1
|
Obermeyer S, Kapoor H, Markusch H, Grasser KD. Transcript elongation by RNA polymerase II in plants: factors, regulation and impact on gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:645-656. [PMID: 36703573 DOI: 10.1111/tpj.16115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Transcriptional elongation by RNA polymerase II (RNAPII) through chromatin is a dynamic and highly regulated step of eukaryotic gene expression. A combination of transcript elongation factors (TEFs) including modulators of RNAPII activity and histone chaperones facilitate efficient transcription on nucleosomal templates. Biochemical and genetic analyses, primarily performed in Arabidopsis, provided insight into the contribution of TEFs to establish gene expression patterns during plant growth and development. In addition to summarising the role of TEFs in plant gene expression, we emphasise in our review recent advances in the field. Thus, mechanisms are presented how aberrant intragenic transcript initiation is suppressed by repressing transcriptional start sites within coding sequences. We also discuss how transcriptional interference of ongoing transcription with neighbouring genes is prevented. Moreover, it appears that plants make no use of promoter-proximal RNAPII pausing in the way mammals do, but there are nucleosome-defined mechanism(s) that determine the efficiency of mRNA synthesis by RNAPII. Accordingly, a still growing number of processes related to plant growth, development and responses to changing environmental conditions prove to be regulated at the level of transcriptional elongation.
Collapse
Affiliation(s)
- Simon Obermeyer
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Henna Kapoor
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Hanna Markusch
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| |
Collapse
|
2
|
Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
Collapse
Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
| |
Collapse
|
3
|
Xu N, Cheng L, Kong Y, Chen G, Zhao L, Liu F. Functional analyses of the NRT2 family of nitrate transporters in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1351998. [PMID: 38501135 PMCID: PMC10944928 DOI: 10.3389/fpls.2024.1351998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Nitrogen is an essential macronutrient for plant growth and development. Nitrate is the major form of nitrogen acquired by most crops and also serves as a vital signaling molecule. Nitrate is absorbed from the soil into root cells usually by the low-affinity NRT1 NO3 - transporters and high-affinity NRT2 NO3 - transporters, with NRT2s serving to absorb NO3 - under NO3 -limiting conditions. Seven NRT2 members have been identified in Arabidopsis, and they have been shown to be involved in various biological processes. In this review, we summarize the spatiotemporal expression patterns, localization, and biotic and abiotic responses of these transporters with a focus on recent advances in the current understanding of the functions of the seven AtNRT2 genes. This review offers beneficial insight into the mechanisms by which plants adapt to changing environmental conditions and provides a theoretical basis for crop research in the near future.
Collapse
Affiliation(s)
- Na Xu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Li Cheng
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Yuan Kong
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Guiling Chen
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Lufei Zhao
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, Shandong, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| |
Collapse
|
4
|
Zhang H, Jin Z, Cui F, Zhao L, Zhang X, Chen J, Zhang J, Li Y, Li Y, Niu Y, Zhang W, Gao C, Fu X, Tong Y, Wang L, Ling HQ, Li J, Xiao J. Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat. Nat Commun 2023; 14:8238. [PMID: 38086830 PMCID: PMC10716289 DOI: 10.1038/s41467-023-44003-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing NRT2 in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.
Collapse
Affiliation(s)
- Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyuan Jin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Long Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinchao Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Yongpeng Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CICMCP, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China.
| | - Junming Li
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China.
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, China.
| |
Collapse
|
5
|
Julian R, Patrick RM, Li Y. Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato. Commun Biol 2023; 6:1225. [PMID: 38044380 PMCID: PMC10694154 DOI: 10.1038/s42003-023-05601-8] [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: 06/16/2022] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same organ revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 in shoots, where an increased level of this repressive mark is observed at genes activated by nitrate. Application of a machine learning approach revealed organ-specific rules regarding the importance of individual histone marks, as H3K36me3 is the most successful mark in predicting gene regulation events in shoots, while H3K4me3 is the strongest individual predictor in roots. Our integrated study substantiates a view that during plant environmental responses, the relationships between histone code dynamics and gene regulation are highly dependent on organ-specific contexts.
Collapse
Affiliation(s)
- Russell Julian
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ryan M Patrick
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Li
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
6
|
Jia Y, Qin D, Zheng Y, Wang Y. Finding Balance in Adversity: Nitrate Signaling as the Key to Plant Growth, Resilience, and Stress Response. Int J Mol Sci 2023; 24:14406. [PMID: 37833854 PMCID: PMC10572113 DOI: 10.3390/ijms241914406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
To effectively adapt to changing environments, plants must maintain a delicate balance between growth and resistance or tolerance to various stresses. Nitrate, a significant inorganic nitrogen source in soils, not only acts as an essential nutrient but also functions as a critical signaling molecule that regulates multiple aspects of plant growth and development. In recent years, substantial advancements have been made in understanding nitrate sensing, calcium-dependent nitrate signal transmission, and nitrate-induced transcriptional cascades. Mounting evidence suggests that the primary response to nitrate is influenced by environmental conditions, while nitrate availability plays a pivotal role in stress tolerance responses. Therefore, this review aims to provide an overview of the transcriptional and post-transcriptional regulation of key components in the nitrate signaling pathway, namely, NRT1.1, NLP7, and CIPK23, under abiotic stresses. Additionally, we discuss the specificity of nitrate sensing and signaling as well as the involvement of epigenetic regulators. A comprehensive understanding of the integration between nitrate signaling transduction and abiotic stress responses is crucial for developing future crops with enhanced nitrogen-use efficiency and heightened resilience.
Collapse
Affiliation(s)
- Yancong Jia
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Debin Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China;
| | - Yulu Zheng
- College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Yang Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
- College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| |
Collapse
|
7
|
Zhang H, Zhang X, Xiao J. Epigenetic Regulation of Nitrogen Signaling and Adaptation in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2725. [PMID: 37514337 PMCID: PMC10386408 DOI: 10.3390/plants12142725] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Nitrogen (N) is a crucial nutrient that plays a significant role in enhancing crop yield. Its availability, including both supply and deficiency, serves as a crucial signal for plant development. However, excessive N use in agriculture leads to environmental and economic issues. Enhancing nitrogen use efficiency (NUE) is, therefore, essential to minimize negative impacts. Prior studies have investigated the genetic factors involved in N responses and the process of low-nitrogen (LN) adaptation. In this review, we discuss recent advances in understanding how epigenetic modifications, including DNA methylation, histone modification, and small RNA, participate in the regulation of N response and LN adaptation. We highlight the importance of decoding the epigenome at various levels to accelerate the functional study of how plants respond to N availability. Understanding the epigenetic control of N signaling and adaptation can lead to new strategies to improve NUE and enhance crop productivity sustainably.
