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Gu H, Pan Z, Jia M, Fang H, Li J, Qi Y, Yang Y, Feng W, Gao X, Ditta A, Khan MKR, Wang W, Cao Y, Wang B. Genome-wide identification and analysis of the cotton ALDH gene family. BMC Genomics 2024; 25:513. [PMID: 38789947 PMCID: PMC11127303 DOI: 10.1186/s12864-024-10388-x] [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: 12/05/2023] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Aldehyde dehydrogenases (ALDHs) are a family of enzymes that catalyze the oxidation of aldehyde molecules into the corresponding carboxylic acid, regulate the balance of aldehydes and protect plants from the poisoning caused by excessive accumulation of aldehydes; however, this gene family has rarely been studied in cotton. RESULTS In the present study, genome-wide identification was performed, and a total of 114 ALDH family members were found in three cotton species, Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii. The ALDH genes were divided into six subgroups by evolutionary analysis. ALDH genes in the same subgroup showed similar gene structures and conserved motifs, but some genes showed significant differences, which may result in functional differences. Chromosomal location analysis and selective pressure analysis revealed that the ALDH gene family had experienced many fragment duplication events. Cis-acting element analysis revealed that this gene family may be involved in the response to various biotic and abiotic stresses. The RT‒qPCR results showed that the expression levels of some members of this gene family were significantly increased under salt stress conditions. Gohir.A11G040800 and Gohir.D06G046200 were subjected to virus-induced gene silencing (VIGS) experiments, and the sensitivity of the silenced plants to salt stress was significantly greater than that of the negative control plants, suggesting that Gohir.A11G040800 and Gohir.D06G046200 may be involved in the response of cotton to salt stress. CONCLUSIONS In total, 114 ALDH genes were identified in three Gossypium species by a series of bioinformatics analysis. Gene silencing of the ALDH genes of G. hirsutum revealed that ALDH plays an important role in the response of cotton to salt stress.
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Affiliation(s)
- Haijing Gu
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Zongjin Pan
- Jiangsu Coastal Area Institute of Agricultural Sciences/Jiangsu Collaborative Innovation Center for Modern Crop Production, Yancheng, Jiangsu, 224002, China
| | - Mengxue Jia
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Junyi Li
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Yingxiao Qi
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Yixuan Yang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
- Nantong Middle School, Nantong, Jiangsu, 226001, China
| | - Wenxiang Feng
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Xin Gao
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Allah Ditta
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - Muhammad K R Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - Wei Wang
- Jiangsu Coastal Area Institute of Agricultural Sciences/Jiangsu Collaborative Innovation Center for Modern Crop Production, Yancheng, Jiangsu, 224002, China.
| | - Yunying Cao
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China.
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China.
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Li S, Wang X, Wang W, Zhang Z, Wang X, Zhang Q, Wang Y. Genome-wide identification and expression analysis of the ALDH gene family and functional analysis of PaALDH17 in Prunus avium. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:633-645. [PMID: 38737320 PMCID: PMC11087402 DOI: 10.1007/s12298-024-01444-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 03/06/2024] [Accepted: 03/22/2024] [Indexed: 05/14/2024]
Abstract
ALDH (Aldehyde dehydrogenase), as an enzyme that encodes the dehydroxidization of aldehydes into corresponding carboxylic acids, played an important role inregulating gene expression in response to many kinds of biotic and abiotic stress, including saline-alkali stress. Saline-alkali stress was a common stress that seriously affected plant growth and productivity. Saline-alkali soil contained the characteristics of high salinity and high pH value, which could cause comprehensive damage such as osmotic stress, ion toxicity, high pH, and HCO3-/CO32- stress. In our study, 18 PaALDH genes were identified in sweet cherry genome, and their gene structures, phylogenetic analysis, chromosome localization, and promoter cis-acting elements were analyzed. Quantitative real-time PCR confirmed that PaALDH17 exhibited the highest expression compared to other members under saline-alkali stress. Subsequently, it was isolated from Prunus avium, and transgenic A. thaliana was successfully obtained. Compared with wild type, transgenic PaALDH17 plants grew better under saline-alkali stress and showed higher chlorophyll content, Superoxide dismutase (SOD), Peroxidase (POD) and Catalase (CAT) enzyme activities, which indicated that they had strong resistance to stress. These results indicated that PaALDH17 improved the resistance of sweet cherries to saline-alkali stress, which in turn improved quality and yields. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01444-7.
