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Zeng BZ, Zhou XT, Gou HM, Che LL, Lu SX, Yang JB, Cheng YJ, Liang GP, Mao J. Molecular Evolution of SNAREs in Vitis vinifera and Expression Analysis under Phytohormones and Abiotic Stress. Int J Mol Sci 2024; 25:5984. [PMID: 38892171 PMCID: PMC11173047 DOI: 10.3390/ijms25115984] [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: 04/21/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
SNARE proteins (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) play a key role in mediating a variety of plant biological processes. Currently, the function of the SNARE gene family in phytohormonal and abiotic stress treatments in grapevine is currently unknown, making it worthwhile to characterize and analyze the function and expression of this family in grapevine. In the present study, 52 VvSNARE genes were identified and predominantly distributed on 18 chromosomes. Secondary structures showed that the VvSNARE genes family irregular random coils and α-helices. The promoter regions of the VvSNARE genes were enriched for light-, abiotic-stress-, and hormone-responsive elements. Intraspecific collinearity analysis identified 10 pairs collinear genes within the VvSNARE family and unveiled a greater number of collinear genes between grapevine and apple, as well as Arabidopsis thaliana, but less associations with Oryza sativa. Quantitative real-time PCR (qRT-PCR) analyses showed that the VvSNARE genes have response to treatments with ABA, NaCl, PEG, and 4 °C. Notably, VvSNARE2, VvSNARE14, VvSNARE15, and VvSNARE17 showed up-regulation in response to ABA treatment. VvSNARE2, VvSNARE15, VvSNARE18, VvSNARE19, VvSNARE20, VvSNARE24, VvSNARE25, and VvSNARE29 exhibited significant up-regulation when exposed to NaCl treatment. The PEG treatment led to significant down-regulation of VvSNARE1, VvSNARE8, VvSNARE23, VvSNARE25, VvSNARE26, VvSNARE31, and VvSNARE49 gene expression. The expression levels of VvSNARE37, VvSNARE44, and VvSNARE46 were significantly enhanced after exposure to 4 °C treatment. Furthermore, subcellular localization assays certified that VvSNARE37, VvSNARE44, and VvSNARE46 were specifically localized at the cell membrane. Overall, this study showed the critical role of the VvSNARE genes family in the abiotic stress response of grapevines, thereby providing novel candidate genes such as VvSNARE37, VvSNARE44, and VvSNARE46 for further exploration in grapevine stress tolerance research.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (B.-z.Z.); (X.-t.Z.); (H.-m.G.); (L.-l.C.); (S.-x.L.); (J.-b.Y.); (Y.-j.C.); (G.-p.L.)
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2
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Li Z, Li Y, Geng L, Wang J, Ouyang Y, Li J. Genome-wide methylation, transcriptome and characteristic metabolites reveal the balance between diosgenin and brassinosteroids in Dioscorea zingiberensis. HORTICULTURE RESEARCH 2024; 11:uhae056. [PMID: 38659444 PMCID: PMC11040209 DOI: 10.1093/hr/uhae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 04/26/2024]
Abstract
Diosgenin (DG) is a bioactive metabolite isolated from Dioscorea species, renowned for its medicinal properties. Brassinosteroids (BRs) are a class of crucial plant steroidal hormones. Cholesterol and campesterol are important intermediates of DG and BR biosynthesis, respectively. DG and BRs are structurally similar components; however, the regulatory network and metabolic interplays have not been fully elucidated. In an effort to decode these complex networks, we conducted a comprehensive study integrating genome-wide methylation, transcriptome and characteristic metabolite data from Dioscorea zingiberensis. Leveraging these data, we were able to construct a comprehensive regulatory network linking DG and BRs. Mass spectrometry results enabled us to clarify the alterations in cholesterol, campesterol, diosgenin, and castasterone (one of the major active BRs). The DG content decreased by 27.72% at 6 h after brassinolide treatment, whereas the content increased by 85.34% at 6 h after brassinazole treatment. Moreover, we pinpointed DG/BR-related genes, such as CASs, CYP90s, and B3-ARFs, implicated in the metabolic pathways of DG and BRs. Moreover, CASs and CYP90s exhibit hypomethylation, which is closely related to their high transcription. These findings provide robust evidence for the homeostasis between DG and BRs. In conclusion, our research revealed the existence of a balance between DG and BRs in D. zingiberensis. Furthermore, our work not only provides new insights into the relationship between the two pathways but also offers a fresh perspective on the functions of secondary metabolites.