Collapse
Affiliation(s)
- Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing 100101, China
| |
Collapse
|
8
|
Zhu H, Han G, Wang J, Xu J, Hong Y, Huang L, Zheng S, Yang J, Chen W. CG hypermethylation of the bHLH39 promoter regulates its expression and Fe deficiency responses in tomato roots. HORTICULTURE RESEARCH 2023; 10:uhad104. [PMID: 37577397 PMCID: PMC10419876 DOI: 10.1093/hr/uhad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/08/2023] [Indexed: 08/15/2023]
Abstract
Iron (Fe) is an essential micronutrient for all organisms, including plants, whose limited bioavailability restricts plant growth, yield, and nutritional quality. While the transcriptional regulation of plant responses to Fe deficiency have been extensively studied, the contribution of epigenetic modulations, such as DNA methylation, remains poorly understood. Here, we report that treatment with a DNA methylase inhibitor repressed Fe deficiency-induced responses in tomato (Solanum lycopersicum) roots, suggesting the importance of DNA methylation in regulating Fe deficiency responses. Dynamic changes in the DNA methylome in tomato roots responding to short-term (12 hours) and long-term (72 hours) Fe deficiency identified many differentially methylated regions (DMRs) and DMR-associated genes. Most DMRs occurred at CHH sites under short-term Fe deficiency, whereas they were predominant at CG sites following long-term Fe deficiency. Furthermore, no correlation was detected between the changes in DNA methylation levels and the changes in transcript levels of the affected genes under either short-term or long-term treatments. Notably, one exception was CG hypermethylation at the bHLH39 promoter, which was positively correlated with its transcriptional induction. In agreement, we detected lower CG methylation at the bHLH39 promoter and lower bHLH39 expression in MET1-RNA interference lines compared with wild-type seedlings. Virus-induced gene silencing of bHLH39 and luciferase reporter assays revealed that bHLH39 is positively involved in the modulation of Fe homeostasis. Altogether, we propose that dynamic epigenetic DNA methylation in the CG context at the bHLH39 promoter is involved in its transcriptional regulation, thus contributing to the Fe deficiency response of tomato.
Collapse
Affiliation(s)
- Huihui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guanghao Han
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jiayi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianli Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiwei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| |
Collapse
|
9
|
Jie L, Sanagi M, Luo Y, Maeda H, Fukao Y, Chiba Y, Yanagisawa S, Yamaguchi J, Takagi J, Sato T. Histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 proteins affect plant growth under nitrogen deficient conditions in Arabidopsis thaliana. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:93-98. [PMID: 38439935 PMCID: PMC10910346 DOI: 10.5511/plantbiotechnology.22.1219a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 03/06/2024]
Abstract
Nitrogen (N) availability is one of the most important factors regulating plant metabolism and growth as it affects global gene expression profiles. Dynamic changes in chromatin structure, including histone modifications and nucleosome assembly/disassembly, have been extensively shown to regulate gene expression under various environmental stresses in plants. However, the involvement of chromatin related changes in plant nutrient responses has been demonstrated only in a few studies to date. In this study, we investigated the function of histone chaperone NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) proteins under N deficient conditions in Arabidopsis. In the nap1;1 nap1;2 nap1;3 triple mutant (m123-1), the expression of N-responsive marker genes and growth of lateral roots were decreased under N deficient conditions. In addition, the m123-1 plants showed a delay in N deficiency-induced leaf senescence. Taken together, these results suggest that NAP1s affect plant growth under N deficient conditions in Arabidopsis.
Collapse
Affiliation(s)
- Linnan Jie
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Miho Sanagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yongming Luo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Haruna Maeda
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoichiro Fukao
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Junji Yamaguchi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junpei Takagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takeo Sato
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
10
|
Lepetit M, Brouquisse R. Control of the rhizobium-legume symbiosis by the plant nitrogen demand is tightly integrated at the whole plant level and requires inter-organ systemic signaling. FRONTIERS IN PLANT SCIENCE 2023; 14:1114840. [PMID: 36968361 PMCID: PMC10033964 DOI: 10.3389/fpls.2023.1114840] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Symbiotic nodules formed on legume roots with rhizobia fix atmospheric N2. Bacteria reduce N2 to NH4 + that is assimilated into amino acids by the plant. In return, the plant provides photosynthates to fuel the symbiotic nitrogen fixation. Symbiosis is tightly adjusted to the whole plant nutritional demand and to the plant photosynthetic capacities, but regulatory circuits behind this control remain poorly understood. The use of split-root systems combined with biochemical, physiological, metabolomic, transcriptomic, and genetic approaches revealed that multiple pathways are acting in parallel. Systemic signaling mechanisms of the plant N demand are required for the control of nodule organogenesis, mature nodule functioning, and nodule senescence. N-satiety/N-deficit systemic signaling correlates with rapid variations of the nodules' sugar levels, tuning symbiosis by C resources allocation. These mechanisms are responsible for the adjustment of plant symbiotic capacities to the mineral N resources. On the one hand, if mineral N can satisfy the plant N demand, nodule formation is inhibited, and nodule senescence is activated. On the other hand, local conditions (abiotic stresses) may impair symbiotic activity resulting in plant N limitation. In these conditions, systemic signaling may compensate the N deficit by stimulating symbiotic root N foraging. In the past decade, several molecular components of the systemic signaling pathways controlling nodule formation have been identified, but a major challenge remains, that is, to understand their specificity as compared to the mechanisms of non-symbiotic plants that control root development and how they contribute to the whole plant phenotypes. Less is known about the control of mature nodule development and functioning by N and C nutritional status of the plant, but a hypothetical model involving the sucrose allocation to the nodule as a systemic signaling process, the oxidative pentose phosphate pathway, and the redox status as potential effectors of this signaling is emerging. This work highlights the importance of organism integration in plant biology.
Collapse
|
11
|
Choi SJ, Lee Z, Jeong E, Kim S, Seo JS, Um T, Shim JS. Signaling pathways underlying nitrogen transport and metabolism in plants. BMB Rep 2023; 56:56-64. [PMID: 36658636 PMCID: PMC9978367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 01/21/2023] Open
Abstract
Nitrogen (N) is an essential macronutrient required for plant growth and crop production. However, N in soil is usually insufficient for plant growth. Thus, chemical N fertilizer has been extensively used to increase crop production. Due to negative effects of N rich fertilizer on the environment, improving N usage has been a major issue in the field of plant science to achieve sustainable production of crops. For that reason, many efforts have been made to elucidate how plants regulate N uptake and utilization according to their surrounding habitat over the last 30 years. Here, we provide recent advances focusing on regulation of N uptake, allocation of N by N transporting system, and signaling pathway controlling N responses in plants. [BMB Reports 2023; 56(2): 56-64].