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Affiliation(s)
- Sitian Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Wanxia Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Zhongxing Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xingbin Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Qingxia Zhang
- College of Agriculture and Forestry Technology, Longdong University, Qingyang, 745000 China
| | - Yanxiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
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Wang X, Wu M, Yu S, Zhai L, Zhu X, Yu L, Zhang Y. Comprehensive analysis of the aldehyde dehydrogenase gene family in Phaseolus vulgaris L. and their response to saline-alkali stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1283845. [PMID: 38450406 PMCID: PMC10915231 DOI: 10.3389/fpls.2024.1283845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Background Aldehyde dehydrogenase (ALDH) scavenges toxic aldehyde molecules by catalyzing the oxidation of aldehydes to carboxylic acids. Although ALDH gene family members in various plants have been extensively studied and were found to regulate plant response to abiotic stress, reports on ALDH genes in the common bean (Phaseolus vulgaris L.) are limited. In this study, we aimed to investigate the effects of neutral (NS) and basic alkaline (AS) stresses on growth, physiological and biochemical indices, and ALDH activity, ALDH gene expression of common bean. In addition, We used bioinformatics techniques to analyze the physical and chemical properties, phylogenetic relationships, gene replication, collinearity, cis-acting elements, gene structure, motifs, and protein structural characteristics of PvALDH family members. Results We found that both NS and AS stresses weakened the photosynthetic performance of the leaves, induced oxidative stress, inhibited common bean growth, and enhanced the antioxidative system to scavenge reactive oxygen species. Furthermore, we our findings revealed that ALDH in the common bean actively responds to NS or AS stress by inducing the expression of PvALDH genes. In addition, using the established classification criteria and phylogenetic analysis, 27 PvALDHs were identified in the common bean genome, belonging to 10 ALDH families. The primary expansion mode of PvALDH genes was segmental duplication. Cis-acting elemental analysis showed that PvALDHs were associated with abiotic stress and phytohormonal responses. Gene expression analysis revealed that the PvALDH gene expression was tissue-specific. For instance, PvALDH3F1 and PvALDH3H1 were highly expressed in flower buds and flowers, respectively, whereas PvALDH3H2 and PvALDH2B4 were highly expressed in green mature pods and young pods, respectively. PvALDH22A1 and PvALDH11A2 were highly expressed in leaves and young trifoliates, respectively; PvALDH18B2 and PvALDH18B3 were highly expressed in stems and nodules, respectively; and PvALDH2C2 and PvALDH2C3 were highly expressed in the roots. PvALDHs expression in the roots responded positively to NS-AS stress, and PvALDH2C3, PvALDH5F1, and PvALDH10A1 were significantly (P < 0.05) upregulated in the roots. Conclusion These results indicate that AS stress causes higher levels of oxidative damage than NS stress, resulting in weaker photosynthetic performance and more significant inhibition of common bean growth. The influence of PvALDHs potentially modulates abiotic stress response, particularly in the context of saline-alkali stress. These findings establish a basis for future research into the potential roles of ALDHs in the common bean.
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Affiliation(s)
- Xiaoqin Wang
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
| | - Mingxu Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
| | - Song Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
- Key Laboratory of Low-carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang, China
| | - Lingxia Zhai
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Keshan, Heilongjiang, China
| | - Xuetian Zhu
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
| | - Lihe Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
- Key Laboratory of Low-carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang, China
| | - Yifei Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University/Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing, Heilongjiang, China
- Key Laboratory of Low-carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang, China
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Baisakh N, Da Silva EA, Pradhan AK, Rajasekaran K. Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1214907. [PMID: 37534296 PMCID: PMC10392829 DOI: 10.3389/fpls.2023.1214907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
Aflatoxin (AF) contamination, caused by Aspergillus flavus, compromises the food safety and marketability of commodities, such as maize, cotton, peanuts, and tree nuts. Multigenic inheritance of AF resistance impedes conventional introgression of resistance traits into high-yielding commercial maize varieties. Several AF resistance-associated quantitative trait loci (QTLs) and markers have been reported from multiple biparental mapping and genome-wide association studies (GWAS) in maize. However, QTLs with large confidence intervals (CI) explaining inconsistent phenotypic variance limit their use in marker-assisted selection. Meta-analysis of published QTLs can identify significant meta-QTLs (MQTLs) with a narrower CI for reliable identification of genes and linked markers for AF resistance. Using 276 out of 356 reported QTLs controlling resistance to A. flavus infection and AF contamination in maize, we identified 58 MQTLs on all 10 chromosomes with a 66.5% reduction in the average CI. Similarly, a meta-analysis of maize genes differentially expressed in response to (a)biotic stresses from the to-date published literature identified 591 genes putatively responding to only A. flavus infection, of which 14 were significantly differentially expressed (-1.0 ≤ Log2Fc ≥ 1.0; p ≤ 0.05). Eight MQTLs were validated by their colocalization with 14 A. flavus resistance-associated SNPs identified from GWAS in maize. A total of 15 genes were physically close between the MQTL intervals and SNPs. Assessment of 12 MQTL-linked SSR markers identified three markers that could discriminate 14 and eight cultivars with resistance and susceptible responses, respectively. A comprehensive meta-analysis of QTLs and differentially expressed genes led to the identification of genes and makers for their potential application in marker-assisted breeding of A. flavus-resistant maize varieties.
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Affiliation(s)
- Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Eduardo A. Da Silva
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - Anjan K. Pradhan
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, Southern Regional Research Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), New Orleans, LA, United States
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Yang Q, Zhang X, Solairaj D, Lin R, Wang K, Zhang H. TMT-Based Proteomic Analysis of Hannaella sinensis-Induced Apple Resistance-Related Proteins. Foods 2023; 12:2637. [PMID: 37509729 PMCID: PMC10378395 DOI: 10.3390/foods12142637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Studies on the molecular mechanism of antagonistic yeasts to control apple postharvest diseases are not comprehensive enough. Our preliminary investigations screened the biocontrol effect of Hannaella sinensis, an antagonistic yeast, and discovered its control efficacy on apple blue mold decay. However, the molecular mechanism of H. sinensis-induced resistance in apple has not been studied. In this study, proteins from apple treated with H. sinensis and sterile saline were analyzed using TMT proteomics technology. It was found that H. sinensis treatment induced the expressions of apple resistance-related proteins. Among the proteins in H. sinensis-induced apple, proteins related to plant defense mechanisms, such as reactive oxygen species scavenging, improvement of plant resistance and synthesis of resistant substances, improvement of plant disease resistance, the degradation of the pathogen cell wall, cell signaling, antibacterial activity, transport of defense-related substances, and protein processing, were differentially regulated. The results of this study revealed the underlying molecular mechanisms of H. sinensis-induced apple resistance at the protein level; the results also provided a theoretical basis for the commercial application of H. sinensis.