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Affiliation(s)
- Zihao Li
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yi Li
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Luyu Geng
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiachen Wang
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaru Li
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
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3
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Hawk T, Zadegan SB, Ozdemir S, Li P, Pantalone V, Staton M, Hewezi T. Conceptual Framework of Epigenetic Analyses of Plant Responses to Sedentary Endoparasitic Nematodes. Methods Mol Biol 2024; 2756:327-341. [PMID: 38427303 DOI: 10.1007/978-1-0716-3638-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Epigenetic modifications including miRNA regulation, DNA methylation, and histone modifications play fundamental roles in establishing the interactions between host plants and parasitic nematodes. Over the past decade, an increasing number of studies revealed the key functions of various components of the plant epigenome in the regulation of gene expression and shaping plant responses to nematode infection. In this chapter, we provide a conceptual framework for methods used to investigate epigenetic regulation during plant-nematode interactions. We focus specifically on current and emerging methods used to study miRNA regulation and function. We also highlight various methods and analytical tools used to profile DNA methylation patterns and histone modification marks at the genome level. Our intention is simply to explain the advantages of various methods and how to overcome some limitations. With rapid development of single-cell sequencing technology and genome editing, advanced and new methodologies are expected to emerge in the near future to further improve our understanding of epigenetic regulation and function during plant-nematode interactions.
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Affiliation(s)
- Tracy Hawk
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | | | - Selin Ozdemir
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Peitong Li
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Meg Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
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4
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Yung WS, Huang C, Li MW, Lam HM. Changes in epigenetic features in legumes under abiotic stresses. THE PLANT GENOME 2023; 16:e20237. [PMID: 35730915 DOI: 10.1002/tpg2.20237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress-resilient crops is crucial for ensuring global food security. Because of their nitrogen-fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next-generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.
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Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Cheng Huang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, P.R. China
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
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5
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Kumar S, Seem K, Kumar S, Singh A, Krishnan SG, Mohapatra T. DNA methylome analysis provides insights into gene regulatory mechanism for better performance of rice under fluctuating environmental conditions: epigenomics of adaptive plasticity. PLANTA 2023; 259:4. [PMID: 37993704 DOI: 10.1007/s00425-023-04272-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
MAIN CONCLUSION Roots play an important role in adaptive plasticity of rice under dry/direct-sown conditions. However, hypomethylation of genes in leaves (resulting in up-regulated expression) complements the adaptive plasticity of Nagina-22 under DSR conditions. Rice is generally cultivated by transplanting which requires plenty of water for irrigation. Such a practice makes rice cultivation a challenging task under global climate change and reducing water availability. However, dry-seeded/direct-sown rice (DSR) has emerged as a resource-saving alternative to transplanted rice (TPR). Though some of the well-adapted local cultivars are used for DSR, only limited success has been achieved in developing DSR varieties mainly because of a limited knowledge of adaptability of rice under fluctuating environmental conditions. Based on better morpho-physiological and agronomic performance of Nagina-22 (N-22) under DSR conditions, N-22 and IR-64 were grown by transplanting and direct-sowing and used for whole genome methylome analysis to unravel the epigenetic basis of adaptive plasticity of rice. Comparative methylome and transcriptome