Collapse
Affiliation(s)
- Su Jeong Choi
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Zion Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Eui Jeong
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Sohyun Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Jun Sung Seo
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea,Corresponding author. Tel: +82-62-530-0507; Fax: +82-62-530-2199; E-mail:
| |
Collapse
|
12
|
Yu Y, Wang Y, Yao Z, Wang Z, Xia Z, Lee J. Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications. Methods Mol Biol 2023; 2665:95-111. [PMID: 37166596 DOI: 10.1007/978-1-0716-3183-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Vital biochemical reactions including photosynthesis to respiration require iron, which should be tightly regulated. Although increasing evidence reveals the importance of epigenetic regulation in gene expression and signaling, the role of histone modifications and chromatin remodeling in plant iron homeostasis is not well understood. In this study, we surveyed publicly available ChIP-seq datasets of Arabidopsis wild-type and mutants defective in key enzymes of histone modification and chromatin remodeling and compared the deposition of epigenetic marks on loci of genes involved in iron regulation. Based on the analysis, we compiled a comprehensive list of iron homeostasis genes with differential enrichment of various histone modifications. This report will provide a resource for future studies to investigate epigenetic regulatory mechanisms of iron homeostasis in plants.
Collapse
Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Yuxin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Zhujun Yao
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Zijun Xia
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China.
| |
Collapse
|
13
|
Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
Collapse
Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
14
|
Zhu Z, Liu Y, Qi J, Sui Z. Identification of epigenetic histone modifications and analysis of histone lysine methyltransferases in Alexandrium pacificum. HARMFUL ALGAE 2022; 119:102323. [PMID: 36344193 DOI: 10.1016/j.hal.2022.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Alexandrium pacificum is a toxic dinoflagellate that can cause harmful algal blooms (HABs). The molecular mechanisms of HABs are still poorly understood, especially at the epigenetics level. Organism growth and metabolic processes are affected by histone modifications, an important mode of epigenetic regulation. In this study, various types of modifications, including methylation, acetylation, ubiquitination, and phosphorylation in A. pacificum cells were identified by using pan-antibodies, mass spectrometry, and an H3 modification multiplex assay kit. The modification abundance of H3K4me2 and H3K27me3 of A. pacificum varied under different growth conditions detected by Western blots. A class of SET domain genes (SDGs) encoding histone lysine methyltransferase was analyzed. A total of 179 SDG members were identified in A. pacificum, of which 53 sequences encoding complete proteins were classified into three categories by phylogenetic analysis, conserved domains and motifs analysis. Expression analysis and real-time polymerase chain reaction validation showed that the expressions of some SDGs were significantly influenced by light, nitrogen, phosphorus and manganese supplements. The results revealed that histone lysine methylation played an important role in responding to HABs inducing conditions. This study provided useful information for the further exploration of the role and regulatory mechanism of SDGs in the rapid growth of A. pacificum.
Collapse
Affiliation(s)
- Zhimei Zhu
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education of China, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education of China, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Juan Qi
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education of China, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education of China, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
15
|
Eshel G, Duppen N, Wang G, Oh D, Kazachkova Y, Herzyk P, Amtmann A, Gordon M, Chalifa‐Caspi V, Oscar MA, Bar‐David S, Marshall‐Colon A, Dassanayake M, Barak S. Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica. THE NEW PHYTOLOGIST 2022; 236:1006-1026. [PMID: 35909295 PMCID: PMC9804903 DOI: 10.1111/nph.18411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress-ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.
Collapse
Affiliation(s)
- Gil Eshel
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Nick Duppen
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Guannan Wang
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Dong‐Ha Oh
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Yana Kazachkova
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Pawel Herzyk
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Anna Amtmann
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Michal Gordon
- Bioinformatics Core Facility, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8410501Israel
| | - Vered Chalifa‐Caspi
- Bioinformatics Core Facility, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8410501Israel
| | - Michelle Arland Oscar
- Blaustein Center for Scientific CooperationBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Shirli Bar‐David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Amy Marshall‐Colon
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Maheshi Dassanayake
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Simon Barak
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| |
Collapse
|
16
|
Bvindi C, Tang L, Lee S, Patrick RM, Yee ZR, Mengiste T, Li Y. Histone methyltransferases SDG33 and SDG34 regulate organ-specific nitrogen responses in tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:1005077. [PMID: 36311072 PMCID: PMC9606235 DOI: 10.3389/fpls.2022.1005077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Histone posttranslational modifications shape the chromatin landscape of the plant genome and affect gene expression in response to developmental and environmental cues. To date, the role of histone modifications in regulating plant responses to environmental nutrient availability, especially in agriculturally important species, remains largely unknown. We describe the functions of two histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen (N) responses of shoots and roots in tomato. By comparing the transcriptomes of CRISPR edited tomato lines sdg33 and sdg34 with wild-type plants under N-supplied and N-starved conditions, we uncovered that SDG33 and SDG34 regulate overlapping yet distinct downstream gene targets. In response to N level changes, both SDG33 and SDG34 mediate gene regulation in an organ-specific manner: in roots, SDG33 and SDG34 regulate a gene network including Nitrate Transporter 1.1 (NRT1.1) and Small Auxin Up-regulated RNA (SAUR) genes. In agreement with this, mutations in sdg33 or sdg34 abolish the root growth response triggered by an N-supply; In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and photosynthetic parameters in response to N. Our analysis thus revealed that SDG33 and SDG34 regulate N-responsive gene expression and physiological changes in an organ-specific manner, thus presenting previously unknown candidate genes as targets for selection and engineering to improve N uptake and usage in crop plants.
Collapse
Affiliation(s)
- Carol Bvindi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Liang Tang
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ryan M. Patrick
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Zheng Rong Yee
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ying Li
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
17
|
Su J, Yao Z, Wu Y, Lee J, Jeong J. Minireview: Chromatin-based regulation of iron homeostasis in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:959840. [PMID: 36186078 PMCID: PMC9523571 DOI: 10.3389/fpls.2022.959840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/31/2022] [Indexed: 05/26/2023]
Abstract
Plants utilize delicate mechanisms to effectively respond to changes in the availability of nutrients such as iron. The responses to iron status involve controlling gene expression at multiple levels. The regulation of iron deficiency response by a network of transcriptional regulators has been extensively studied and recent research has shed light on post-translational control of iron homeostasis. Although not as considerably investigated, an increasing number of studies suggest that histone modification and DNA methylation play critical roles during iron deficiency and contribute to fine-tuning iron homeostasis in plants. This review will focus on the current understanding of chromatin-based regulation on iron homeostasis in plants highlighting recent studies in Arabidopsis and rice. Understanding iron homeostasis in plants is vital, as it is not only relevant to fundamental biological questions, but also to agriculture, biofortification, and human health. A comprehensive overview of the effect and mechanism of chromatin-based regulation in response to iron status will ultimately provide critical insights in elucidating the complexities of iron homeostasis and contribute to improving iron nutrition in plants.
