation throughout plant evolution have not been assessed so far. To address this question, we compared ethanol fermentation in species representing subsequent steps in plant evolution and related it to the structural features and transcriptional regulation of the two enzymes involved: pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH). We observed that, despite the conserved ability to produce ethanol upon hypoxia in distant phyla, transcriptional regulation of the enzymes involved is not conserved in ancient plant lineages, whose ADH homologues do not share structural features distinctive for acetaldehyde/ethanol-processing enzymes. Moreover, Arabidopsis mutants devoid of ADH expression exhibited enhanced PDC activity and retained substantial ethanol production under hypoxic conditions. Therefore, we concluded that, whereas ethanol production is a highly conserved adaptation to low oxygen, its catalysis and regulation in land plants probably involve components that will be identified in the future.
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Affiliation(s)
- Liem T Bui
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Giacomo Novi
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | | | - Cristina Iannuzzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Anna Mensuali
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Françoise Corbineau
- UMR 7622 CNRS-UPMC, Biologie du développement, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Beatrice Giuntoli
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- Biology Department, University of Pisa, Pisa, Italy
| | | | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Francesco Licausi
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- Biology Department, University of Pisa, Pisa, Italy
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38
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Dumont S, Rivoal J. Consequences of Oxidative Stress on Plant Glycolytic and Respiratory Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:166. [PMID: 30833954 PMCID: PMC6387960 DOI: 10.3389/fpls.2019.00166] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/31/2019] [Indexed: 05/03/2023]
Abstract
Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are present at low and controlled levels under normal conditions. These reactive molecules can increase to high levels under various biotic and abiotic conditions, resulting in perturbation of the cellular redox state that can ultimately lead to oxidative or nitrosative stress. In this review, we analyze the various effects that result from alterations of redox homeostasis on plant glycolytic pathway and tricarboxylic acid (TCA) cycle. Most documented modifications caused by ROS or RNS are due to the presence of redox-sensitive cysteine thiol groups in proteins. Redox modifications include Cys oxidation, disulfide bond formation, S-glutathionylation, S-nitrosylation, and S-sulfhydration. A growing number of proteomic surveys and biochemical studies document the occurrence of ROS- or RNS-mediated modification in enzymes of glycolysis and the TCA cycle. In a few cases, these modifications have been shown to affect enzyme activity, suggesting an operational regulatory mechanism in vivo. Further changes induced by oxidative stress conditions include the proposed redox-dependent modifications in the subcellular distribution of a putative redox sensor, NAD-glyceraldehyde-3P dehydrogenase and the micro-compartmentation of cytosolic glycolytic enzymes. Data from the literature indicate that oxidative stress may induce complex changes in metabolite pools in central carbon metabolism. This information is discussed in the context of our understanding of plant metabolic response to oxidative stress.
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Dumont S, Bykova NV, Khaou A, Besserour Y, Dorval M, Rivoal J. Arabidopsis thaliana alcohol dehydrogenase is differently affected by several redox modifications. PLoS One 2018; 13:e0204530. [PMID: 30252897 PMCID: PMC6155552 DOI: 10.1371/journal.pone.0204530] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
In plant cells, many stresses, including low oxygen availability, result in a higher production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). These molecules can lead to redox-dependent post-translational modification of proteins Cys residues. Here, we studied the effect of different redox modifications on alcohol dehydrogenase (ADH) from Arabidopsis thaliana. ADH catalyzes the last step of the ethanol fermentation pathway used by plants to cope with energy deficiency during hypoxic stress. Arabidopsis suspension cell cultures showed decreased ADH activity upon exposure to H2O2, but not to the thiol oxidizing agent diamide. We purified recombinant ADH and observed a significant decrease in the enzyme activity by treatments with H2O2 and diethylamine NONOate (DEA/NO). Treatments leading to the formation of a disulfide bond between ADH and glutathione (protein S-glutathionylation) had no negative effect on the enzyme activity. LC-MS/MS analysis showed that Cys47 and Cys243 could make a stable disulfide bond with glutathione, suggesting redox sensitivity of these residues. Mutation of ADH Cys47 to Ser caused an almost complete loss of the enzyme activity while the Cys243 to Ser mutant had increased specific activity. Incubation of ADH with NAD+ or NADH prevented inhibition of the enzyme by H2O2 or DEA/NO. These results suggest that binding of ADH with its cofactors may limit availability of Cys residues to redox modifications. Our study demonstrates that ADH from A. thaliana is subject to different redox modifications. Implications of ADH sensitivity to ROS and RNS during hypoxic stress conditions are discussed.