analyses indicated a large number (4078) of genes regulated through DNA methylation/demethylation in N-22 under DSR conditions. Gene × environment interactions play important roles in adaptive plasticity of rice under direct-sown conditions. While genes for pectinesterase, LRK10, C2H2 zinc-finger protein, splicing factor, transposable elements, and some of the unannotated proteins were hypermethylated, the genes for regulation of transcription, protein phosphorylation, etc. were hypomethylated in CG context in the root of N-22, which played important roles in providing adaptive plasticity to N-22 under DSR conditions. Hypomethylation leading to up-regulation of gene expression in the leaf complements the adaptive plasticity of N-22 under DSR conditions. Moreover, differential post-translational modification of proteins and chromatin assembly/disassembly through DNA methylation in CHG context modulate adaptive plasticity of N-22. These findings would help developing DSR cultivars for increased water-productivity and ecological efficiency.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Archana Singh
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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6
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Fang C, Yang M, Tang Y, Zhang L, Zhao H, Ni H, Chen Q, Meng F, Jiang J. Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean. Proc Natl Acad Sci U S A 2023; 120:e2303836120. [PMID: 37871213 PMCID: PMC10622917 DOI: 10.1073/pnas.2303836120] [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: 03/07/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase-hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9-mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation of cis-regulatory elements (CREs) within the ACRs can change the balance of the expression level and/or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
| | - Mingyu Yang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Yuecheng Tang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Ling Zhang
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun130033, China
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
| | - Hejia Ni
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Qingshan Chen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Fanli Meng
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
- Department of Horticulture, Michigan State University, East Lansing, MI48824
- Michigan State University AgBioResearch, East Lansing, MI48824
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7
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Dwivedi SL, Quiroz LF, Reddy ASN, Spillane C, Ortiz R. Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs. Int J Mol Sci 2023; 24:15205. [PMID: 37894886 PMCID: PMC10607462 DOI: 10.3390/ijms242015205] [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: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, SE, Sweden
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8
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Forte FP, Malinowska M, Nagy I, Schmid J, Dijkwel P, Hume DE, Johnson RD, Simpson WR, Asp T. Methylome changes in Lolium perenne associated with long-term colonisation by the endophytic fungus Epichloë sp. LpTG-3 strain AR37. FRONTIERS IN PLANT SCIENCE 2023; 14:1258100. [PMID: 37810388 PMCID: PMC10557135 DOI: 10.3389/fpls.2023.1258100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023]
Abstract
Epichloë spp. often form mutualistic interactions with cool-season grasses, such as Lolium perenne. However, the molecular mechanisms underlying this interaction remain poorly understood. In this study, we employed reduced representation bisulfite sequencing method (epiGBS) to investigate the impact of the Epichloë sp. LpTG-3 strain AR37 on the methylome of L. perenne across multiple grass generations and under drought stress conditions. Our results showed that the presence of the endophyte leads to a decrease in DNA methylation across genomic features, with differentially methylated regions primarily located in intergenic regions and CHH contexts. The presence of the endophyte was consistently associated with hypomethylation in plants across generations. This research sheds new light on the molecular mechanisms governing the mutualistic interaction between Epichloë sp. LpTG-3 strain AR37 and L. perenne. It underscores the role of methylation changes associated with endophyte infection and suggests that the observed global DNA hypomethylation in L. perenne may be influenced by factors such as the duration of the endophyte-plant association and the accumulation of genetic and epigenetic changes over time.
