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Yin W, Huang Z, Zhong Q, Tang L, Wu R, Li S, Mao Y, Zhu X, Wang C, Rao Y, Wang Y. The Mining of Genetic Loci and the Analysis of Candidate Genes to Identify the Physical and Chemical Markers of Anti-Senescence in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3812. [PMID: 38005709 PMCID: PMC10674301 DOI: 10.3390/plants12223812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
Premature senescence is a common occurrence in rice production, and seriously affects rice plants' nutrient utilization and growth. A total of 120 recombinant inbred lines (RILs) were obtained from successive self-crossing of F12 generations derived from Huazhan and Nekken2. The superoxide dismutase (SOD) activity, malondialdehyde (MDA), content and catalase (CAT) activity related to the anti-senescence traits and enzyme activity index of rice were measured for QTL mapping using 4858 SNPs. Thirteen QTLs related to anti-senescence were found, among which the highest LOD score was 5.70. Eighteen anti-senescence-related genes were found in these regions, and ten of them differed significantly between the parents. It was inferred that LOC_Os01g61500, LOC_Os01g61810, and LOC_Os04g40130 became involved in the regulation of the anti-senescence molecular network upon upregulation of their expression levels. The identified anti-senescence-related QTLs and candidate genes provide a genetic basis for further research on the mechanism of the molecular network that regulates premature senescence.
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Affiliation(s)
- Wenjing Yin
- National Key Laboratory of Rice Biological Breeding, China National Rice Research Institute, Hangzhou 310006, China; (W.Y.); (S.L.); (Y.M.); (X.Z.)
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Zhao Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Qianqian Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Luyao Tang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Richeng Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Sanfeng Li
- National Key Laboratory of Rice Biological Breeding, China National Rice Research Institute, Hangzhou 310006, China; (W.Y.); (S.L.); (Y.M.); (X.Z.)
| | - Yijian Mao
- National Key Laboratory of Rice Biological Breeding, China National Rice Research Institute, Hangzhou 310006, China; (W.Y.); (S.L.); (Y.M.); (X.Z.)
| | - Xudong Zhu
- National Key Laboratory of Rice Biological Breeding, China National Rice Research Institute, Hangzhou 310006, China; (W.Y.); (S.L.); (Y.M.); (X.Z.)
| | - Changchun Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (Z.H.); (Q.Z.); (L.T.); (R.W.)
| | - Yuexing Wang
- National Key Laboratory of Rice Biological Breeding, China National Rice Research Institute, Hangzhou 310006, China; (W.Y.); (S.L.); (Y.M.); (X.Z.)
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Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut. Int J Mol Sci 2021; 23:ijms23010246. [PMID: 35008672 PMCID: PMC8745729 DOI: 10.3390/ijms23010246] [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: 11/19/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/18/2022] Open
Abstract
Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response.
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Lin Y, Liu G, Xue Y, Guo X, Luo J, Pan Y, Chen K, Tian J, Liang C. Functional Characterization of Aluminum (Al)-Responsive Membrane-Bound NAC Transcription Factors in Soybean Roots. Int J Mol Sci 2021; 22:12854. [PMID: 34884659 PMCID: PMC8657865 DOI: 10.3390/ijms222312854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
The membrane-bound NAC transcription (NTL) factors have been demonstrated to participate in the regulation of plant development and the responses to multiple environmental stresses. This study is aimed to functionally characterize soybean NTL transcription factors in response to Al-toxicity, which is largely uncharacterized. The qRT-PCR assays in the present study found that thirteen out of fifteen GmNTL genes in the soybean genome were up-regulated by Al toxicity. However, among the Al-up-regulated GmNTLs selected from six duplicate gene pairs, only overexpressing GmNTL1, GmNTL4, and GmNTL10 could confer Arabidopsis Al resistance. Further comprehensive functional characterization of GmNTL4 showed that the expression of this gene in response to Al stress depended on root tissues, as well as the Al concentration and period of Al treatment. Overexpression of GmNTL4 conferred Al tolerance of transgenic Arabidopsis in long-term (48 and 72 h) Al treatments. Moreover, RNA-seq assay identified 517 DEGs regulated by GmNTL4 in Arabidopsis responsive to Al stress, which included MATEs, ALMTs, PMEs, and XTHs. These results suggest that the function of GmNTLs in Al responses is divergent, and GmNTL4 might confer Al resistance partially by regulating the expression of genes involved in organic acid efflux and cell wall modification.