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Affiliation(s)
- Sébastien Dumont
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Natalia V. Bykova
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Alexia Khaou
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Yasmine Besserour
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Maude Dorval
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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40
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Tan CS, Hassan M, Mohamed Hussein ZA, Ismail I, Ho KL, Ng CL, Zainal Z. Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:359-368. [PMID: 29304481 DOI: 10.1016/j.plaphy.2017.12.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/23/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme that belongs to MDR (medium-chain dehydrogenases/reductases) superfamily that catalyses the first oxidative step of geraniol degradation pathway in citral biosynthesis. Kinetic analysis revealed that rPmNeDH has a high specificity for allylic primary alcohols with backbone ≤10 carbons. rPmNeDH has ∼3 fold higher affinity towards nerol (cis-3,7-dimethyl-2,6-octadien-1-ol) than its trans-isomer, geraniol. To our knowledge, this is the first alcohol dehydrogenase with higher preference towards nerol, suggesting that nerol can be effective substrate for citral biosynthesis in P. minor. The rPmNeDH crystal structure (1.54 Å) showed high similarity with enzyme structures from MDR superfamily. Structure guided mutation was conducted to describe the relationships between substrate specificity and residue substitutions in the active site. Kinetics analyses of wild-type rPmNeDH and several active site mutants demonstrated that the substrate specificity of rPmNeDH can be altered by changing any selected active site residues (Asp280, Leu294 and Ala303). Interestingly, the L294F, A303F and A303G mutants were able to revamp the substrate preference towards geraniol. Furthermore, mutant that exhibited a broader substrate range was also obtained. This study demonstrates that P. minor may have evolved to contain enzyme that optimally recognise cis-configured nerol as substrate. rPmNeDH structure provides new insights into the substrate specificity and active site plasticity in MDR superfamily.
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Affiliation(s)
- Cheng Seng Tan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Zeti Azura Mohamed Hussein
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
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Käsbauer CL, Pathuri IP, Hensel G, Kumlehn J, Hückelhoven R, Proels RK. Barley ADH-1 modulates susceptibility to Bgh and is involved in chitin-induced systemic resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:281-287. [PMID: 29275209 DOI: 10.1016/j.plaphy.2017.12.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
The plant primary energy metabolism is profoundly reorganized under biotic stress conditions and there is increasing evidence for a role of the fermentative pathway in biotic interactions. Previously we showed via transient gene silencing or overexpression a function of barley alcohol dehydrogenase 1 (HvADH-1) in the interaction of barley with the parasitic fungus Blumeria graminis f.sp. hordei (Bgh). Here we extend our studies on stable transgenic barley events over- or under-expressing HvADH-1 to analyse ADH-1 functions at the level of whole plants. Knock-down (KD) of HvADH-1 by dsRNA interference resulted in reduced and overexpression of HvADH-1 in strongly increased HvADH-1 enzyme activity in leaves of stable transgenic barley plants. The KD of HvADH-1 coincided with a reduced susceptibility to Bgh of both excised leaves and leaves of intact plants. Overexpression (OE) of HvADH-1 results in increased susceptibility to Bgh when excised leaves but not when whole seedlings were inoculated. When first leaves of 10-day-old barley plants were treated with a chitin elicitor, we observed a reduced enzyme activity of ADH-1/-1 homodimers at 48 h after treatment in the second, systemic leaf for empty vector controls and HvADH-1 KD events, but not for the HvADH-1 OE events. Reduced ADH-1 activity in the systemic leaf of empty vector controls and HvADH-1 KD events coincided with chitin-induced resistance to Bgh. Taken together, stable HvADH-1 (KD) or systemic down-regulation of ADH-1/-1 activity by chitin treatment modulated the pathogen response of barley to the biotrophic fungal parasite Bgh and resulted in less successful infections by Bgh.
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Affiliation(s)
- Christoph L Käsbauer
- Chair of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Freising-Weihenstephan, Germany
| | - Indira Priyadarshini Pathuri
- Chair of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Freising-Weihenstephan, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Freising-Weihenstephan, Germany.
| | - Reinhard K Proels
- Chair of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Freising-Weihenstephan, Germany.