Collapse
Affiliation(s)
- Justin Su
- Department of Biology, Amherst College, Amherst, MA, United States
| | - Zhujun Yao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Yixuan Wu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Jeeyon Jeong
- Department of Biology, Amherst College, Amherst, MA, United States
| |
Collapse
|
18
|
Xing G, Jin M, Qu R, Zhang J, Han Y, Han Y, Wang X, Li X, Ma F, Zhao X. Genome-wide investigation of histone acetyltransferase gene family and its responses to biotic and abiotic stress in foxtail millet (Setaria italica [L.] P. Beauv). BMC PLANT BIOLOGY 2022; 22:292. [PMID: 35701737 PMCID: PMC9199193 DOI: 10.1186/s12870-022-03676-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/01/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Modification of histone acetylation is a ubiquitous and reversible process in eukaryotes and prokaryotes and plays crucial roles in the regulation of gene expression during plant development and stress responses. Histone acetylation is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT plays an essential regulatory role in various growth and development processes by modifying the chromatin structure through interactions with other histone modifications and transcription factors in eukaryotic cells, affecting the transcription of genes. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana and Oryza sativa. However, little information is available on the HAT genes in foxtail millet (Setaria italica [L.] P. Beauv). RESULTS In this study, 24 HAT genes (SiHATs) were identified and divided into four groups with conserved gene structures via motif composition analysis. Phylogenetic analysis of the genes was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa, and foxtail millet; 19 and 2 orthologous gene pairs were individually identified. Moreover, all identified HAT gene pairs likely underwent purified selection based on their non-synonymous/synonymous nucleotide substitutions. Using published transcriptome data, we found that SiHAT genes were preferentially expressed in some tissues and organs. Stress responses were also examined, and data showed that SiHAT gene transcription was influenced by drought, salt, low nitrogen, and low phosphorus stress, and that the expression of four SiHATs was altered as a result of infection by Sclerospora graminicola. CONCLUSIONS Results indicated that histone acetylation may play an important role in plant growth and development and stress adaptations. These findings suggest that SiHATs play specific roles in the response to abiotic stress and viral infection. This study lays a foundation for further analysis of the biological functions of SiHATs in foxtail millet.
Collapse
Affiliation(s)
- Guofang Xing
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, 030031, Taiyuan, China
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Minshan Jin
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Ruifang Qu
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Jiewei Zhang
- Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, 100097, Beijing, China
| | - Yuanhuai Han
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Yanqing Han
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Xingchun Wang
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Xukai Li
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Fangfang Ma
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China.
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China.
| | - Xiongwei Zhao
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China.
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China.
| |
Collapse
|
19
|
Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
Collapse
Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| |
Collapse
|
20
|
Vanderstraeten L, Sanchez-Muñoz R, Depaepe T, Auwelaert F, Van Der Straeten D. Mix-and-match: an improved, fast and accessible protocol for hypocotyl micrografting of Arabidopsis seedlings with systemic ACC responses as a case study. PLANT METHODS 2022; 18:24. [PMID: 35246176 PMCID: PMC8896378 DOI: 10.1186/s13007-022-00859-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Grafting is a technique widely used in horticulture that also has been applied in agriculture. In plant physiology, grafting facilitates the elucidation of mechanisms underlying growth and developmental processes, through the construction of chimeric plants with organs of different genotypes. Despite its small size, the model species Arabidopsis thaliana is very amenable for grafting, which can be useful to investigate transport of nutrients, amino acids or secondary metabolites between different tissues, or to investigate developmental processes depending on root-to-shoot communication, such as shoot branching, root and shoot plasticity upon shade avoidance, or disease resistance. Nevertheless, grafting protocols are usually technically challenging and training is required to achieve a reasonable success rate. Additionally, specialized tools and equipment are often needed, such as chips to accommodate the grafted plantlets or collars to maintain the contact between root and shoot. RESULTS In this methodology paper, we provide a fast, easy, accessible, and specialized equipment-free protocol that enables high success ratios. Critical steps and notes are detailed, easing the implementation of the procedure for non-trained researchers. An example of the protocol application by three independent non-trained researchers shows that this method allows to achieve a 90-100% of grafting efficiency after 6 days post-grafting recovery. In addition, the grafting of Col-0 with the acs8x mutant, depleted in 1-aminocyclopropane-1-carboxylic acid (ACC), the biosynthetic precursor of the phytohormone ethylene, provides an example of the application of this optimized protocol, showing the suitability of the process to study long-distance transport processes. CONCLUSIONS We present an optimized protocol for hypocotyl grafting of 4-day-old Arabidopsis thaliana seedlings. The combination of conditions yields a grafting success of 90-100% and provides an easy and accessible methodology, reducing the time frame, and without the necessity of acquiring specialized equipment. The presented protocol is simple, fast and highly efficient, easing the inclusion of hypocotyl grafting assays in any research project. In addition, the description of the protocol is detailed to a level ensuring that even non-trained researchers, are sufficiently prepared to adopt the grafting methodology.
Collapse
Affiliation(s)
- L Vanderstraeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
| | - R Sanchez-Muñoz
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
| | - T Depaepe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
| | - F Auwelaert
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
| | - D Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium.
| |
Collapse
|
21
|
Hu QQ, Shu JQ, Li WM, Wang GZ. Role of Auxin and Nitrate Signaling in the Development of Root System Architecture. FRONTIERS IN PLANT SCIENCE 2021; 12:690363. [PMID: 34858444 PMCID: PMC8631788 DOI: 10.3389/fpls.2021.690363] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/25/2021] [Indexed: 06/12/2023]
Abstract
The plant root is an important storage organ that stores indole-3-acetic acid (IAA) from the apical meristem, as well as nitrogen, which is obtained from the external environment. IAA and nitrogen act as signaling molecules that promote root growth to obtain further resources. Fluctuations in the distribution of nitrogen in the soil environment induce plants to develop a set of strategies that effectively improve nitrogen use efficiency. Auxin integrates the information regarding the nitrate status inside and outside the plant body to reasonably distribute resources and sustainably construct the plant root system. In this review, we focus on the main factors involved in the process of nitrate- and auxin-mediated regulation of root structure to better understand how the root system integrates the internal and external information and how this information is utilized to modify the root system architecture.