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Affiliation(s)
- Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xi Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Dhanasekaran Solairaj
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Rouling Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
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Munim Twaij B, Jameel Ibraheem L, Al-Shammari RHH, Hasan M, Akter Khoko R, Sunzid Ahomed M, Prodhan SH, Nazmul Hasan M. Identification and characterization of aldehyde dehydrogenase (ALDH) gene superfamily in garlic and expression profiling in response to drought, salinity, and ABA. Gene 2023; 860:147215. [PMID: 36709878 DOI: 10.1016/j.gene.2023.147215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/31/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
In response to biotic and abiotic stressors, aldehydes are detoxified and converted to carboxylic acids by aldehyde dehydrogenases (ALDHs), which are enzymes that use NAD+/NADP+ as cofactors. Garlic (Allium sativum L.) has not yet undergone a systematic examination of the ALDH superfamily, despite the genome sequence having been made public. In this investigation, we identified, characterized, and profiled the expression of the garlic ALDH gene family over the entire genome. The ALDH Gene Nomenclature Committee (AGNC) classification was used to classify and name the 34 ALDH genes that were discovered. Except for chromosome 8, all AsALDH genes were dispersed across the chromosomes. AsALDH genes have various localizations, according to predictions about subcellular localization. The AsALDH proteins are more varied and closely related to rice than to Arabidopsis, according to a study of conserved motifs and phylogenetic relationships. The presence of stress modulation pathways is indicated by the abundance of stress-related cis-elements in the AsALDH genes' promoter regions. Analysis of the RNA-seq data showed that AsALDHs expressed differently in various tissues and at various developmental stages. Nine AsALDHs were chosen for study using RT-qPCR, and the results revealed that the majority of the genes were upregulated in response to ABA and downregulated in response to salinity and drought. The results of this study improved our knowledge of the traits, evolutionary background, and biological functions of AsALDHs genes in growth and development.
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Affiliation(s)
- Baan Munim Twaij
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq.
| | | | | | - Mahmudul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Roksana Akter Khoko
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Md Sunzid Ahomed
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Shamsul H Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
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Ronchi A, Foscari A, Zaina G, De Paoli E, Incerti G. Self-DNA Early Exposure in Cultivated and Weedy Setaria Triggers ROS Degradation Signaling Pathways and Root Growth Inhibition. PLANTS (BASEL, SWITZERLAND) 2023; 12:1288. [PMID: 36986976 PMCID: PMC10058795 DOI: 10.3390/plants12061288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
The accumulation of fragmented extracellular DNA reduces conspecific seed germination and plantlet growth in a concentration-dependent manner. This self-DNA inhibition was repeatedly reported, but the underlying mechanisms are not fully clarified. We investigated the species-specificity of self-DNA inhibition in cultivated vs. weed congeneric species (respectively, Setaria italica and S. pumila) and carried out a targeted real-time qPCR analysis under the hypothesis that self-DNA elicits molecular pathways that are responsive to abiotic stressors. The results of a cross-factorial experiment on root elongation of seedlings exposed to self-DNA, congeneric DNA, and heterospecific DNA from Brassica napus and Salmon salar confirmed a significantly higher inhibition by self-DNA as compared to non-self-treatments, with the latter showing a magnitude of the effect consistent with the phylogenetic distance between the DNA source and the target species. Targeted gene expression analysis highlighted an early activation of genes involved in ROS degradation and management (FSD2, ALDH22A1, CSD3, MPK17), as well as deactivation of scaffolding molecules acting as negative regulators of stress signaling pathways (WD40-155). While being the first exploration of early response to self-DNA inhibition at molecular level on C4 model plants, our study highlights the need for further investigation of the relationships between DNA exposure and stress signaling pathways by discussing potential applications for species-specific weed control in agriculture.
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Affiliation(s)
- Alessia Ronchi
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34100 Trieste, Italy
- Department of Agrifood, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Alessandro Foscari
- Department of Agrifood, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Giusi Zaina
- Department of Agrifood, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Emanuele De Paoli
- Department of Agrifood, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Guido Incerti
- Department of Agrifood, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
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Zhang X, Zhong J, Cao L, Ren C, Yu G, Gu Y, Ruan J, Zhao S, Wang L, Ru H, Cheng L, Wang Q, Zhang Y. Genome-wide characterization of aldehyde dehydrogenase gene family members in groundnut ( Arachis hypogaea) and the analysis under saline-alkali stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1097001. [PMID: 36875623 PMCID: PMC9978533 DOI: 10.3389/fpls.2023.1097001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Groundnut or peanut (Arachis hypogaea) is a legume crop. Its seeds are rich in protein and oil. Aldehyde dehydrogenase (ALDH, EC: 1.2.1.3) is an important enzyme involved in detoxification of aldehyde and cellular reactive oxygen species, as well as in attenuation of lipid peroxidation-meditated cellular toxicity under stress conditions. However, few studies have been identified and analyzed about ALDH members in Arachis hypogaea. In the present study, 71 members of the ALDH superfamily (AhALDH) were identified using the reference genome obtained from the Phytozome database. A systematic analysis of the evolutionary relationship, motif, gene structure, cis-acting elements, collinearity, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and expression patterns was conducted to understand the structure and function of AhALDHs. AhALDHs exhibited tissue-specific expression, and quantitative real-time PCR identified significant differences in the expression levels of AhALDH members under saline-alkali stress. The results revealed that some AhALDHs members could be involved in response to abiotic stress. Our findings on AhALDHs provide insights for further study.
