1
|
Zhao Y, Zhang Y, Li S, Tan S, Cao J, Wang HL, Luo J, Guo H, Zhang Z, Li Z. Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research. J Mol Biol 2024; 436:168530. [PMID: 38462130 DOI: 10.1016/j.jmb.2024.168530] [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: 01/04/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Through an extensive literature survey, we have upgraded the Leaf Senescence Database (LSD v5.0; https://ngdc.cncb.ac.cn/lsd/), a curated repository of comprehensive senescence-associated genes (SAGs) and their corresponding mutants. Since its inception in 2010, LSD undergoes frequent updates to encompass the latest advances in leaf senescence research and its current version comprises a high-quality collection of 31,740 SAGs and 1,209 mutants from 148 species, which were manually searched based on robust experimental evidence and further categorized according to their functions in leaf senescence. Furthermore, LSD was greatly enriched with comprehensive annotations for the SAGs through meticulous curation using both manual and computational methods. In addition, it was equipped with user-friendly web interfaces that facilitate text queries, BLAST searches, and convenient download of SAG sequences for localized analysis. Users can effortlessly navigate the database to access a plethora of information, including literature references, mutants, phenotypes, multi-omics data, miRNA interactions, homologs in other plants, and cross-links to various databases. Taken together, the upgraded version of LSD stands as the most comprehensive and informative plant senescence-related database to date, incorporating the largest collection of SAGs and thus bearing great utility for a wide range of studies related to plant senescence.
Collapse
Affiliation(s)
- Yaning Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yang Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shichun Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jie Cao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jingchu Luo
- College of Life Sciences, Peking University, Beijing 100871, China; Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Zhang Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| |
Collapse
|
2
|
Guo C, Huang Z, Chen J, Yu G, Wang Y, Wang X. Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model. PLANTS (BASEL, SWITZERLAND) 2024; 13:1276. [PMID: 38732491 PMCID: PMC11085074 DOI: 10.3390/plants13091276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Deep learning has emerged as a powerful tool for investigating intricate biological processes in plants by harnessing the potential of large-scale data. Gene regulation is a complex process that transcription factors (TFs), cooperating with their target genes, participate in through various aspects of biological processes. Despite its significance, the study of gene regulation has primarily focused on a limited number of notable instances, leaving numerous aspects and interactions yet to be explored comprehensively. Here, we developed DEGRN (Deep learning on Expression for Gene Regulatory Network), an innovative deep learning model designed to decipher gene interactions by leveraging high-dimensional expression data obtained from bulk RNA-Seq and scRNA-Seq data in the model plant Arabidopsis. DEGRN exhibited a compared level of predictive power when applied to various datasets. Through the utilization of DEGRN, we successfully identified an extensive set of 3,053,363 high-quality interactions, encompassing 1430 TFs and 13,739 non-TF genes. Notably, DEGRN's predictive capabilities allowed us to uncover novel regulators involved in a range of complex biological processes, including development, metabolism, and stress responses. Using leaf senescence as an example, we revealed a complex network underpinning this process composed of diverse TF families, including bHLH, ERF, and MYB. We also identified a novel TF, named MAF5, whose expression showed a strong linear regression relation during the progression of senescence. The mutant maf5 showed early leaf decay compared to the wild type, indicating a potential role in the regulation of leaf senescence. This hypothesis was further supported by the expression patterns observed across four stages of leaf development, as well as transcriptomics analysis. Overall, the comprehensive coverage provided by DEGRN expands our understanding of gene regulatory networks and paves the way for further investigations into their functional implications.
Collapse
Affiliation(s)
| | | | | | | | | | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (C.G.); (Z.H.); (J.C.); (G.Y.); (Y.W.)
| |
Collapse
|
3
|
Tian D, Xu T, Kang H, Luo H, Wang Y, Chen M, Li R, Ma L, Wang Z, Hao L, Tang B, Zou D, Xiao J, Zhao W, Bao Y, Zhang Z, Song S. Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications. ABIOTECH 2024; 5:94-106. [PMID: 38576435 PMCID: PMC10987443 DOI: 10.1007/s42994-023-00134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/18/2023] [Indexed: 04/06/2024]
Abstract
Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems, including the constituent elements within and among species. Through various efforts in genomic data archiving, integrative analysis and value-added curation, the National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), has successfully established and currently maintains a vast amount of database resources. This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts. Here, we present a comprehensive overview of central repositories dedicated to archiving, presenting, and sharing plant omics data, introduce knowledgebases focused on variants or gene-based functional insights, highlight species-specific multiple omics database resources, and briefly review the online application tools. We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00134-4.