Collapse
|
22
|
Plants' Epigenetic Mechanisms and Abiotic Stress. Genes (Basel) 2021; 12:genes12081106. [PMID: 34440280 PMCID: PMC8394019 DOI: 10.3390/genes12081106] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are sessile organisms that need to adapt to constantly changing environmental conditions. Unpredictable climate change places plants under a variety of abiotic stresses. Studying the regulation of stress-responsive genes can help to understand plants’ ability to adapt to fluctuating environmental conditions. Changes in epigenetic marks such as histone modifications and DNA methylation are known to regulate gene expression by their dynamic variation in response to stimuli. This can then affect their phenotypic plasticity, which helps with the adaptation of plants to adverse conditions. Epigenetic marks may also provide a mechanistic basis for stress memory, which enables plants to respond more effectively and efficiently to recurring stress and prepare offspring for potential future stresses. Studying epigenetic changes in addition to genetic factors is important to better understand the molecular mechanisms underlying plant stress responses. This review summarizes the epigenetic mechanisms behind plant responses to some main abiotic stresses.
Collapse
|
23
|
Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
Collapse
|
24
|
Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O’Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. PLANT PHYSIOLOGY 2021; 186:696-714. [PMID: 33582801 PMCID: PMC8154064 DOI: 10.1093/plphys/kiab047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/14/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
Collapse
Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O’Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
- Author for communication:
| |
Collapse
|
25
|
Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O'Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. PLANT PHYSIOLOGY 2021; 186:696-714. [PMID: 33582801 DOI: 10.1101/822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
Collapse
Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O'Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| |
Collapse
|
26
|
Fan X, Liu L, Qian K, Chen J, Zhang Y, Xie P, Xu M, Hu Z, Yan W, Wu Y, Xu G, Fan X. Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice. BMC PLANT BIOLOGY 2021; 21:211. [PMID: 33975546 PMCID: PMC8111971 DOI: 10.1186/s12870-021-02953-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Nitrogen (N) is an important nutrient for plant growth, development, and agricultural production. Nitrogen stress could induce epigenetic changes in plants. In our research, overexpression of the OsNAR2.1 line was used as a testing target in rice plants with high nitrogen-use efficiency to study the changes of rice methylation and growth in respond of the endogenous and external nitrogen stress. RESULTS Our results showed that external N deficiency could decrease seed N content and plant growth of the overexpression line. During the filial growth, we found that the low parent seed nitrogen (LPSN) in the overexpression line could lead to a decrease in the filial seed nitrogen content, total plant nitrogen content, yield, and OsNAR2.1 expression (28, 35, 23, and 55%, respectively) compared with high parent seed nitrogen (HPSN) in high nitrogen external supply. However, such decreases were not observed in wild type. Furthermore, methylation sequencing results showed that LPSN caused massive gene methylation changes, which enriched in over 20 GO pathways in the filial overexpression line, and the expression of OsNAR2.1 in LPSN filial overexpression plants was significantly reduced compared to HPSN filial plants in high external N, which was not shown in wild type. CONCLUSIONS We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1, resulting in a heritable phenotype of N deficiency over two generations of the overexpression line.
Collapse
Affiliation(s)
- Xiaoru Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Laihua Liu
- Vazyme Biotech Co Ltd, Nanjing, 210033, China
| | - Kaiyun Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingguang Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- School of Agriculture, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuyue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Man Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - WenKai Yan
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yufeng Wu
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China.
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
27
|
Safi A, Medici A, Szponarski W, Martin F, Clément-Vidal A, Marshall-Colon A, Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3881-3901. [PMID: 33758916 PMCID: PMC8096604 DOI: 10.1093/jxb/erab114] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/22/2021] [Indexed: 05/04/2023]
Abstract
Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.
Collapse
Affiliation(s)
- Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Correspondence: or
| | - Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | - Florence Martin
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Clément-Vidal
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Amy Marshall-Colon
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
- Present address: Department of Plant Biology, University of Illinois at Urbana -Champaign, Urbana, IL, USA
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Frédéric Gaymard
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, and Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Julie Leclercq
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gloria Coruzzi
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Correspondence: or
| |
Collapse
|
28
|
Li A, Hu B, Chu C. Epigenetic regulation of nitrogen and phosphorus responses in plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153363. [PMID: 33508741 DOI: 10.1016/j.jplph.2021.153363] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) and phosphorus (P) are two of the most important nutrients for plant growth and crop yields. In the last decade, plenty of studies have revealed the genetic factors and their regulatory networks which are involved in N and/or P uptake and utilization in different model plant species, especially in Arabidopsis and rice. However, increasing evidences have shown that epigenetic regulation also plays a vital role in modulating plant responses to nutrient availability. In this review, we make a brief summary of epigenetic regulation including histone modifications, DNA methylation, and other chromatin structure alterations in tuning N and P responses. We also give an outlook for future research directions to comprehensively dissect the involvement of epigenetic regulation in modulating nutrient response in plants.
Collapse
Affiliation(s)
- Aifu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
29
|
Islam S, Zhang J, Zhao Y, She M, Ma W. Genetic regulation of the traits contributing to wheat nitrogen use efficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110759. [PMID: 33487345 DOI: 10.1016/j.plantsci.2020.110759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.
Collapse
Affiliation(s)
- Shahidul Islam
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Yun Zhao
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia.
| |
Collapse
|
30
|
Foroozani M, Vandal MP, Smith AP. H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants. PLANTA 2021; 253:4. [PMID: 33387051 DOI: 10.1007/s00425-020-03520-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The H3K4me3 histone mark in plants functions in the regulation of gene expression and transcriptional memory, and influences numerous developmental processes and stress responses. Plants execute developmental programs and respond to changing environmental conditions via adjustments in gene expression, which are modulated in part by chromatin structure dynamics. Histone modifications alter chromatin in precise ways on a global scale, having the potential to influence the expression of numerous genes. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a prominent histone modification that is dogmatically associated with gene activity, but more recently has also been linked to gene repression. As in other eukaryotes, the distribution of H3K4me3 in plant genomes suggests it plays a central role in gene expression regulation, however the underlying mechanisms are not fully understood. Transcript levels of many genes related to flowering, root, and shoot development are affected by dynamic H3K4me3 levels, as are those for a number of stress-responsive and stress memory-related genes. This review examines the current understanding of how H3K4me3 functions in modulating plant responses to developmental and environmental cues.
Collapse
Affiliation(s)
- Maryam Foroozani
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matthew P Vandal
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
| |
Collapse
|
31
|
Bartusch K, Melnyk CW. Insights Into Plant Surgery: An Overview of the Multiple Grafting Techniques for Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:613442. [PMID: 33362838 PMCID: PMC7758207 DOI: 10.3389/fpls.2020.613442] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/20/2020] [Indexed: 05/28/2023]
Abstract
Plant grafting, the ancient practice of cutting and joining different plants, is gaining popularity as an elegant way to generate chimeras that combine desirable traits. Grafting was originally developed in woody species, but the technique has evolved over the past century to now encompass a large number of herbaceous species. The use of plant grafting in science is accelerating in part due to the innovative techniques developed for the model plant Arabidopsis thaliana. Here, we review these developments and discuss the advantages and limitations associated with grafting various Arabidopsis tissues at diverse developmental stages.