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Affiliation(s)
- Xiaoming Zhang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
- Agricultural College, Northeast Agricultural University, Harbin, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jingwen Zhong
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Liang Cao
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chunyuan Ren
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Gaobo Yu
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanhua Gu
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Jingwen Ruan
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Siqi Zhao
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Lei Wang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Haishun Ru
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Lili Cheng
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qi Wang
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yuxian Zhang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Soybean Mechanized Production, Ministry of Agriculture and Rural Affairs, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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10
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Zhao X, Huang LJ, Sun XF, Zhao LL, Wang PC. Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:785702. [PMID: 35310664 PMCID: PMC8924449 DOI: 10.3389/fpls.2022.785702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/07/2022] [Indexed: 05/26/2023]
Abstract
Soil aridification and desertification are particularly prominent in China's karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H2O2), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4.1.13, E3.2.1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.
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Affiliation(s)
- Xin Zhao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Juan Huang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xiao-Fu Sun
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Li Zhao
- College of Animal Science, Guizhou University, Guiyang, China
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11
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Raza H, Khan MR, Zafar SA, Kirch HH, Bartles D. Aldehyde dehydrogenase 3I1 gene is recruited in conferring multiple abiotic stress tolerance in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:85-94. [PMID: 34670007 DOI: 10.1111/plb.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Plant growth and productivity is restricted by a multitude of abiotic stresses. These stresses negatively affect physiological and metabolic pathways, leading to the production of many harmful substances like ROS, lipid peroxides and aldehydes. This study was conducted to investigate the role of Arabidopsis ALDH3I1 gene in multiple abiotic stress tolerance. Transgenic tobacco plants were generated that overexpress the ALDH3I1 gene driven by the CaMV35S promoter and evaluated under different abiotic stresses, namely salt, drought, cold and oxidative stress. Tolerance to stress was evaluated based on responses of various growth and physiological traits under stress condition. Transgenic plants displayed elevated ALDH3I1 transcript levels compared to WT plants. The constitutive ectopic expression of ALDH3I1 conferred increased tolerance to salt, drought, cold and oxidative stresses in transgenic plants, along with improved plant growth. Transgenic plants overexpressing ALDH3I1 had higher chlorophyll content, photosynthesis rate and proline, and less accumulation of ROS and malondialdehyde compared to the WT, which contributed to stress tolerance in transgenic plants. Our results further revealed that ALDH3I1 had a positive effect on CO2 assimilation rate in plants under abiotic stress conditions. Overall, this study revealed that ALDH3I1 positively regulates abiotic stress tolerance in plants, and has future implications in producing transgenic cereal and horticultural plants tolerant to abiotic stresses.
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Affiliation(s)
- H Raza
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - M R Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - S A Zafar
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - H H Kirch
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - D Bartles
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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12
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Carmona-Molero R, Jimenez-Lopez JC, Caballo C, Gil J, Millán T, Die JV. Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea. PLANTS 2021; 10:plants10112429. [PMID: 34834791 PMCID: PMC8619295 DOI: 10.3390/plants10112429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 11/04/2021] [Indexed: 11/23/2022]
Abstract
Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs.
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Affiliation(s)
- Rocío Carmona-Molero
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of Plants, EEZ-CSIC, 18008 Granada, Spain;
- Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth 6009, Australia
| | - Cristina Caballo
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, 14080 Córdoba, Spain;
| | - Juan Gil
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Teresa Millán
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Jose V. Die
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
- Correspondence:
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13
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Fan Y, Lai D, Yang H, Xue G, He A, Chen L, Feng L, Ruan J, Xiang D, Yan J, Cheng J. Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.). BMC Genomics 2021; 22:778. [PMID: 34717536 PMCID: PMC8557513 DOI: 10.1186/s12864-021-08095-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08095-y.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.,School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.
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Huangfu Y, Pan J, Li Z, Wang Q, Mastouri F, Li Y, Yang S, Liu M, Dai S, Liu W. Genome-wide identification of PTI1 family in Setaria italica and salinity-responsive functional analysis of SiPTI1-5. BMC PLANT BIOLOGY 2021; 21:319. [PMID: 34217205 PMCID: PMC8254068 DOI: 10.1186/s12870-021-03077-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/27/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND PTI1 (Pto-interacting 1) protein kinase belongs to the receptor-like cytoplasmic kinase (RLCK) group of receptor-like protein kinases (RLK), but lack extracellular and transmembrane domains. PTI1 was first identified in tomato (Solanum lycopersicum) and named SlPTI1, which has been reported to interact with bacterial effector Pto, a serine/threonine protein kinase involved in plant resistance to bacterial disease. Briefly, the host PTI1 specifically recognizes and interacts with the bacterial effector AvrPto, which triggers hypersensitive cell death to inhibit the pathogen growth in the local infection site. Previous studies have demonstrated that PTI1 is associated with oxidative stress and hypersensitivity. RESULTS We identified 12 putative PTI1 genes from the genome of foxtail millet (Setaria italica) in this study. Gene replication analysis indicated that both segmental replication events played an important role in the expansion of PTI1 gene family in foxtail millet. The PTI1 family members of model plants, i.e. S. italica, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), maize (Zea mays), S. lycopersicum, and soybean (Glycine max), were classified into six major categories according to the phylogenetic analysis, among which the PTI1 family members in foxtail millet showed higher degree of homology with those of rice and maize. The analysis of a complete set of SiPTI1 genes/proteins including classification, chromosomal location, orthologous relationships and duplication. The tissue expression characteristics revealed that SiPTI1 genes are mainly expressed in stems and leaves. Experimental qRT-PCR results demonstrated that 12 SiPTI1 genes were induced by multiple stresses. Subcellular localization visualized that all of foxtail millet SiPTI1s were localized to the plasma membrane. Additionally, heterologous expression of SiPTI1-5 in yeast and E. coli enhanced their tolerance to salt stress. CONCLUSIONS Our results contribute to a more comprehensive understanding of the roles of PTI1 protein kinases and will be useful in prioritizing particular PTI1 for future functional validation studies in foxtail millet.