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Affiliation(s)
- Flavia Pilar Forte
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
| | - Marta Malinowska
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
| | - Jan Schmid
- Ferguson Street Laboratories, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Paul Dijkwel
- Ferguson Street Laboratories, Palmerston North, New Zealand
| | - David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
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9
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Li M, Ou M, He X, Ye H, Ma J, Liu H, Yang H, Zhao P. DNA methylation role in subgenome expression dominance of Juglans regia and its wild relative J. mandshurica. PLANT PHYSIOLOGY 2023; 193:1313-1329. [PMID: 37403190 DOI: 10.1093/plphys/kiad394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023]
Abstract
Subgenome expression dominance plays a crucial role in the environmental adaptation of polyploids. However, the epigenetic molecular mechanism underlying this process has not been thoroughly investigated, particularly in perennial woody plants. Persian walnut (Juglans regia) and its wild relative, Manchurian walnut (Juglans mandshurica), are woody plants of great economic importance and are both paleopolyploids that have undergone whole-genome duplication events. In this study, we explored the characteristics of subgenome expression dominance in these 2 Juglans species and examined its epigenetic basis. We divided their genomes into dominant subgenome (DS) and submissive subgenome (SS) and found that the DS-specific genes might play critical roles in biotic stress response or pathogen defense. We comprehensively elucidated the characteristics of biased gene expression, asymmetric DNA methylation, transposable elements (TEs), and alternative splicing (AS) events of homoeologous gene pairs between subgenomes. The results showed that biased expression genes (BEGs) in 2 Juglans species were mainly related to external stimuli response, while non-BEGs were related to complexes that might be involved in signal transduction. DS genes had higher expression and more AS events while having less DNA methylation and TEs than homoeologous genes from the SS in the 2 Juglans species. Further studies showed that DNA methylation might contribute to the biased expression of gene pairs by modifying LTR/TIR/nonTIR TEs and improving the AS efficiency of corresponding precursor mRNAs in a particular context. Our study contributes to understanding the epigenetic basis of subgenome expression dominance and the environmental adaptation of perennial woody plants.
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Affiliation(s)
- Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Mengwei Ou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xiaozhou He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huijuan Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
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10
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Vigneaud J, Kohler A, Sow MD, Delaunay A, Fauchery L, Guinet F, Daviaud C, Barry KW, Keymanesh K, Johnson J, Singan V, Grigoriev I, Fichot R, Conde D, Perales M, Tost J, Martin FM, Allona I, Strauss SH, Veneault-Fourrey C, Maury S. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. THE NEW PHYTOLOGIST 2023; 238:2561-2577. [PMID: 36807327 DOI: 10.1111/nph.18734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.
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Affiliation(s)
- Julien Vigneaud
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Annegret Kohler
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Mamadou Dia Sow
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Laure Fauchery
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Frederic Guinet
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Kerrie W Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Francis M Martin
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
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11
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Piya S, Pantalone V, Zadegan SB, Shipp S, Lakhssassi N, Knizia D, Krishnan HB, Meksem K, Hewezi T. Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development. MOLECULAR PLANT PATHOLOGY 2023; 24:628-636. [PMID: 36975024 DOI: 10.1111/mpp.13327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 05/18/2023]
Abstract
Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | | | - Sarah Shipp
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, Missouri, USA
- Plant Genetics Research, USDA Agricultural Research Service, Columbia, Missouri, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
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12
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Mazarei M, Routray P, Piya S, Stewart CN, Hewezi T. Overexpression of soybean GmNAC19 and GmGRAB1 enhances root growth and water-deficit stress tolerance in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1186292. [PMID: 37324708 PMCID: PMC10264791 DOI: 10.3389/fpls.2023.1186292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is an important crop in agricultural production where water shortage limits yields in soybean. Root system plays important roles in water-limited environments, but the underlying mechanisms are largely unknown. In our previous study, we produced a RNA-seq dataset generated from roots of soybean at three different growth stages (20-, 30-, and 44-day-old plants). In the present study, we performed a transcriptome analysis of the RNA-seq data to select candidate genes with probable association with root growth and development. Candidate genes were functionally examined in soybean by overexpression of individual genes using intact soybean composite plants with transgenic hairy roots. Root growth and biomass in the transgenic composite plants were significantly increased by overexpression of the GmNAC19 and GmGRAB1 transcriptional factors, showing up to 1.8-fold increase in root length and/or 1.7-fold increase in root fresh/dry weight. Furthermore, greenhouse-grown transgenic composite plants had significantly higher seed yield by about 2-fold than control plants. Expression profiling in different developmental stages and tissues showed that GmNAC19 and GmGRAB1 were most highly expressed in roots, displaying a distinct root-preferential expression. Moreover, we found that under water-deficit conditions, overexpression of GmNAC19 enhanced water stress tolerance in transgenic composite plants. Taken together, these results provide further insights into the agricultural potential of these genes for development of soybean cultivars with improved root growth and enhanced tolerance to water-deficit conditions.