Collapse
Affiliation(s)
- Kai Bartusch
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Charles W. Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| |
Collapse
|
32
|
Genome-Wide Differential DNA Methylation and miRNA Expression Profiling Reveals Epigenetic Regulatory Mechanisms Underlying Nitrogen-Limitation-Triggered Adaptation and Use Efficiency Enhancement in Allotetraploid Rapeseed. Int J Mol Sci 2020; 21:ijms21228453. [PMID: 33182819 PMCID: PMC7697602 DOI: 10.3390/ijms21228453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 12/15/2022] Open
Abstract
Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1, NRT1.5, NRT1.7, NRT2.1/NAR2.1, and Gln1;1, and repressed the transcriptional levels of CLCa, NRT1.8, and NIA1. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-SCL6 and miR160-ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.
Collapse
|
33
|
Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:10241-10258. [PMID: 32941642 PMCID: PMC7544207 DOI: 10.1093/nar/gkaa745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
Collapse
Affiliation(s)
- Natalia I Reim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
34
|
Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses. Int J Mol Sci 2020; 21:ijms21207457. [PMID: 33050358 PMCID: PMC7589735 DOI: 10.3390/ijms21207457] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 01/17/2023] Open
Abstract
Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.
Collapse
|
35
|
Han X, Wu K, Fu X, Liu Q. Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture. ABIOTECH 2020; 1:255-275. [PMID: 36304130 PMCID: PMC9590520 DOI: 10.1007/s42994-020-00027-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/20/2020] [Indexed: 01/25/2023]
Abstract
The agricultural green revolution of the 1960s boosted cereal crop yield was in part due to cultivation of semi-dwarf green revolution varieties. The semi-dwarf plants resist lodging and require high nitrogen (N) fertilizer inputs to maximize yield. To produce higher grain yield, inorganic fertilizer has been overused by Chinese farmers in intensive crop production. With the ongoing increase in the food demand of global population and the environmental pollution, improving crop productivity with reduced N supply is a pressing challenge. Despite a great deal of research efforts, to date only a few genes that improve N use efficiency (NUE) have been identified. The molecular mechanisms underlying the coordination of plant growth, carbon (C) and N assimilation is still not fully understood, thus preventing significant improvement. Recent advances have shed light on how explore NUE within an overall plant biology system that considered the co-regulation of plant growth, C and N metabolisms as a whole, rather than focusing specifically on N uptake and assimilation. There are several potential approaches to improve NUE discussed in this review. Increasing knowledge of how plants sense and respond to changes in N availability, as well as identifying new targets for breeding strategies to simultaneously improve NUE and grain yield, could usher in a new green revolution.
Collapse
Affiliation(s)
- Xiang Han
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Kun Wu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qian Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| |
Collapse
|
36
|
Liu KH, Diener A, Lin Z, Liu C, Sheen J. Primary nitrate responses mediated by calcium signalling and diverse protein phosphorylation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4428-4441. [PMID: 31985788 PMCID: PMC7382375 DOI: 10.1093/jxb/eraa047] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/24/2020] [Indexed: 05/04/2023]
Abstract
Nitrate, the major source of inorganic nitrogen for plants, is a critical signal controlling nutrient transport and assimilation and adaptive growth responses throughout the plant. Understanding how plants perceive nitrate and how this perception is transduced into responses that optimize growth are important for the rational improvement of crop productivity and for mitigating pollution from the use of fertilizers. This review highlights recent findings that reveal key roles of cytosolic-nuclear calcium signalling and dynamic protein phosphorylation via diverse mechanisms in the primary nitrate response (PNR). Nitrate-triggered calcium signatures as well as the critical functions of subgroup III calcium-sensor protein kinases, a specific protein phosphatase 2C, and RNA polymerase II C-terminal domain phosphatase-like 3 are discussed. Moreover, genome-wide meta-analysis of nitrate-regulated genes encoding candidate protein kinases and phosphatases for modulating critical phosphorylation events in the PNR are elaborated. We also consider how phosphoproteomics approaches can contribute to the identification of putative regulatory protein kinases in the PNR. Exploring and integrating experimental strategies, new methodologies, and comprehensive datasets will further advance our understanding of the molecular and cellular mechanisms underlying the complex regulatory processes in the PNR.
Collapse
Affiliation(s)
- Kun-Hsiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
- Correspondence:
| | - Andrew Diener
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ziwei Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
37
|
Thi Nong H, Tateishi R, Suriyasak C, Kobayashi T, Oyama Y, Chen WJ, Matsumoto R, Hamaoka N, Iwaya-Inoue M, Ishibashi Y. Effect of Seedling Nitrogen Condition on Subsequent Vegetative Growth Stages and Its Relationship to the Expression of Nitrogen Transporter Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2020; 9:E861. [PMID: 32646051 PMCID: PMC7412562 DOI: 10.3390/plants9070861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022]
Abstract
Nitrogen (N) deficiency is one of the most common problems in soils, limiting crop growth and production. However, the effects of N limitation in seedlings on vegetative growth remain poorly understood. Here, we show that N limitation in rice seedlings restricted vegetative growth but not yield. Aboveground parts were affected mainly during the period of tillering, but belowground parts were sensitive throughout vegetative growth, especially during panicle development. At the tillering stage, N-limited plants had a significantly lower N content in shoots, but not in roots. On the other hand, N content in roots during the panicle development stage was significantly lower in N-limited plants. This distinct response was driven by significant changes in expression of N transporter genes during growth. Under N limitation, N translocation from roots to shoots was greatly sped up by systemic expression of N transporter genes to obtain balanced growth. N limitation during the seedling stage did not reduce any yield components. We conclude that the N condition during the seedling stage affects physiological responses such as N translocation through the expression of N transporter genes.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yushi Ishibashi
- Graduate school of Bioresource and Bioenviromental Sciences, Kyushu University, Mootoka 774, Fukuoka 819–0395, Japan; (H.T.N.); (R.T.); (C.S.); (T.K.); (Y.O.); (W.J.C.); (R.M.); (N.H.); (M.I.-I.)
| |
Collapse
|
38
|
Chaput V, Martin A, Lejay L. Redox metabolism: the hidden player in carbon and nitrogen signaling? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3816-3826. [PMID: 32064525 DOI: 10.1093/jxb/eraa078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/12/2020] [Indexed: 05/05/2023]
Abstract
While decades of research have considered redox metabolism as purely defensive, recent results show that reactive oxygen species (ROS) are necessary for growth and development. Close relationships have been found between the regulation of nitrogen metabolism and ROS in response to both carbon and nitrogen availability. Root nitrate uptake and nitrogen metabolism have been shown to be regulated by a signal from the oxidative pentose phosphate pathway (OPPP) in response to carbon signaling. As a major source of NADP(H), the OPPP is critical to maintaining redox balance under stress situations. Furthermore, recent results suggest that at least part of the regulation of the root nitrate transporter by nitrogen signaling is also linked to the redox status of the plant. This leads to the question of whether there is a more general role of redox metabolism in the regulation of nitrogen metabolism by carbon and nitrogen. This review highlights the role of the OPPP in carbon signaling and redox metabolism, and the interaction between redox and nitrogen metabolism. We discuss how redox metabolism could be an important player in the regulation of nitrogen metabolism in response to carbon/nitrogen interaction and the implications for plant adaptation to extreme environments and future crop development.