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Torrens-Spence MP, Pluskal T, Li FS, Carballo V, Weng JK. Complete Pathway Elucidation and Heterologous Reconstitution of Rhodiola Salidroside Biosynthesis. MOLECULAR PLANT 2018; 11:205-217. [PMID: 29277428 DOI: 10.1016/j.molp.2017.12.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Accepted: 12/12/2017] [Indexed: 05/05/2023]
Abstract
Salidroside is a bioactive tyrosine-derived phenolic natural product found in medicinal plants under the Rhodiola genus. In addition to their anti-fatigue and anti-anoxia roles in traditional medicine, Rhodiola total extract and salidroside have also displayed medicinal properties as anti-cardiovascular diseases and anti-cancer agents. The resulting surge in global demand of Rhodiola plants and salidroside has driven some species close to extinction. Here, we report the full elucidation of the Rhodiola salidroside biosynthetic pathway utilizing the first comprehensive transcriptomics and metabolomics datasets for Rhodiola rosea. Unlike the previously proposed pathway involving separate decarboxylation and deamination enzymatic steps from tyrosine to the key intermediate 4-hydroxyphenylacetaldehyde (4-HPAA), Rhodiola contains a pyridoxal phosphate-dependent 4-HPAA synthase that directly converts tyrosine to 4-HPAA. We further identified genes encoding the subsequent 4-HPAA reductase and tyrosol:UDP-glucose 8-O-glucosyltransferase, respectively, to complete salidroside biosynthesis in Rhodiola. We show that heterologous production of salidroside can be achieved in the yeast Saccharomyces cerevisiae as well as the plant Nicotiana benthamiana through transgenic expression of Rhodiola salidroside biosynthetic genes. This study provides new tools for engineering sustainable production of salidroside in heterologous hosts.
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Affiliation(s)
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Fu-Shuang Li
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Valentina Carballo
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Yi SY, Ku SS, Sim HJ, Kim SK, Park JH, Lyu JI, So EJ, Choi SY, Kim J, Ahn MS, Kim SW, Park H, Jeong WJ, Lim YP, Min SR, Liu JR. An Alcohol Dehydrogenase Gene from Synechocystis sp. Confers Salt Tolerance in Transgenic Tobacco. FRONTIERS IN PLANT SCIENCE 2017; 8:1965. [PMID: 29204151 PMCID: PMC5698875 DOI: 10.3389/fpls.2017.01965] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/31/2017] [Indexed: 06/01/2023]
Abstract
Synechocystis salt-responsive gene 1 (sysr1) was engineered for expression in higher plants, and gene construction was stably incorporated into tobacco plants. We investigated the role of Sysr1 [a member of the alcohol dehydrogenase (ADH) superfamily] by examining the salt tolerance of sysr1-overexpressing (sysr1-OX) tobacco plants using quantitative real-time polymerase chain reactions, gas chromatography-mass spectrometry, and bioassays. The sysr1-OX plants exhibited considerably increased ADH activity and tolerance to salt stress conditions. Additionally, the expression levels of several stress-responsive genes were upregulated. Moreover, airborne signals from salt-stressed sysr1-OX plants triggered salinity tolerance in neighboring wild-type (WT) plants. Therefore, Sysr1 enhanced the interconversion of aldehydes to alcohols, and this occurrence might affect the quality of green leaf volatiles (GLVs) in sysr1-OX plants. Actually, the Z-3-hexenol level was approximately twofold higher in sysr1-OX plants than in WT plants within 1-2 h of wounding. Furthermore, analyses of WT plants treated with vaporized GLVs indicated that Z-3-hexenol was a stronger inducer of stress-related gene expression and salt tolerance than E-2-hexenal. The results of the study suggested that increased C6 alcohol (Z-3-hexenol) induced the expression of resistance genes, thereby enhancing salt tolerance of transgenic plants. Our results revealed a role for ADH in salinity stress responses, and the results provided a genetic engineering strategy that could improve the salt tolerance of crops.