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Affiliation(s)
- Yan Lin
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Guoxuan Liu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Yingbing Xue
- Department of Resources and Environmental Sciences, College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China;
| | - Xueqiong Guo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Jikai Luo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Yaoliang Pan
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Kang Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
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Singh CK, Singh D, Taunk J, Chaudhary P, Tomar RSS, Chandra S, Singh D, Pal M, Konjengbam NS, Singh MP, Singh Sengar R, Sarker A. Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:693630. [PMID: 34531881 PMCID: PMC8438445 DOI: 10.3389/fpls.2021.693630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/30/2021] [Indexed: 05/28/2023]
Abstract
Aluminium stress causes plant growth retardation and engenders productivity loss under acidic soil conditions. This study accentuates morpho-physiological and molecular bases of aluminium (Al) tolerance within and between wild (ILWL-15) and cultivated (L-4602 and BM-4) lentil species. Morpho-physiological studies revealed better cyto-morphology of tolerant genotypes over sensitive under Al3+ stress conditions. Mitotic lesions were observed in root cells under these conditions. Transcriptome analysis under Al3+ stress revealed 30,158 specifically up-regulated genes in different comparison groups showing contigs between 15,305 and 18,861 bp. In tolerant genotypes, top up-regulated differentially expressed genes (DEGs) were found to be involved in organic acid synthesis and exudation, production of antioxidants, callose synthesis, protein degradation, and phytohormone- and calcium-mediated signalling under stress conditions. DEGs associated with epigenetic regulation and Al3+ sequestration inside vacuole were specifically upregulated in wild and cultivars, respectively. Based on assembled unigenes, an average of 6,645.7 simple sequence repeats (SSRs) and 14,953.7 high-quality single nucleotide polymorphisms (SNPs) were spotted. By quantitative real-time polymerase chain reaction (qRT-PCR), 12 selected genes were validated. Gene ontology (GO) annotation revealed a total of 8,757 GO terms in three categories, viz., molecular, biological, and cellular processes. Kyoto Encyclopaedia of Genes and Genomes pathway scanning also revealed another probable pathway pertaining to metacaspase-1,-4, and -9 for programmed cell death under Al-stress conditions. This investigation reveals key inter- and intraspecies metabolic pathways associated with Al-stress tolerance in lentil species that can be utilised in designing future breeding programmes to improve lentil and related species towards Al3+ stress.
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Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Dharmendra Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Shivani Chandra
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University—Imphal, Umiam, India
| | - M. Premjit Singh
- College of Agriculture, Central Agricultural University—Imphal, Iroisemba, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut, India
| | - Ashutosh Sarker
- International Center for Agriculture Research in the Dry Areas, New Delhi, India
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Xiao D, Li X, Zhou YY, Wei L, Keovongkod C, He H, Zhan J, Wang AQ, He LF. Transcriptome analysis reveals significant difference in gene expression and pathways between two peanut cultivars under Al stress. Gene 2021; 781:145535. [PMID: 33631240 DOI: 10.1016/j.gene.2021.145535] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 12/31/2022]
Abstract
Aluminum (Al) toxicity is an important factor in limiting peanut growth on acidic soil. The molecular mechanisms underlying peanut responses to Al stress are largely unknown. In this study, we performed transcriptome analysis of the root tips (0-1 cm) of peanut cultivar ZH2 (Al-sensitive) and 99-1507 (Al-tolerant) respectively. Root tips of peanuts that treated with 100 μM Al for 8 h and 24 h were analyzed by RNA-Seq, and a total of 8,587 differentially expressed genes (DEGs) were identified. GO and KEGG pathway analysis excavated a group of important Al-responsive genes related to organic acid transport, metal cation transport, transcription regulation and programmed cell death (PCD). These homologs were promising targets to modulate Al tolerance in peanuts. It was found that the rapid transcriptomic response to Al stress in 99-1507 helped to activate effective Al tolerance mechanisms. Protein and protein interaction analysis indicated that MAPK signal transduction played important roles in the early response to Al stress in peanuts. Moreover, weighted correlation network analysis (WGCNA) identified a predicted EIL (EIN3-like) gene with greatly increased expression as an Al-associated gene, and revealed a link between ethylene signaling transduction and Al resistance related genes in peanut, which suggested the enhanced signal transduction mediated the rapid transcriptomic responses. Our results revealed key pathways and genes associated with Al stress, and improved the understanding of Al response in peanut.