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Affiliation(s)
- Yongguan Huangfu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Jiaowen Pan
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Zhen Li
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Qingguo Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Fatemeh Mastouri
- Bota Bioscience, 325 Vassar st. Suite 2a, Cambridge, MA, 02139, USA
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Stephen Yang
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, MD, 20850, USA
| | - Min Liu
- Shandong Agriculture and Engineering University, Jinan, 250100, Shandong, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Wei Liu
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, China.
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15
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Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
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16
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Lv J, Sun D, Yan D, Ti X, Liu P, Li J. Quantitative Trait Loci Mapping and Marker Identification for Low Salinity Tolerance Trait in the Swimming Crab ( Portunus trituberculatus). Front Genet 2019; 10:1193. [PMID: 31850064 PMCID: PMC6900548 DOI: 10.3389/fgene.2019.01193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/28/2019] [Indexed: 01/17/2023] Open
Abstract
Low salinity is one of the most important abiotic factors that directly affect the abundance of the swimming crab, Portunus trituberculatus. Quantitative trait loci (QTL) mapping could be helpful in identifying the markers and genes involved in low salinity tolerance. In this study, two QTLs of low salt tolerance were mapped on linkage group 17 (LG17, 2.6-5.2 cM) based on a high-density linkage map. Ninety-five markers related to low salinity tolerance were identified via association analysis, and seventy-nine low salt-related candidate genes (including ammonium transport, aldehyde dehydrogenase, and glucosyltransferase) were screened from draft genome of the species via these markers. This represents the first report of QTL mapping for low salinity tolerance in the swimming crab, which may be useful to elucidate salinity adaptation mechanisms.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dongfang Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Deping Yan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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17
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K M, V C. Phytoconstituents in the Management of Pesticide Induced Parkinson’s Disease- A Review. ACTA ACUST UNITED AC 2019. [DOI: 10.13005/bpj/1770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent studies have suggested that environmental factors have a crucial role in triggering and/ or propagating the pathological changes in Parkinson’s disease (PD). Although many studies have been and being performed by utilizing MPTP like chemicals to study the effectiveness of new extracts and compounds in PD, a little focus was made on the role of pesticides. Since agricultural fields account for 37.7% of land area worldwide and the use of pesticides is an important risk factor in neurodegeneration, there is a crucial need to focus on the association between pesticides and PD. Benomyl, a benzimidazole fungicide is being widely used in India in cultivation of tropical crops. Studies prove the chronic exposure of benomyl leads to aldehyde dehydrogenase inhibition caused DOPAL toxicity, subsequently leading to dopamine degradation and Parkinson’s disease. Till date, there is no remedy for pesticide induced Parkinson’s disease. This review provides an insight of the pathophysiological aspects of pesticide induced Parkinson’s disease and also enlightens the importance of aldehyde dehydrogenase enzyme in neuroprotection.
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Affiliation(s)
- Manasa K
- Department of Pharmacology, SRM College of Pharmacy, SRMIST, Kattankulathur-603203
| | - Chitra V
- Department of Pharmacology, SRM College of Pharmacy, SRMIST, Kattankulathur-603203
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18
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Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants. J Mol Biol 2018; 431:576-592. [PMID: 30580036 DOI: 10.1016/j.jmb.2018.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 11/23/2022]
Abstract
Heterokonts, Alveolata protists, green algae from Charophyta and Chlorophyta divisions, and all Embryophyta plants possess an aldehyde dehydrogenase (ALDH) gene named ALDH12. Here, we provide a biochemical characterization of two ALDH12 family members from the lower plant Physcomitrella patens and higher plant Zea mays. We show that ALDH12 encodes an NAD+-dependent glutamate γ-semialdehyde dehydrogenase (GSALDH), which irreversibly converts glutamate γ-semialdehyde (GSAL), a mitochondrial intermediate of the proline and arginine catabolism, to glutamate. Sedimentation equilibrium and small-angle X-ray scattering analyses reveal that in solution both plant GSALDHs exist as equilibrium between a domain-swapped dimer and the dimer-of-dimers tetramer. Plant GSALDHs share very low-sequence identity with bacterial, fungal, and animal GSALDHs (classified as ALDH4), which are the closest related ALDH superfamily members. Nevertheless, the crystal structure of ZmALDH12 at 2.2-Å resolution shows that nearly all key residues involved in the recognition of GSAL are identical to those in ALDH4, indicating a close functional relationship with ALDH4. Phylogenetic analysis suggests that the transition from ALDH4 to ALDH12 occurred during the evolution of the endosymbiotic plant ancestor, prior to the evolution of green algae and land plants. Finally, ALDH12 expression in maize and moss is downregulated in response to salt and drought stresses, possibly to maintain proline levels. Taken together, these results provide molecular insight into the biological roles of the plant ALDH12 family.