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Affiliation(s)
- Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Pratyush Routray
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
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13
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Tehrani N, Mitra RM. Plant pathogens and symbionts target the plant nucleus. Curr Opin Microbiol 2023; 72:102284. [PMID: 36868049 DOI: 10.1016/j.mib.2023.102284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 03/05/2023]
Abstract
In plant-microbe interactions, symbionts and pathogens live within plants and attempt to avoid triggering plant defense responses. In order to do so, these microbes have evolved multiple mechanisms that target components of the plant cell nucleus. Rhizobia-induced symbiotic signaling requires the function of specific legume nucleoporins within the nuclear pore complex. Symbiont and pathogen effectors harbor nuclear localization sequences that facilitate movement across nuclear pores, allowing these proteins to target transcription factors that function in defense. Oomycete pathogens introduce proteins that interact with plant pre-mRNA splicing components in order to alter host splicing of defense-related transcripts. Together, these functions indicate that the nucleus is an active site of symbiotic and pathogenic functioning in plant-microbe interactions.
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14
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Liu J, Chen S, Liu M, Chen Y, Fan W, Lee S, Xiao H, Kudrna D, Li Z, Chen X, Peng Y, Tian K, Zhang B, Wing RA, Zhang J, Wang X. Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max. Int J Mol Sci 2022; 23:7371. [PMID: 35806374 PMCID: PMC9266934 DOI: 10.3390/ijms23137371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Alternative splicing (AS) is a ubiquitous phenomenon among eukaryotic intron-containing genes, which greatly contributes to transcriptome and proteome diversity. Here we performed the isoform sequencing (Iso-Seq) of soybean underground tissues inoculated and uninoculated with Rhizobium and obtained 200,681 full-length transcripts covering 26,183 gene loci. It was found that 80.78% of the multi-exon loci produced more than one splicing variant. Comprehensive analysis of these identified 7874 differentially splicing events with highly diverse splicing patterns during nodule development, especially in defense and transport-related processes. We further profiled genes with differential isoform usage and revealed that 2008 multi-isoform loci underwent stage-specific or simultaneous major isoform switches after Rhizobium inoculation, indicating that AS is a vital way to regulate nodule development. Moreover, we took the lead in identifying 1563 high-confidence long non-coding RNAs (lncRNAs) in soybean, and 157 of them are differentially expressed during nodule development. Therefore, our study uncovers the landscape of AS during the soybean-Rhizobium interaction and provides systematic transcriptomic data for future study of multiple novel directions in soybean.
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Affiliation(s)
- Jing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Shengcai Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Min Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
| | - Yimian Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Wei Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Han Xiao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Zixin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
| | - Xu Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Yaqi Peng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Kewei Tian
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Bao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
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15
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Pecrix Y, Sallet E, Moreau S, Bouchez O, Carrere S, Gouzy J, Jardinaud MF, Gamas P. DNA demethylation and hypermethylation are both required for late nodule development in Medicago. NATURE PLANTS 2022; 8:741-749. [PMID: 35817824 DOI: 10.1038/s41477-022-01188-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Plant epigenetic regulations are involved in transposable element silencing, developmental processes and responses to the environment1-7. They often involve modifications of DNA methylation, particularly through the DEMETER (DME) demethylase family and RNA-dependent DNA methylation (RdDM)8. Root nodules host rhizobia that can fix atmospheric nitrogen for the plant's benefit in nitrogen-poor soils. The development of indeterminate nodules, as in Medicago truncatula, involves successive waves of gene activation9-12, control of which raises interesting questions. Using laser capture microdissection (LCM) coupled to RNA-sequencing (SYMbiMICS data11), we previously identified 4,309 genes (termed NDD) activated in the nodule differentiation and nitrogen fixation zones, 36% of which belong to co-regulated genomic regions dubbed symbiotic islands13. We found MtDME to be upregulated in the differentiation zone and required for nodule development, and we identified 474 differentially methylated regions hypomethylated in the nodule by analysing ~2% of the genome4. Here, we coupled LCM and whole-genome bisulfite sequencing for a comprehensive view of DNA methylation, integrated with gene expression at the tissue level. Furthermore, using CRISPR-Cas9 mutagenesis of MtDRM2, we showed the importance of RdDM for CHH hypermethylation and nodule development. We thus proposed a model of DNA methylation dynamics during nodule development.