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Affiliation(s)
- So Young Yi
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Institute of Agricultural Science, Chungnam National University, Daejeon, South Korea
| | - Seong Sub Ku
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Hee-Jung Sim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Sang-Kyu Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Ji Hyun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jae Il Lyu
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Eun Jin So
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - So Yeon Choi
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jonghyun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Myung Suk Ahn
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Suk Weon Kim
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Hyunwoo Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Won Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, South Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jang Ryol Liu
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
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44
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Song Y, Liu L, Li G, An L, Tian L. Trichostatin A and 5-Aza-2'-Deoxycytidine influence the expression of cold-induced genes in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1389828. [PMID: 29027833 PMCID: PMC5703259 DOI: 10.1080/15592324.2017.1389828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The expression of cold-induced genes is critical for plants to survive under freezing stress. However, the underlying mechanisms for the decision of when, where, and which genes to express are unclear when a plant meets a sudden temperature drop. Previous studies have demonstrated epigenetics to play a central role in the regulation of gene expression in plant responses to environmental stress. DNA methylation and histone deacetylation are the two most important epigenetic modifications. This study was conducted to investigate the effects of inhibiting DNA methylation and histone deacetylation on gene expression, and to explore the potential role of epigenetics in plant responses to cold stress. The results revealed that histone deacetylase inhibitors (trichostatin A) and DNA methylation inhibitors (5-Aza-2'-deoxycytosine) treatment enhanced cold tolerance. DNA microarray analysis and the gene ontology method revealed 76 cold-induced differently expressed genes in Arabidopsis thaliana seedlings that were treated to 0°C for 24 h following Trichostatin A and 5-Aza-2'-Deoxycytidine. Furthermore, analyses of metabolic pathways and transcription factors of 3305 differentially expressed genes were performed. Each four metabolic pathways were significantly affected (p < 0.01) by Trichostatin A and 5-Aza-2'-Deoxycytidine. Finally, 10 genes were randomly selected and verified via qPCR analysis. Our study indicated that Trichostatin A and 5-Aza-2'-Deoxycytidine can improve the plant cold resistance and influence the expression of the cold-induced gene in A. thaliana. This result will advance our understanding of plant freezing responses and may provide a helpful strategy for cold tolerance improvement in crops.
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Affiliation(s)
- Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
- CONTACT Lining Tian ; Yuan Song Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, The South of Tianshui Road 222#, Lanzhou City, China Lanzhou 730000
| | - Lijun Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Gaopeng Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Lining Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, Canada, N5V4T3
- CONTACT Lining Tian ; Yuan Song Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, The South of Tianshui Road 222#, Lanzhou City, China Lanzhou 730000
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45
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Vicente VA, Weiss VA, Bombassaro A, Moreno LF, Costa FF, Raittz RT, Leão AC, Gomes RR, Bocca AL, Fornari G, de Castro RJA, Sun J, Faoro H, Tadra-Sfeir MZ, Baura V, Balsanelli E, Almeida SR, Dos Santos SS, Teixeira MDM, Soares Felipe MS, do Nascimento MMF, Pedrosa FO, Steffens MB, Attili-Angelis D, Najafzadeh MJ, Queiroz-Telles F, Souza EM, De Hoog S. Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis. Front Microbiol 2017; 8:1924. [PMID: 29062304 PMCID: PMC5640708 DOI: 10.3389/fmicb.2017.01924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/21/2017] [Indexed: 01/16/2023] Open
Abstract
Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23 Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-α contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species.
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Affiliation(s)
- Vania A Vicente
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Vinícius A Weiss
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Leandro F Moreno
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Flávia F Costa
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto T Raittz
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C Leão
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Anamelia L Bocca
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - Gheniffer Fornari
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Helisson Faoro
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Valter Baura
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Sandro R Almeida
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Suelen S Dos Santos
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Marcus de Melo Teixeira
- Department of Cell Biology, University of Brasília, Brasilia, Brazil.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Maria S Soares Felipe
- Department of Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasilia, Brazil
| | | | - Fabio O Pedrosa
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Maria B Steffens
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Flávio Queiroz-Telles
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Clinical Hospital of the Federal University of Paraná, Curitiba, Brazil
| | - Emanuel M Souza
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Sybren De Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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Differential expression by chromatin modifications of alcohol dehydrogenase 1 of Chorispora bungeana in cold stress. Gene 2017; 636:1-16. [PMID: 28912063 DOI: 10.1016/j.gene.2017.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/03/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022]
Abstract
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene. H3K9 acetylation and H3K4 trimethylation increased throughout the gene and in the proximal promoter region, respectively. Moreover, increased Ser5P and Ser2P polymerase II accumulation further indicated changes in the transcription initiation and elongation of CbADH1 were due to the cold stress. Taken together, our results suggested that CbADH1 is highly expressed during cold stress, and is regulated by epigenetic modifications. This study expands our understanding of the regulation of gene expression by epigenetic modifications in response to environmental cues.