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Affiliation(s)
- Dong Xiao
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China; Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, PR China.
| | - Xia Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Yun-Yi Zhou
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Li Wei
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Chanthaphoone Keovongkod
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Huyi He
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, PR China
| | - Jie Zhan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China; Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, PR China
| | - Ai-Qin Wang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China; Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, PR China
| | - Long-Fei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China; Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, PR China.
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Barros VA, Chandnani R, de Sousa SM, Maciel LS, Tokizawa M, Guimaraes CT, Magalhaes JV, Kochian LV. Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils. FRONTIERS IN PLANT SCIENCE 2020; 11:565339. [PMID: 33281841 PMCID: PMC7688899 DOI: 10.3389/fpls.2020.565339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 06/01/2023]
Abstract
Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.
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Affiliation(s)
- Vanessa A. Barros
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Laiane S. Maciel
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mutsutomo Tokizawa
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Jurandir V. Magalhaes
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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Hernandez Y, Goswami K, Sanan‐Mishra N. Stress induced dynamic adjustment of conserved miR164:NAC module. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:134-151. [PMID: 37283725 PMCID: PMC10168063 DOI: 10.1002/pei3.10027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 06/08/2023]
Abstract
Aims including the rationale Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood. Methods In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets. Key results It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (-2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co-expression assay validated that gma-miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC-TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions. Main conclusion Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC-TF module may play an important role in determining the adaptive response of plants to stress.
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Affiliation(s)
- Yuniet Hernandez
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Kavita Goswami
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Neeti Sanan‐Mishra
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
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Han R, Wei Y, Xie Y, Liu L, Jiang C, Yu Y. Quantitative phosphoproteomic analysis provides insights into the aluminum-responsiveness of Tamba black soybean. PLoS One 2020; 15:e0237845. [PMID: 32813721 PMCID: PMC7437914 DOI: 10.1371/journal.pone.0237845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/04/2020] [Indexed: 01/01/2023] Open
Abstract
Aluminum (Al3+) toxicity is one of the most important limitations to agricultural production worldwide. The overall response of plants to Al3+ stress has been documented, but the contribution of protein phosphorylation to Al3+ detoxicity and tolerance in plants is unclear. Using a combination of tandem mass tag (TMT) labeling, immobilized metal affinity chromatography (IMAC) enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS), Al3+-induced phosphoproteomic changes in roots of Tamba black soybean (TBS) were investigated in this study. The Data collected in this study are available via ProteomeXchange with the identifier PXD019807. After the Al3+ treatment, 189 proteins harboring 278 phosphosites were significantly changed (fold change > 1.2 or < 0.83, p < 0.05), with 88 upregulated, 96 downregulated and 5 up-/downregulated. Enrichment and protein interaction analyses revealed that differentially phosphorylated proteins (DPPs) under the Al3+ treatment were mainly related to G-protein-mediated signaling, transcription and translation, transporters and carbohydrate metabolism. Particularly, DPPs associated with root growth inhibition or citric acid synthesis were identified. The results of this study provide novel insights into the molecular mechanisms of TBS post-translational modifications in response to Al3+ stress.
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Affiliation(s)
- Rongrong Han
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, China
| | - Yunmin Wei
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, China
| | - Yonghong Xie
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, China
| | - Lusheng Liu
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, China
| | - Caode Jiang
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, China
| | - Yongxiong Yu
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, China