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19
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Pan J, Li Z, Wang Q, Garrell AK, Liu M, Guan Y, Zhou W, Liu W. Comparative proteomic investigation of drought responses in foxtail millet. BMC PLANT BIOLOGY 2018; 18:315. [PMID: 30497407 PMCID: PMC6267058 DOI: 10.1186/s12870-018-1533-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Foxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture facing various adversities, it's urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level. RESULTS In this research, a total of 2474 differentially expressed proteins were identified by quantitative proteomic analysis after subjecting foxtail millet seedlings to drought conditions. 321 of these 2474 proteins exhibited significant expression changes, including 252 up-regulated proteins and 69 down-regulated proteins. The resulting proteins could then be divided into different categories, such as stress and defense responses, photosynthesis, carbon metabolism, ROS scavenging, protein synthesis, etc., according to Gene Ontology annotation. Proteins implicated in fatty acid and amino acid metabolism, polyamine biosynthesis, hormone metabolism, and cell wall modifications were also identified. These obtained differential proteins and their possible biological functions under drought stress all suggested that various physiological and metabolic processes might function cooperatively to configure a new dynamic homeostasis in organisms. The expression patterns of five drought-responsive proteins were further validated using western blot analysis. The qRT-PCR was also carried out to analyze the transcription levels of 21 differentially expressed proteins. The results showed large inconsistency in the variation between proteins and the corresponding mRNAs, which showed once again that post-transcriptional modification performs crucial roles in regulating gene expression. CONCLUSION The results offered a valuable inventory of proteins that may be involved in drought response and adaption, and provided a regulatory network of different metabolic pathways under stress stimulation. This study will illuminate the stress tolerance mechanisms of foxtail millet, and shed some light on crop germplasm breeding and innovation.
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Affiliation(s)
- Jiaowen Pan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
| | - Zhen Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
| | - Qingguo Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
| | | | - Min Liu
- Shandong Agriculture and Engineering University, Jinan, 250100 Shandong China
| | - Yanan Guan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 Shandong China
| | | | - Wei Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250100 Shandong China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 Shandong China
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20
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Abdul W, Aliyu SR, Lin L, Sekete M, Chen X, Otieno FJ, Yang T, Lin Y, Norvienyeku J, Wang Z. Family-Four Aldehyde Dehydrogenases Play an Indispensable Role in the Pathogenesis of Magnaporthe oryzae. FRONTIERS IN PLANT SCIENCE 2018; 9:980. [PMID: 30135691 PMCID: PMC6092734 DOI: 10.3389/fpls.2018.00980] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/15/2018] [Indexed: 05/22/2023]
Abstract
The oxidative degradation of lipids through lipid peroxidation processes results in the generation of free fatty acid radicals. These free radicals including reactive oxygen species (ROS) serve as a substrate for generating reactive aldehydes. The accumulation of free fatty acid radicals, ROS, and reactive aldehydes in cell compartments beyond physiological threshold levels tends to exert a damaging effect on proximal membranes and distal tissues. Living organisms deploy a wide array of efficient enzymes including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and aldehyde dehydrogenases (ALDHs) for scavenging reactive molecules and intermediates produced from membrane lipid peroxidation events. Although the contributions of SOD, CAT, and POD to the pathogenesis of microbial plant pathogens are well known, the influence of ALDH genes on the morphological and infectious development of plant pathogenic microbes is not well understood. In this study, we deployed RNA interference (RNAi) techniques and successfully silenced two putative family-four aldehyde dehydrogenase genes potassium-activated aldehyde dehydrogenase (MoKDCDH) and delta-1-pyrrorine-5-carboxylate dehydrogenase (MoP5CDH) in the rice blast pathogen Magnaporthe oryzae. The results obtained from the phenotypic analysis of individual knock-down strains showed that the RNAi-mediated inactivation of MoKDCDH and MoP5CDH triggered a significant reduction in conidiogenesis and vegetative growth of ΔMokdcdh and ΔMop5cdh strains. We further observed that downregulating the expression of MoKDCDH and MoP5CDH severely compromised the pathogenesis of the rice blast fungus. Also, the disruption of MoKDCDH and MoP5CDH M. oryzae undermined membrane integrity and rendered the mutant strains highly sensitive to membrane stress inducing osmolytes. However, the MoKDCDH and MoP5CDH knock-down strains generated in this study displayed unaltered cell wall integrity and thus suggested that family-four ALDHs play a dispensable role in enforcing cell wall-directed stress tolerance in M. oryzae. From these results, we deduced that family-four ALDHs play a conserved role in fostering membrane integrity in M. oryzae possibly by scavenging reactive aldehydes, fatty acid radicals, and other alcohol derivatives. The observation that downregulating the expression activities of MoKDCDH had a lethal effect on potential mutants further emphasized the need for comprehensive and holistic evaluation of the numerous ALDHs amassed by the rice blast fungus for their possible engagement as suitable targets as antiblast agents.