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Affiliation(s)
- Y Pecrix
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - E Sallet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - S Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - O Bouchez
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - S Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - J Gouzy
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - M-F Jardinaud
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - P Gamas
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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16
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Song JH, Montes-Luz B, Tadra-Sfeir MZ, Cui Y, Su L, Xu D, Stacey G. High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation. FRONTIERS IN PLANT SCIENCE 2022; 13:820348. [PMID: 35498680 PMCID: PMC9048599 DOI: 10.3389/fpls.2022.820348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Nodule organogenesis in legumes is regulated temporally and spatially through gene networks. Genome-wide transcriptome, proteomic, and metabolomic analyses have been used previously to define the functional role of various plant genes in the nodulation process. However, while significant progress has been made, most of these studies have suffered from tissue dilution since only a few cells/root regions respond to rhizobial infection, with much of the root non-responsive. To partially overcome this issue, we adopted translating ribosome affinity purification (TRAP) to specifically monitor the response of the root cortex to rhizobial inoculation using a cortex-specific promoter. While previous studies have largely focused on the plant response within the root epidermis (e.g., root hairs) or within developing nodules, much less is known about the early responses within the root cortex, such as in relation to the development of the nodule primordium or growth of the infection thread. We focused on identifying genes specifically regulated during early nodule organogenesis using roots inoculated with Bradyrhizobium japonicum. A number of novel nodulation gene candidates were discovered, as well as soybean orthologs of nodulation genes previously reported in other legumes. The differential cortex expression of several genes was confirmed using a promoter-GUS analysis, and RNAi was used to investigate gene function. Notably, a number of differentially regulated genes involved in phytohormone signaling, including auxin, cytokinin, and gibberellic acid (GA), were also discovered, providing deep insight into phytohormone signaling during early nodule development.
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Affiliation(s)
- Jae Hyo Song
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Bruna Montes-Luz
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Michelle Zibetti Tadra-Sfeir
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Yaya Cui
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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17
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Beamer ZG, Routray P, Choi WG, Spangler MK, Lokdarshi A, Roberts DM. Aquaporin family lactic acid channel NIP2;1 promotes plant survival under low oxygen stress in Arabidopsis. PLANT PHYSIOLOGY 2021; 187:2262-2278. [PMID: 34890456 PMCID: PMC8644545 DOI: 10.1093/plphys/kiab196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/28/2021] [Indexed: 05/05/2023]
Abstract
Under anaerobic stress, Arabidopsis thaliana induces the expression of a collection of core hypoxia genes that encode proteins for an adaptive response. Among these genes is NIP2;1, which encodes a member of the "Nodulin 26-like Intrinsic Protein" (NIP) subgroup of the aquaporin superfamily of membrane channel proteins. NIP2;1 expression is limited to the "anoxia core" region of the root stele under normal growth conditions, but shows substantial induction (up to 1,000-fold by 2-4 h of hypoxia) by low oxygen stress, and accumulation in all root tissues. During hypoxia, NIP2;1-GFP accumulates predominantly on the plasma membrane by 2 h, is distributed between the plasma and internal membranes during sustained hypoxia, and remains elevated in root tissues through 4 h of reoxygenation recovery. In response to hypoxia challenge, T-DNA insertion mutant nip2;1 plants exhibit elevated lactic acid within root tissues, reduced efflux of lactic acid, and reduced acidification of the external medium compared to wild-type plants. Previous biochemical evidence demonstrates that NIP2;1 has lactic acid channel activity, and our work supports the hypothesis that NIP2;1 prevents lactic acid toxicity by facilitating release of cellular lactic acid from the cytosol to the apoplast, supporting eventual efflux to the rhizosphere. In evidence, nip2;1 plants demonstrate poorer survival during argon-induced hypoxia stress. Expressions of the ethanolic fermentation transcript Alcohol Dehydrogenase1 and the core hypoxia-induced transcript Alanine Aminotransferase1 are elevated in nip2;1, and expression of the Glycolate Oxidase3 transcript is reduced, suggesting NIP2;1 lactic acid efflux regulates other pyruvate and lactate metabolism pathways.