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Apriana A, Sisharmini A, Aswidinnoor H, Trijatmiko KR, Sudarsono S. Promoter deletion analysis reveals root-specific expression of the alkenal reductase gene (OsAER1) in Oryza sativa. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:376-391. [PMID: 32172746 DOI: 10.1071/fp18237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/12/2019] [Indexed: 06/10/2023]
Abstract
Root-specific promoters are useful in plant genetic engineering, primarily to improve water and nutrient absorption. The aim of this study was to clone and characterise the promoter of the Oryza sativa L. alkenal reductase (OsAER1) gene encoding 2-alkenal reductase, an NADPH-dependent oxidoreductase. Expression analysis using quantitative real-time PCR confirmed the root-specific expression of the OsAER1 gene. Subsequently, a 3082-bp fragment of the OsAER1 promoter was isolated from a local Indonesian rice cultivar, Awan Kuning. Sequencing and further nucleotide sequence analysis of the 3082-bp promoter fragment (PA-5) revealed the presence of at least 10 root-specific cis-regulatory elements putatively responsible for OsAER1 root-specific expression. Using the 3082-bp promoter fragment to drive the expression of the GUS reporter transgene confirmed that the OsAER1 promoter is root-specific. Further, the analysis indicated that OsAER1 promoter activity was absent in leaves, petioles and shoots during sprouting, vegetative, booting and generative stages of rice development. In contrast, the promoter activity was present in anthers and aleurone layers of immature seeds 7-20 days after anthesis. Moreover, there was no promoter activity observed in the aleurone layers of mature seeds. The OsAER1 promoter activity is induced by Al-toxicity, NaCl and submergence stresses, indicating the OsAER1 promoter activity is induced by those stresses. Exogenous treatments of transgenic plants carrying the PA-5 promoter construct with abscisic acid and indoleacetic acid also induced expression of the GUS reporter transgene, indicating the role of plant growth regulators in controlling OsAER1 promoter activity. Promoter deletion analysis was conducted to identify the cis-acting elements of the promoter responsible for controlling root-specific expression. The GUS reporter gene was fused with various deletion fragments of the OsAER1 promoter and the resulting constructs were transformed in rice plants to generate transgenic plants. The results of this analysis indicated that cis-acting elements controlling root-specific expression are located between -1562 to -1026bp of the OsAER1 CDS. Here we discusses the results of the conducted analyses, the possible role of OsAER1 in rice growth and development, possible contributions and the potential usage of these findings in future plant research.
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Affiliation(s)
- Aniversari Apriana
- PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jalan Raya Ciampea, Bogor, Indonesia; and Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jalan Tentara Pelajar 3A, Bogor, Indonesia
| | - Atmitri Sisharmini
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jalan Tentara Pelajar 3A, Bogor, Indonesia
| | - Hajrial Aswidinnoor
- PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jalan Raya Ciampea, Bogor, Indonesia
| | - Kurniawan R Trijatmiko
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jalan Tentara Pelajar 3A, Bogor, Indonesia; and Corresponding authors. Emails: ;
| | - Sudarsono Sudarsono
- PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jalan Raya Ciampea, Bogor, Indonesia; and Corresponding authors. Emails: ;
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Krasnov GS, Dmitriev AA, Zyablitsin AV, Rozhmina TA, Zhuchenko AA, Kezimana P, Snezhkina AV, Fedorova MS, Novakovskiy RO, Pushkova EN, Povkhova LV, Bolsheva NL, Kudryavtseva AV, Melnikova NV. Aluminum Responsive Genes in Flax ( Linum usitatissimum L.). BIOMED RESEARCH INTERNATIONAL 2019; 2019:5023125. [PMID: 30941364 PMCID: PMC6421055 DOI: 10.1155/2019/5023125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/22/2018] [Accepted: 12/12/2018] [Indexed: 01/08/2023]
Abstract
Flax (Linum usitatissimum L.) is a multipurpose crop which is used for the production of textile, oils, composite materials, pharmaceuticals, etc. Soil acidity results in a loss of seed and fiber production of flax, and aluminum toxicity is a major factor that depresses plant growth and development in acid conditions. In the present work, we evaluated gene expression alterations in four flax genotypes with diverse tolerance to aluminum exposure. Using RNA-Seq approach, we revealed genes that are differentially expressed under aluminum stress in resistant (Hermes, TMP1919) and sensitive (Lira, Orshanskiy) cultivars and selectively confirmed the identified alterations using qPCR. To search for differences in response to aluminum between resistant and sensitive genotypes, we developed the scoring that allowed us to suggest the involvement of MADS-box and NAC transcription factors regulating plant growth and development and enzymes participating in cell wall modifications in aluminum tolerance in flax. Using Gene Ontology (GO) enrichment analysis, we revealed that glutathione metabolism, oxidoreductase, and transmembrane transporter activities are the most affected by the studied stress in flax. Thus, we identified genes that are involved in aluminum response in resistant and sensitive genotypes and suggested genes that contribute to flax tolerance to the aluminum stress.