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Affiliation(s)
- Waheed Abdul
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sami R. Aliyu
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Lin
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Malota Sekete
- Department of Crop Science, Faculty of Agriculture, National University of Lesotho, Lesotho, Southern Africa
| | - Xiaomin Chen
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Frankline J. Otieno
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tao Yang
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yahong Lin
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Justice Norvienyeku
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Justice Norvienyeku, Zonghua Wang,
| | - Zonghua Wang
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian and Taiwan Joint Center for Ecological Control of Crop Pests, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Justice Norvienyeku, Zonghua Wang,
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Wang W, Jiang W, Liu J, Li Y, Gai J, Li Y. Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response. BMC Genomics 2017; 18:518. [PMID: 28687067 PMCID: PMC5501352 DOI: 10.1186/s12864-017-3908-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 06/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses. However, the comprehensive analysis of ALDH superfamily in soybean (Glycine max) has been limited. RESULTS In present study, a total of 53 GmALDHs were identified in soybean, and grouped into 10 ALDH families according to the ALDH Gene Nomenclature Committee and phylogenetic analysis. These groupings were supported by their gene structures and conserved motifs. Soybean ALDH superfamily expanded mainly by whole genome duplication/segmental duplications. Gene network analysis identified 1146 putative co-functional genes of 51 GmALDHs. Gene Ontology (GO) enrichment analysis suggested the co-functional genes of these 51 GmALDHs were enriched (FDR < 1e-3) in the process of lipid metabolism, photosynthesis, proline catabolism, and small molecule catabolism. In addition, 22 co-functional genes of GmALDHs are related to plant response to water deprivation/water transport. GmALDHs exhibited various expression patterns in different soybean tissues. The expression levels of 13 GmALDHs were significantly up-regulated and 14 down-regulated in response to water deficit. The occurrence frequencies of three drought-responsive cis-elements (ABRE, CRT/DRE, and GTGCnTGC/G) were compared in GmALDH genes that were up-, down-, or non-regulated by water deficit. Higher frequency of these three cis-elements was observed for the group of up-regulated GmALDH genes as compared to the group of down- or non- regulated GmALDHs by drought stress, implying their potential roles in the regulation of soybean response to drought stress. CONCLUSIONS A total of 53 ALDH genes were identified in soybean genome and their phylogenetic relationships and duplication patterns were analyzed. The potential functions of GmALDHs were predicted by analyses of their co-functional gene networks, gene expression profiles, and cis-regulatory elements. Three GmALDH genes, including GmALDH3H2, GmALDH12A2 and GmALDH18B3, were highly induced by drought stress in soybean leaves. Our study provides a foundation for future investigations of GmALDH gene function in soybean.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture) / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Wei Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture) / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Juge Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture) / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Yang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture) / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture) / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture) / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu China
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Sheshadri SA, Nishanth MJ, Simon B. Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta. FRONTIERS IN PLANT SCIENCE 2016; 7:1725. [PMID: 27933071 PMCID: PMC5122738 DOI: 10.3389/fpls.2016.01725] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/02/2016] [Indexed: 05/07/2023]
Abstract
Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants.
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Affiliation(s)
| | | | - Bindu Simon
- School of Chemical and Biotechnology, SASTRA UniversityThanjavur, India
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Missihoun TD, Kotchoni SO, Bartels D. Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots. PLoS One 2016; 11:e0165867. [PMID: 27798665 PMCID: PMC5087895 DOI: 10.1371/journal.pone.0165867] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/19/2016] [Indexed: 11/22/2022] Open
Abstract
Plant aldehyde dehydrogenases (ALDHs) play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.
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Affiliation(s)
- Tagnon D. Missihoun
- Department of Biology, Rutgers University, Camden, New Jersey, United States of America
- * E-mail: (SOK); (TDM)
| | - Simeon O. Kotchoni
- Department of Biology, Rutgers University, Camden, New Jersey, United States of America
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, United States of America
- * E-mail: (SOK); (TDM)
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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Li W, Chen M, Wang E, Hu L, Hawkesford MJ, Zhong L, Chen Z, Xu Z, Li L, Zhou Y, Guo C, Ma Y. Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice. BMC Genomics 2016; 17:797. [PMID: 27733118 PMCID: PMC5062844 DOI: 10.1186/s12864-016-3113-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 09/23/2016] [Indexed: 01/07/2023] Open
Abstract
Background Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycling of amino acids in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) has strong resistance to stresses and has been proposed as an ideal material for use in the study of the physiological mechanisms of abiotic stress tolerance in plants. Although the genome sequence of foxtail millet (Setaria italica) is available, the characteristics and functions of abiotic stress-related genes remain largely unknown for this species. Results A total of 37 putative ATG (autophagy-associated genes) genes in the foxtail millet genome were identified. Gene duplication analysis revealed that both segmental and tandem duplication events have played significant roles in the expansion of the ATG gene family in foxtail millet. Comparative synteny mapping between the genomes of foxtail millet and rice suggested that the ATG genes in both species have common ancestors, as their ATG genes were primarily located in similar syntenic regions. Gene expression analysis revealed the induced expression of 31 SiATG genes by one or more phytohormone treatments, 26 SiATG genes by drought, salt and cold, 24 SiATG genes by darkness and 25 SiATG genes by nitrogen starvation. Results of qRT-PCR showing that among 37 SiATG genes, the expression level of SiATG8a was the highest after nitrogen starvation treatment 24 h, suggesting its potential role in tolerance to nutrient starvation. Moreover, the heterologous expression of SiATG8a in rice improved nitrogen starvation tolerance. Compared to wild type rice, the transgenic rice performed better and had higher aboveground total nitrogen content when the plants were grown under nitrogen starvation conditions. Conclusions Our results deepen understanding about the characteristics and functions of ATG genes in foxtail millet and also identify promising new genetic resources that should be of use in future efforts to develop varieties of foxtail millet and other crop species that have resistance to nitrogen deficiency stress. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3113-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weiwei Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Erhui Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Liqin Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Malcolm J Hawkesford