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Affiliation(s)
- Zachary G Beamer
- Department of Biochemistry and Cellular, and Molecular Biology, the University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Won-Gyu Choi
- Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, Nevada 89557, USA
| | - Margaret K Spangler
- Department of Biochemistry and Cellular, and Molecular Biology, the University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Ansul Lokdarshi
- Department of Biochemistry and Cellular, and Molecular Biology, the University of Tennessee, Knoxville, Tennessee 37996, USA
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18
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Li Y, Wang J, Elzo MA, Fan H, Du K, Xia S, Shao J, Lai T, Hu S, Jia X, Lai S. Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits. Curr Issues Mol Biol 2021; 43:1558-1575. [PMID: 34698087 PMCID: PMC8929151 DOI: 10.3390/cimb43030110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022] Open
Abstract
DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit.
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Affiliation(s)
- Yanhong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Huimei Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Kun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Siqi Xia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Jiahao Shao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Tianfu Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Shenqiang Hu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Xianbo Jia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Songjia Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
- Correspondence:
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Bennett M, Cleaves K, Hewezi T. Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones. Int J Mol Sci 2021; 22:ijms22189681. [PMID: 34575855 PMCID: PMC8470644 DOI: 10.3390/ijms22189681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. We characterized the spatiotemporal expression patterns of genes involved in de novo methylation, methyl maintenance, and active demethylation in roots, shoots, and reproductive organs using β-glucuronidase (GUS) reporter lines. Promoters of DNA demethylases were generally more highly active at the mature root tissues, whereas the promoters of genes involved in DNA methylation were more highly active at fast-growing root tissues. The promoter activity also implies that methylation status in shoot apex, leaf primordia, floral organs, and developing embryos is under tight equilibrium through the activity of genes involved in DNA methylation and demethylation. The promoter activity of DNA methylation and demethylation-related genes in response to various phytohormone treatments revealed that phytohormones can alter DNA methylation status in specific and redundant ways. Overall, our results illustrate that DNA methylation and demethylation pathways act synergistically and antagonistically in various tissues and in response to phytohormone treatments and point to the existence of hormone-linked methylome regulation mechanisms that may contribute to tissue differentiation and development.
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Wang S, Yan W, Yang X, Zhang J, Shi Q. Comparative methylome reveals regulatory roles of DNA methylation in melon resistance to Podosphaera xanthii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110954. [PMID: 34134849 DOI: 10.1016/j.plantsci.2021.110954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Powdery mildew caused by Podosphaera xanthii (P. xanthii) severely endangers melon (Cucumis melo L.) production, while the mechanistic understanding about its resistance to powdery mildew remains largely limited. In this study, we integrated transcriptomic and methylomic analyses to explore whether DNA methylation was involved in modulating transcriptional acclimation of melon to P. xanthii infection. Net photosynthetic rate (Pn), stomatal conductance (Gs), actual photochemical efficiency (ФPSII) and maximum PSII quantum yield (Fv/Fm) were significantly decreased in P. xanthii-infected plants relative to uninfected ones (Control), revealing apparent physiological disorders. Totally 4808 differentially expressed genes (DEGs) were identified by global analysis of gene expression in Control and P. xanthii-infected plants. Comparative methylome uncovered that 932 DEGs were associated with hypermethylation, while 603 DEGs were associated with hypomethylation in melon upon P. xanthii infection. Among these differential methylation-involved DEGs, a set of resistance-related genes including R genes and candidate genes in metabolic and defense pathways were further identified, demonstrating that DNA methylation might function as a new regulatory layer for melon resistance to P. xanthii infection. Altogether our study sheds new insights into the molecular mechanisms of melon against powdery mildew and provides some potential targets for improving melon disease resistance in future.