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Affiliation(s)
- George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander V. Zyablitsin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow 115598, Russia
| | - Parfait Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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11
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Kundu A, Das S, Basu S, Kobayashi Y, Kobayashi Y, Koyama H, Ganesan M. GhSTOP1, a C2H2 type zinc finger transcription factor is essential for aluminum and proton stress tolerance and lateral root initiation in cotton. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:35-44. [PMID: 30098101 DOI: 10.1111/plb.12895] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/04/2018] [Indexed: 05/25/2023]
Abstract
Aluminum (Al) and proton (H+ ) ions are major acid soil stress factors deleteriously affecting plant root growth and crop yield. In our preliminary studies, cotton (Gossypium hirsutum L.) seedlings displayed very sensitive phenotypes to Al and H+ rhizotoxicities. Based on previous Arabidopsis results, we aimed to characterise the Al stress responsive Sensitive to Proton rhizotoxicity 1 (GhSTOP1) transcription system in cotton using RNAi-mediated down-regulation. With the help of seed embryo apex explants, we developed transgenic cotton plants overexpressing a GhSTOP1-RNAi cassette with NPTII selection. Kanamycin-tolerant T1 seedlings were further considered for Al and H+ stress tolerance studies. Down-regulation of the GhSTOP1 increased sensitivity to Al and proton rhizotoxicities, and root growth was significantly reduced in RNAi lines. The expression profile of GhALMT1 (Aluminum-activated Malate Transporter 1), GhMATE (Multidrug and Toxic Compound Extrusion), GhALS3 (Aluminium Sensitive 3) and key genes involved in the GABA shunt were down-regulated in the transgenic RNAi lines. Additionally, the lateral root initiation process was delayed and expression of GhNAC1, which is involved in lateral roots, was also suppressed in transgenic lines. Besides, overexpression of GhSTOP1 in Arabidopsis accelerated root growth and AtMATE and AtALMT1 expression under Al stress conditions. These analyses indicate that GhSTOP1 is essential for the expression of several genes which are necessary for acid soil tolerance mechanisms and lateral root initiation.
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Affiliation(s)
- A Kundu
- Department of Life Sciences, Presidency University Kolkata, West Bengal, India
| | - S Das
- Department of Life Sciences, Presidency University Kolkata, West Bengal, India
| | - S Basu
- Department of Life Sciences, Presidency University Kolkata, West Bengal, India
| | - Y Kobayashi
- Department of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Y Kobayashi
- Department of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - H Koyama
- Department of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - M Ganesan
- Department of Life Sciences, Presidency University Kolkata, West Bengal, India
- Department of Applied Biological Sciences, Gifu University, Gifu, Japan
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12
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Jing L, Li J, Song Y, Zhang J, Chen Q, Han Q. Characterization of a Potential Ripening Regulator, SlNAC3, from Solanum Lycopersicum. Open Life Sci 2018; 13:518-526. [PMID: 33817122 PMCID: PMC7874718 DOI: 10.1515/biol-2018-0062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022] Open
Abstract
NAC (for NAM, ATAF1-2, and CUC2) proteins are one of the largest transcription factor families in plants. They have various functions and are closely related to developmental processes of fruits. Tomato (Solanum lycopersicum) is a model plant for studies of fruit growth patterns. In this study, the functional characteristics and action mechanisms of a new NAC-type transcription factor, SlNAC3 (SGN-U568609), were examined to determine its role in tomato development and ripening. The SlNAC3 protein was produced by prokaryotic expression and used to immunize New Zealand white rabbits to obtain a specific polyclonal antibody against SlNAC3. By co-immunoprecipitation and MALDI-TOF-MS assays, we showed that there was an interaction between the SlNAC3 protein and Polygalacturonase-2 (PG-2), which is related to the ripening and softening of fruit. Chromatin immunoprecipitation assays revealed the genome of the highly stress-tolerant Solanum pennellii chromosome 10 (sequence ID, HG975449.1), further demonstrating that SlNAC3 is a negative regulator of drought and salinity stress resistance in tomato, consistent with previous reports. These results indicate that SlNAC3 is not only involved in abiotic stress, but also plays a necessary role in mediating tomato ripening.
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Affiliation(s)
- Le Jing
- Engineering Research Center for Molecular Diagnosis, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming650500, Yunnan, People’s Republic of China
| | - Jie Li
- Engineering Research Center for Molecular Diagnosis, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming650500, Yunnan, People’s Republic of China
| | - Yuzhu Song
- Engineering Research Center for Molecular Diagnosis, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming650500, Yunnan, People’s Republic of China
| | - Jinyang Zhang
- Engineering Research Center for Molecular Diagnosis, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming650500, Yunnan, People’s Republic of China
| | - Qiang Chen
- Engineering Research Center for Molecular Diagnosis, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming650500, Yunnan, People’s Republic of China
| | - Qinqin Han
- Engineering Research Center for Molecular Diagnosis, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming650500, Yunnan, People’s Republic of China
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