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Li Zhong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Zhu Chen
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230000, China
| | - Zhaoshi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Liancheng Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yongbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
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Kirankumar TV, Madhusudhan KV, Nareshkumar A, Kiranmai K, Lokesh U, Venkatesh B, Sudhakar C. Expression Analysis of Aldo-Keto Reductase 1 (<i>AKR1</i>) in Foxtail Millet (<i>Setaria italica</i> L.) Subjected to Abiotic Stresses. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/ajps.2016.73044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Duan Z, Zhang D, Zhang J, Di H, Wu F, Hu X, Meng X, Luo K, Zhang J, Wang Y. Co-transforming bar and CsALDH Genes Enhanced Resistance to Herbicide and Drought and Salt Stress in Transgenic Alfalfa (Medicago sativa L.). FRONTIERS IN PLANT SCIENCE 2015; 6:1115. [PMID: 26734025 PMCID: PMC4679862 DOI: 10.3389/fpls.2015.01115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 11/25/2015] [Indexed: 05/24/2023]
Abstract
Drought and high salinity are two major abiotic factors that restrict the productivity of alfalfa. By application of the Agrobacterium-mediated transformation method, an oxidative responsive gene, CsALDH12A1, from the desert grass Cleistogenes songorica together with the bar gene associated with herbicide resistance, were co-transformed into alfalfa (Medicago sativa L.). From the all 90 transformants, 16 were positive as screened by spraying 1 mL L(-1) 10% Basta solution and molecularly diagnosis using PCR. Real-time PCR analysis indicated that drought and salt stress induced high CsALDH expression in the leaves of the transgenic plants. The CsALDH expression levels under drought (15 d) and salt stress (200 mM NaCl) were 6.11 and 6.87 times higher than in the control plants, respectively. In comparison to the WT plants, no abnormal phenotypes were observed among the transgenic plants, which showed significant enhancement of tolerance to 15 d of drought and 10 d of salinity treatment. Evaluation of the physiological and biochemical indices during drought and salt stress of the transgenic plants revealed relatively lower Na(+) content and higher K(+) content in the leaves relative to the WT plants, a reduction of toxic on effects and maintenance of osmotic adjustment. In addition, the transgenic plants could maintain a higher relative water content level, higher shoot biomass, fewer changes in the photosystem, decreased membrane injury, and a lower level of osmotic stress. These results indicate that the co-expression of the introduced bar and CsALDH genes enhanced the herbicide, drought and salt tolerance of alfalfa and therefore can potentially be used as a novel genetic resource for the future breeding programs to develop new cultivars.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jiyu Zhang
- State Key Laborotary of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
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Zhao C, Wang D, Feng B, Gou M, Liu X, Li Q. Identification and characterization of aldehyde dehydrogenase 9 from Lampetra japonica and its protective role against cytotoxicity. Comp Biochem Physiol B Biochem Mol Biol 2015; 187:102-9. [DOI: 10.1016/j.cbpb.2015.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/16/2014] [Accepted: 05/07/2015] [Indexed: 11/16/2022]
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Končitíková R, Vigouroux A, Kopečná M, Andree T, Bartoš J, Šebela M, Moréra S, Kopečný D. Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7. Biochem J 2015; 468:109-23. [PMID: 25734422 DOI: 10.1042/bj20150009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aldehyde dehydrogenases (ALDHs) are responsible for oxidation of biogenic aldehyde intermediates as well as for cell detoxification of aldehydes generated during lipid peroxidation. So far, 13 ALDH families have been described in plants. In the present study, we provide a detailed biochemical characterization of plant ALDH2 and ALDH7 families by analysing maize and pea ALDH7 (ZmALDH7 and PsALDH7) and four maize cytosolic ALDH(cALDH)2 isoforms RF2C, RF2D, RF2E and RF2F [the first maize ALDH2 was discovered as a fertility restorer (RF2A)]. We report the crystal structures of ZmALDH7, RF2C and RF2F at high resolution. The ZmALDH7 structure shows that the three conserved residues Glu(120), Arg(300) and Thr(302) in the ALDH7 family are located in the substrate-binding site and are specific to this family. Our kinetic analysis demonstrates that α-aminoadipic semialdehyde, a lysine catabolism intermediate, is the preferred substrate for plant ALDH7. In contrast, aromatic aldehydes including benzaldehyde, anisaldehyde, cinnamaldehyde, coniferaldehyde and sinapaldehyde are the best substrates for cALDH2. In line with these results, the crystal structures of RF2C and RF2F reveal that their substrate-binding sites are similar and are formed by an aromatic cluster mainly composed of phenylalanine residues and several nonpolar residues. Gene expression studies indicate that the RF2C gene, which is strongly expressed in all organs, appears essential, suggesting that the crucial role of the enzyme would certainly be linked to the cell wall formation using aldehydes from phenylpropanoid pathway as substrates. Finally, plant ALDH7 may significantly contribute to osmoprotection because it oxidizes several aminoaldehydes leading to products known as osmolytes.
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Affiliation(s)
- Radka Končitíková
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Armelle Vigouroux
- ‡Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Martina Kopečná
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Tomáš Andree
- †Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Jan Bartoš
- §Centre of Plant Structural and Functional Genomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Marek Šebela
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Solange Moréra
- ‡Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - David Kopečný
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
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Muthamilarasan M, Prasad M. Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015. [PMID: 25239219 DOI: 10.1007/s00122-014-2399-325239219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.
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Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
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Muthamilarasan M, Prasad M. Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1-14. [PMID: 25239219 DOI: 10.1007/s00122-014-2399-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 05/18/2023]
Abstract
Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.
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Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
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