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Affiliation(s)
- Shuoshuo Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Weihao Yan
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Xiaoyu Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Jiayu Zhang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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21
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Ramos-Cruz D, Troyee AN, Becker C. Epigenetics in plant organismic interactions. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102060. [PMID: 34087759 DOI: 10.1016/j.pbi.2021.102060] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 05/26/2023]
Abstract
Plants are hubs of organismic interactions. They constantly engage in beneficial or competitive interactions with fungi, oomycetes, bacteria, insects, nematodes, and other plants. To adjust the molecular processes necessary for the establishment and maintenance of beneficial interactions and for the defense against pathogens and herbivores, plants have evolved intricate regulatory mechanisms. Besides the canonical plant immune system that acts as the primary defense, epigenetic mechanisms have started to emerge as another regulatory entity and as a target of pathogens trying to overcome the plant's defenses. In this review, we highlight recent advances in understanding the contribution of various epigenetic components and of epigenetic diversity to plant-organismic interactions.
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Affiliation(s)
- Daniela Ramos-Cruz
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - A Niloya Troyee
- Department of Evolutionary Ecology, Doñana Biological Station, CSIC, 41092 Sevilla, Spain
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria; Genetics, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany.
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22
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Piya S, Lopes-Caitar VS, Kim W, Pantalone V, Krishnan HB, Hewezi T. Title: Hypermethylation of miRNA Genes During Nodule Development. Front Mol Biosci 2021; 8:616623. [PMID: 33928115 PMCID: PMC8076613 DOI: 10.3389/fmolb.2021.616623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022] Open
Abstract
DNA methylation has recently emerged as a powerful regulatory mechanism controlling the expression of key regulators of various developmental processes, including nodulation. However, the functional role of DNA methylation in regulating the expression of microRNA (miRNA) genes during the formation and development of nitrogen-fixing nodules remains largely unknown. In this study, we profiled DNA methylation patterns of miRNA genes during nodule formation, development, and early senescence stages in soybean (Glycine max) through the analysis of methylC-seq data. Absolute DNA methylation levels in the CG, CHH, and CHH sequence contexts over the promoter and primary transcript regions of miRNA genes were significantly higher in the nodules compared with the corresponding root tissues at these three distinct nodule developmental stages. We identified a total of 82 differentially methylated miRNAs in the nodules compared with roots. Differential DNA methylation of these 82 miRNAs was detected only in the promoter (69), primary transcript region (3), and both in the promoter and primary transcript regions (10). The large majority of these differentially methylated miRNAs were hypermethylated in nodules compared with the corresponding root tissues and were found mainly in the CHH context and showed stage-specific methylation patterns. Differentially methylated regions in the promoters of 25 miRNAs overlapped with transposable elements, a finding that may explain the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis of a set of promoter-differentially methylated miRNAs pointed to a negative association between DNA methylation and miRNA expression. Gene Ontology and pathways analyses indicate that changes in DNA methylation of miRNA genes are reprogrammed and contribute to nodule development through indirect regulation of genes involved in cellular processes and pathways with well-established roles in nodulation.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | | | - Won‐Seok Kim
- Plant Science Division, University of Missouri, Columbia, MO, United States
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Hari B. Krishnan
- Plant Science Division, University of Missouri, Columbia, MO, United States
- Plant Genetics Research, USDA-Agricultural Research Service, Columbia, MO, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
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23
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Lakhssassi N, Zhou Z, Liu S, Piya S, Cullen MA, El Baze A, Knizia D, Patil GB, Badad O, Embaby MG, Meksem J, Lakhssassi A, AbuGhazaleh A, Hewezi T, Meksem K. Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6969-6987. [PMID: 32898219 DOI: 10.1093/jxb/eraa402] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mallory A Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Gunvant B Patil
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Mohamed G Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, Nancy, France
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
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