Collapse
Affiliation(s)
- Valentin Chaput
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Antoine Martin
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Laurence Lejay
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
39
|
Abstract
To investigate factors influencing pre-mRNA splicing in plants, we conducted a forward genetic screen using an alternatively-spliced GFP reporter gene in Arabidopsis thaliana. This effort generated a collection of sixteen mutants impaired in various splicing-related proteins, many of which had not been recovered in any prior genetic screen or implicated in splicing in plants. The factors are predicted to act at different steps of the spliceosomal cycle, snRNP biogenesis pathway, transcription, and mRNA transport. We have described eleven of the mutants in recent publications. Here we present the final five mutants, which are defective, respectively, in RNA-BINDING PROTEIN 45D (rbp45d), DIGEORGE SYNDROME CRITICAL REGION 14 (dgcr14), CYCLIN-DEPENDENT KINASE G2 (cdkg2), INTERACTS WITH SPT6 (iws1) and CAP BINDING PROTEIN 80 (cbp80). We provide RNA-sequencing data and analyses of differential gene expression and alternative splicing patterns for the cbp80 mutant and for several previously published mutants, including smfa and new alleles of cwc16a, for which such information was not yet available. Sequencing of small RNAs from the cbp80 mutant highlighted the necessity of wild-type CBP80 for processing of microRNA (miRNA) precursors into mature miRNAs. Redundancy tests of paralogs encoding several of the splicing factors revealed their functional non-equivalence in the GFP reporter gene system. We discuss the cumulative findings and their implications for the regulation of pre-mRNA splicing efficiency and alternative splicing in plants. The mutant collection provides a unique resource for further studies on a coherent set of splicing factors and their roles in gene expression, alternative splicing and plant development.
Collapse
|
40
|
Zou X, Liu MY, Wu WH, Wang Y. Phosphorylation at Ser28 stabilizes the Arabidopsis nitrate transporter NRT2.1 in response to nitrate limitation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:865-876. [PMID: 31342638 DOI: 10.1111/jipb.12858] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Nitrate is one of the main inorganic nitrogen sources for plants. Nitrate absorption from soils is achieved through the combined activities of specific nitrate transporters. Nitrate transporter 2.1 (NRT2.1) is the major component of the root high-affinity nitrate transport system in Arabidopsis thaliana. Studies to date have mainly focused on transcriptional control of NRT2.1. Here, we show that NRT2.1 protein stability is also regulated in response to nitrogen nutrition availability. When seedlings were transferred to nitrate-limited conditions, the apparent half-life of NRT2.1 in roots increased from 3 to 9 h. This stabilization of NRT2.1 protein occurred rapidly, even prior to the transcriptional stimulation of NRT2.1. Furthermore, we revealed that phosphorylation at serine 28 (Ser28) of NRT2.1 is involved in regulating the stability of this protein. Substitution of Ser28 by alanine resulted in unstable NRT2.1, and this loss-of-phosphorylation mutant (NRT2.1S28A ) failed to complement the growth-restricted phenotype of the nrt2.1 mutant when a low concentration of nitrate was the sole nitrogen source. These results demonstrate that phosphorylation at Ser28 is crucial for NRT2.1 protein stabilization and accumulation in response to nitrate limitation.
Collapse
Affiliation(s)
- Xue Zou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Meng-Yuan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei-Hua Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
41
|
Medina CA, Hawkins C, Liu XP, Peel M, Yu LX. Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa ( Medicago sativa L.). Int J Mol Sci 2020; 21:ijms21093361. [PMID: 32397526 PMCID: PMC7247575 DOI: 10.3390/ijms21093361%20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 05/28/2023] Open
Abstract
Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.
Collapse
Affiliation(s)
- Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
| | - Charles Hawkins
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Xiang-Ping Liu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: College of Animal Science & Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163316, Heilongjiang, China
| | - Michael Peel
- United States Department of Agriculture-Agricultural Research Service, Forage and Range Research Lab, Logan, UT 84322, USA;
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
| |
Collapse
|
42
|
Medina CA, Hawkins C, Liu XP, Peel M, Yu LX. Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa ( Medicago sativa L.). Int J Mol Sci 2020; 21:E3361. [PMID: 32397526 PMCID: PMC7247575 DOI: 10.3390/ijms21093361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.
Collapse
Affiliation(s)
- Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
| | - Charles Hawkins
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Xiang-Ping Liu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: College of Animal Science & Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163316, Heilongjiang, China
| | - Michael Peel
- United States Department of Agriculture-Agricultural Research Service, Forage and Range Research Lab, Logan, UT 84322, USA;
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
| |
Collapse
|
43
|
Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG. Epigenetic regulation in plant abiotic stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:563-580. [PMID: 31872527 DOI: 10.1111/jipb.12901] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/20/2020] [Indexed: 05/18/2023]
Abstract
In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress-responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross-talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.
Collapse
Affiliation(s)
- Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| |
Collapse
|
44
|
Asim M, Ullah Z, Oluwaseun A, Wang Q, Liu H. Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana. Int J Mol Sci 2020; 21:E2880. [PMID: 32326090 PMCID: PMC7215989 DOI: 10.3390/ijms21082880] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
Nitrate (NO3-) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO3-) supply tends to promote auxin translocation from shoots to roots and vice-versa. This nitrate mediated auxin biosynthesis regulating lateral roots growth is induced by the nitrate transporters and its downstream transcription factors. Most nitrate responsive genes (short-term and long-term) are involved in signalling overlap between nitrate and auxin, thereby inducing lateral roots initiation, emergence, and development. Moreover, in the auxin signalling pathway, the varying nitrate supply regulates lateral roots development by modulating the auxin accumulation in the roots. Here, we focus on the roles of nitrate responsive genes in mediating auxin biosynthesis in Arabidopsis root, and the mechanism involved in the transport of auxin at different nitrate levels. In addition, this review also provides an insight into the significance of nitrate responsive regulatory module and their downstream transcription factors in root system architecture in the model plant Arabidopsis thaliana.