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An integrated analysis based on transcriptome and proteome reveals deastringency-related genes in CPCNA persimmon. Sci Rep 2017; 7:44671. [PMID: 28304376 PMCID: PMC5356345 DOI: 10.1038/srep44671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/13/2017] [Indexed: 01/22/2023] Open
Abstract
Persimmon fruits accumulate a large amount of proanthocyanidins (PAs) during development. PAs cause a dry or puckering sensation due to its astringency. Pollination constant and non-astringent (PCNA) persimmon fruits can lose astringency during fruit ripening. However, little is known about the mechanism of natural de-astringency of Chinese PCNA (CPCNA). To gain insight into the molecular events of CPCNA natural de-astringency, we used mRNA-seq and iTRAQ-based quantitative proteomic analysis to measure changes in genes and proteins expression at two key stages of natural astringency removal (i.e. 10 and 20 weeks after bloom) and water-treated (i.e. 40 °C·12 h) de-astringency fruits. Our analyses show that the three predominantly process in CPCNA de-astringency: (1) water treatment strongly up-regulates glycolysis/acetaldehyde metabolism, (2) expression of genes/proteins involved in PA biosynthetic pathway was remarkably reduced in natural and water-treated de-astringency, (3) sugar metabolism and ethylene related pathway were quite abundant in natural de-astringency. We also found ethylene-related TFs were quite abundant in natural de-astringency, followed by WRKY and NAC transcription factors. These results provide an initial understanding of the predominantly biological processes underlying the natural de-astringency and "coagulation effect" in CPCNA.
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Guan C, Du X, Zhang Q, Ma F, Luo Z, Yang Y. DkPK Genes Promote Natural Deastringency in C-PCNA Persimmon by Up-regulating DkPDC and DkADH Expression. FRONTIERS IN PLANT SCIENCE 2017; 8:149. [PMID: 28243247 PMCID: PMC5303730 DOI: 10.3389/fpls.2017.00149] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/24/2017] [Indexed: 05/09/2023]
Abstract
The astringency of Chinese pollination-constant non-astringent (C-PCNA) persimmon (Diospyros kaki Thunb.) can be naturally removed on the tree. This process is controlled by a single locus and is dominant against other types of persimmons; therefore, this variant is an important candidate for commercial cultivation and the breeding of PCNA cultivars. In our previous study, six full-length coding sequences (CDS) for pyruvate kinase genes (DkPK1-6) were isolated, and DkPK1 is thought to be involved in the natural deastringency of C-PCNA persimmon fruit. Here, we characterize the eight other DkPK genes (DkPK7-14) from C-PCNA persimmon fruit based on transcriptome data. The transcript changes in DkPK7-14 genes and correlations with the proanthocyanidin (PA) content were investigated during different fruit development stages in C-PCNA, J-PCNA, and non-PCNA persimmon; DkPK7 and DkPK8 exhibited up-regulation patterns during the last developmental stage in C-PCNA persimmon that was negatively correlated with the decrease in soluble PAs. Phylogenetic analysis and subcellular localization analysis revealed that DkPK7 and DkPK8 are cytosolic proteins. Notably, DkPK7 and DkPK8 were ubiquitously expressed in various persimmon organs and abundantly up-regulated in seeds. Furthermore, transient over-expression of DkPK7 and DkPK8 in persimmon leaves led to a significant decrease in the content of soluble PAs but a significant increase in the expression levels of the pyruvate decarboxylase (DkPDC) and alcohol dehydrogenase genes (DkADH), which are closely related to acetaldehyde metabolism. The accumulated acetaldehyde that results from the up-regulation of the DkPDC and DkADH genes can combine with soluble PAs to form insoluble PAs, resulting in the removal of astringency from persimmon fruit. Thus, we suggest that both DkPK7 and DkPK8 are likely to be involved in natural deastringency via the up-regulation of DkPDC and DkADH expression during the last developmental stage in C-PCNA persimmon.