Collapse
Affiliation(s)
- Muhammad Asim
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zia Ullah
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Aluko Oluwaseun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
| | - Haobao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.)
| |
Collapse
|
45
|
Bartusch K, Trenner J, Melnyk CW, Quint M. Cut and paste: temperature-enhanced cotyledon micrografting for Arabidopsis thaliana seedlings. PLANT METHODS 2020; 16:12. [PMID: 32042304 PMCID: PMC7001232 DOI: 10.1186/s13007-020-0562-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/27/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Cotyledon micrografting represents a useful tool for studying the central role of cotyledons during early plant development, especially their interplay with other plant organs with regard to long distance transport. While hypocotyl micrografting methods are well-established, cotyledon micrografting is still inefficient. By optimizing cotyledon micrografting, we aim for higher success rates and increased throughput in the model species Arabidopsis thaliana. RESULTS We established a cut and paste cotyledon surgery procedure on a flat and solid but moist surface which improved handling of small seedlings. By applying a specific cutting and joining pattern, throughput was increased up to 40 seedlings per hour. The combination of short-day photoperiods and low light intensities for germination and long days plus high light intensities, elevated temperature and vertical plate positioning after grafting significantly increased 'ligation' efficiency. In particular high temperatures affected success rates favorably. Altogether, we achieved up to 92% grafting success in A. thaliana. Reconnection of vasculature was demonstrated by transport of a vasculature-specific dye across the grafting site. Phloem and xylem reconnection were completed 3-4 and 4-6 days after grafting, respectively, in a temperature-dependent manner. We observed that plants with grafted cotyledons match plants with intact cotyledons in biomass production and rosette development. CONCLUSIONS This cut and paste cotyledon-to-petiole micrografting protocol simplifies the handling of plant seedlings in surgery, increases the number of grafted plants per hour and greatly improves success rates for A. thaliana seedlings. The developed cotyledon micrografting method is also suitable for other plant species of comparable size.
Collapse
Affiliation(s)
- Kai Bartusch
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences, Ulls gränd 1, 765 51 Uppsala, Sweden
| | - Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
| | - Charles W. Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, Ulls gränd 1, 765 51 Uppsala, Sweden
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
| |
Collapse
|
46
|
Abstract
Uptake, assimilation, and recycling of nutrients are essential for optimal plant growth and development. A large number of studies have contributed significantly to highlight the major features that shape an efficient utilization of nutrients in plants, especially at the transcriptional level. However, only a few examples have explored the epigenetic mechanisms that are intrinsically associated to the transcriptional reprogramming events in response to nutritional fluctuations. In this review, we gather the chromatin-based mechanisms that have been described in response to variations of nutrients availability. At this time of genome and epigenome editing, such mechanisms could potentially represent new targets for crop improvement.
Collapse
Affiliation(s)
- David Séré
- BPMP, CNRS, INRA, SupAgro, University of Montpellier, Montpellier, France
| | - Antoine Martin
- BPMP, CNRS, INRA, SupAgro, University of Montpellier, Montpellier, France
- CONTACT Antoine Martin BPMP, CNRS, INRA, SupAgro, University of Montpellier, Montpellier, France
| |
Collapse
|
47
|
Li Y, Brooks M, Yeoh-Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM. SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling. PLANT PHYSIOLOGY 2020; 182:215-227. [PMID: 31641075 PMCID: PMC6945839 DOI: 10.1104/pp.19.00682] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 05/04/2023]
Abstract
Chromatin modification has gained increased attention for its role in the regulation of plant responses to environmental changes, but the specific mechanisms and molecular players remain elusive. Here, we show that the Arabidopsis (Arabidopsis thaliana) histone methyltransferase SET DOMAIN GROUP8 (SDG8) mediates genome-wide changes in H3K36 methylation at specific genomic loci functionally relevant to nitrate treatments. Moreover, we show that the specific H3K36 methyltransferase encoded by SDG8 is required for canonical RNA processing, and that RNA isoform switching is more prominent in the sdg8-5 deletion mutant than in the wild type. To demonstrate that SDG8-mediated regulation of RNA isoform expression is functionally relevant, we examined a putative regulatory gene, CONSTANS, CO-like, and TOC1 101 (CCT101), whose nitrogen-responsive isoform-specific RNA expression is mediated by SDG8. We show by functional expression in shoot cells that the different RNA isoforms of CCT101 encode distinct regulatory proteins with different effects on genome-wide transcription. We conclude that SDG8 is involved in plant responses to environmental nitrogen supply, affecting multiple gene regulatory processes including genome-wide histone modification, transcriptional regulation, and RNA processing, and thereby mediating developmental and metabolic processes related to nitrogen use.
Collapse
Affiliation(s)
- Ying Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Matthew Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Jenny Yeoh-Wang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rachel M McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Tara M Rock
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Chang In Moon
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, French National Institute for Agricultural Research, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | | | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| |
Collapse
|
48
|
Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
Collapse
Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
| |
Collapse
|
49
|
Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. MOLECULAR PLANT 2019; 12:1545-1560. [PMID: 31526863 DOI: 10.1016/j.molp.2019.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 05/13/2023]
Abstract
Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
Collapse
Affiliation(s)
- José M Alvarez
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tao Zhang
- Yangzhou University, Yangzhou, China
| | - Diana E Gras
- Instituto de Agrobiotecnologia del Litoral, CONICET, Santa Fe, Argentina
| | - Francisco J Herrera
- University of California, Berkeley, CA, USA; Trancura Biosciences, Inc., San Francisco, CA 94158, USA
| | - Viviana Araus
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - José A O'Brien
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Plant Biology and Horticulture, Michigan State University, MI 48824, USA
| | | |
Collapse
|
50
|
Huang XY, Li M, Luo R, Zhao FJ, Salt DE. Epigenetic regulation of sulfur homeostasis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4171-4182. [PMID: 31087073 DOI: 10.1093/jxb/erz218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
Plants have evolved sophisticated mechanisms for adaptation to fluctuating availability of nutrients in soil. Such mechanisms are of importance for plants to maintain homeostasis of nutrient elements for their development and growth. The molecular mechanisms controlling the homeostasis of nutrient elements at the genetic level have been gradually revealed, including the identification of regulatory factors and transporters responding to nutrient stresses. Recent studies have suggested that such responses are controlled not only by genetic regulation but also by epigenetic regulation. In this review, we present recent studies on the involvement of DNA methylation, histone modifications, and non-coding RNA-mediated gene silencing in the regulation of sulfur homeostasis and the response to sulfur deficiency. We also discuss the potential effect of sulfur-containing metabolites such as S-adenosylmethionine on the maintenance of DNA and histone methylation.
Collapse
Affiliation(s)
- Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengzhen Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Rongjian Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| |
Collapse
|