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Affiliation(s)
- Changfei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology – Ministry of Education, Huazhong Agricultural UniversityWuhan, China
| | - Xiaoyun Du
- Institute of Pomology, Yantai Academy of Agricultural SciencesYantai, China
- *Correspondence: Yong Yang, Xiaoyun Du,
| | - Qinglin Zhang
- Key Laboratory of Horticultural Plant Biology – Ministry of Education, Huazhong Agricultural UniversityWuhan, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology – Ministry of Education, Huazhong Agricultural UniversityWuhan, China
| | - Yong Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- *Correspondence: Yong Yang, Xiaoyun Du,
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Gravot A, Richard G, Lime T, Lemarié S, Jubault M, Lariagon C, Lemoine J, Vicente J, Robert-Seilaniantz A, Holdsworth MJ, Manzanares-Dauleux MJ. Hypoxia response in Arabidopsis roots infected by Plasmodiophora brassicae supports the development of clubroot. BMC PLANT BIOLOGY 2016; 16:251. [PMID: 27835985 PMCID: PMC5106811 DOI: 10.1186/s12870-016-0941-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/01/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The induction of alcohol fermentation in roots is a plant adaptive response to flooding stress and oxygen deprivation. Available transcriptomic data suggest that fermentation-related genes are also frequently induced in roots infected with gall forming pathogens, but the biological significance of this induction is unclear. In this study, we addressed the role of hypoxia responses in Arabidopsis roots during infection by the clubroot agent Plasmodiophora brassicae. RESULTS The hypoxia-related gene markers PYRUVATE DECARBOXYLASE 1 (PDC1), PYRUVATE DECARBOXYLASE 2 (PDC2) and ALCOHOL DEHYDROGENASE 1 (ADH1) were induced during secondary infection by two isolates of P. brassicae, eH and e2. PDC2 was highly induced as soon as 7 days post inoculation (dpi), i.e., before the development of gall symptoms, and GUS staining revealed that ADH1 induction was localised in infected cortical cells of root galls at 21 dpi. Clubroot symptoms were significantly milder in the pdc1 and pdc2 mutants compared with Col-0, but a null T-DNA insertional mutation of ADH1 did not affect clubroot susceptibility. The Arg/N-end rule pathway of ubiquitin-mediated proteolysis controls oxygen sensing in plants. Mutants of components of this pathway, ate1 ate2 and prt6, that both exhibit constitutive hypoxia responses, showed enhanced clubroot symptoms. In contrast, gall development was reduced in quintuple and sextuple mutants where the activity of all oxygen-sensing Group VII Ethylene Response Factor transcription factors (ERFVIIs) is absent (erfVII and prt6 erfVII). CONCLUSIONS Our data demonstrate that the induction of PDC1 and PDC2 during the secondary infection of roots by P. brassicae contributes positively to clubroot development, and that this is controlled by oxygen-sensing through ERFVIIs. The absence of any major role of ADH1 in symptom development may also suggest that PDC activity could contribute to the formation of galls through the activation of a PDH bypass.
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Affiliation(s)
- Antoine Gravot
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France.
| | - Gautier Richard
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Tanguy Lime
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Séverine Lemarié
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Mélanie Jubault
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Christine Lariagon
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Jocelyne Lemoine
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Jorge Vicente
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Michael J Holdsworth
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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Baluška F, Yokawa K, Mancuso S, Baverstock K. Understanding of anesthesia - Why consciousness is essential for life and not based on genes. Commun Integr Biol 2016; 9:e1238118. [PMID: 28042377 PMCID: PMC5193047 DOI: 10.1080/19420889.2016.1238118] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/05/2016] [Accepted: 09/14/2016] [Indexed: 01/14/2023] Open
Abstract
Anesthesia and consciousness represent 2 mysteries not only for biology but also for physics and philosophy. Although anesthesia was introduced to medicine more than 160 y ago, our understanding of how it works still remains a mystery. The most prevalent view is that the human brain and its neurons are necessary to impose the effects of anesthetics. However, the fact is that all life can be anesthesized. Numerous theories have been generated trying to explain the major impact of anesthetics on our human-specific consciousness; switching it off so rapidly, but no single theory resolves this enduring mystery. The speed of anesthetic actions precludes any direct involvement of genes. Lipid bilayers, cellular membranes, and critical proteins emerge as the most probable primary targets of anesthetics. Recent findings suggest, rather surprisingly, that physical forces underlie both the anesthetic actions on living organisms as well as on consciousness in general.
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Affiliation(s)
| | - Ken Yokawa
- IZMB, University of Bonn, Kirschalle, Bonn, Germany
| | - Stefano Mancuso
- Department of Plant, Soil and Environmental Science & LINV, University of Florence, Sesto Fiorentino, Italy
| | - Keith Baverstock
- Department of Environmental Science, University of Eastern Finland, Kuopio, Finland
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