Collapse
Affiliation(s)
- Dongmei Tian
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Tianyi Xu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Hailong Kang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hong Luo
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Yanqing Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Meili Chen
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Rujiao Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Lina Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Zhonghuang Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lili Hao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Bixia Tang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenming Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| |
Collapse
|
4
|
Zhang JF, Wang YY, He L, Yan JY, Liu YY, Ruan ZY, Liu WC, Yi L, Ren F. PHR1 involved in the regulation of low phosphate-induced leaf senescence by modulating phosphorus homeostasis in Arabidopsis. PLANT, CELL & ENVIRONMENT 2024; 47:799-816. [PMID: 38111215 DOI: 10.1111/pce.14790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/09/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023]
Abstract
Phosphorus (P) is a crucial macronutrient for plant growth, development, and reproduction. The effects of low P (LP) stress on leaf senescence and the role of PHR1 in LP-induced leaf senescence are still unknown. Here, we report that PHR1 plays a crucial role in LP-induced leaf senescence, showing delayed leaf senescence in phr1 mutant and accelerated leaf senescence in 35S:PHR1 transgenic Arabidopsis under LP stress. The transcriptional profiles indicate that 763 differentially expressed SAGs (DE-SAGs) were upregulated and 134 DE-SAGs were downregulated by LP stress. Of the 405 DE-SAGs regulated by PHR1, 27 DE-SAGs were involved in P metabolism and transport. PHR1 could bind to the promoters of six DE-SAGs (RNS1, PAP17, SAG113, NPC5, PLDζ2, and Pht1;5), and modulate them in LP-induced senescing leaves. The analysis of RNA content, phospholipase activity, acid phosphatase activity, total P and phosphate content also revealed that PHR1 promotes P liberation from senescing leaves and transport to young tissues under LP stress. Our results indicated that PHR1 is one of the crucial modulators for P recycling and redistribution under LP stress, and the drastic decline of P level is at least one of the causes of early senescence in P-deficient leaves.
Collapse
Affiliation(s)
- Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - You-Yi Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Le He
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jing-Yi Yan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ying-Ying Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhao-Yang Ruan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Wen-Cheng Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Long Yi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- School of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| |
Collapse
|
5
|
Li S, Zhao Y, Tan S, Li Z. Non-coding RNAs and leaf senescence: Small molecules with important roles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108399. [PMID: 38277833 DOI: 10.1016/j.plaphy.2024.108399] [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: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Non-coding RNAs (ncRNAs) are a special class of functional RNA molecules that are not translated into proteins. ncRNAs have emerged as pivotal regulators of diverse developmental processes in plants. Recent investigations have revealed the association of ncRNAs with the regulation of leaf senescence, a complex and tightly regulated developmental process. However, a comprehensive review of the involvement of ncRNAs in the regulation of leaf senescence is still lacking. This manuscript aims to summarize the molecular mechanisms underlying ncRNAs-mediated leaf senescence and the potential applications of ncRNAs to manipulate the onset and progression of leaf senescence. Various classes of ncRNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are discussed in terms of their regulatory mechanisms in leaf senescence. Furthermore, we explore the interactions between ncRNA and the key regulators of senescence, including transcription factors as well as core components in phytohormone signaling pathways. We also discuss the possible challenges and approaches related to ncRNA-mediated leaf senescence. This review contributes to a further understanding of the intricate regulatory network involving ncRNAs in leaf senescence.
Collapse
Affiliation(s)
- Shichun Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
6
|
Yang S, Zong W, Shi L, Li R, Ma Z, Ma S, Si J, Wu Z, Zhai J, Ma Y, Fan Z, Chen S, Huang H, Zhang D, Bao Y, Li R, Xie J. PPGR: a comprehensive perennial plant genomes and regulation database. Nucleic Acids Res 2024; 52:D1588-D1596. [PMID: 37933857 PMCID: PMC10767873 DOI: 10.1093/nar/gkad963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023] Open
Abstract
Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.cncb.ac.cn/ppgr/) to address this critical gap, by collecting, integrating, analyzing and visualizing genomic, gene regulation and functional data of perennial plants. PPGR currently includes 60 species, 847 million protein-protein/TF (transcription factor)-target interactions, 9016 transcriptome samples under various environmental conditions and genetic backgrounds. Noteworthy is the focus on genes that regulate wood production, seasonal dormancy, terpene biosynthesis and leaf senescence representing a wealth of information derived from experimental data, literature mining, public databases and genomic predictions. Furthermore, PPGR incorporates a range of multi-omics search and analysis tools to facilitate browsing and application of these extensive datasets. PPGR represents a comprehensive and high-quality resource for perennial plants, substantiated by an illustrative case study that demonstrates its capacity in unraveling gene functions and shedding light on potential regulatory processes.
Collapse
Affiliation(s)
- Sen Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Wenting Zong
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingling Shi
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Ruisi Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Zhenshu Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Shubao Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Jingna Si
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Zhijing Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Jinglan Zhai
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yingke Ma
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Zhuojing Fan
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Sisi Chen
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, China
| | - Deqiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rujiao Li
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
7
|
Kim SH, Yoon J, Kim H, Lee SJ, Paek NC. Rice Basic Helix-Loop-Helix 079 (OsbHLH079) Delays Leaf Senescence by Attenuating ABA Signaling. RICE (NEW YORK, N.Y.) 2023; 16:60. [PMID: 38093151 PMCID: PMC10719235 DOI: 10.1186/s12284-023-00673-w] [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: 09/07/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Leaf senescence represents the final phase of leaf development and is characterized by a highly organized degenerative process involving the active translocation of nutrients from senescing leaves to growing tissues or storage organs. To date, a large number of senescence-associated transcription factors (sen-TFs) have been identified that regulate the initiation and progression of leaf senescence. Many of these TFs, including NAC (NAM/ATAF1/2/CUC2), WRKY, and MYB TFs, have been implicated in modulating the expression of downstream senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs) under the control of phytohormones. However, the involvement of basic helix-loop-helix (bHLH) TFs in leaf senescence has been less investigated. Here, we show that OsbHLH079 delays both natural senescence and dark-induced senescence: Overexpression of OsbHLH079 led to a stay-green phenotype, whereas osbhlh079 knockout mutation displayed accelerated leaf senescence. Similar to other sen-TFs, OsbHLH079 showed a gradual escalation in expression as leaves underwent senescence. During this process, the mRNA levels of SAGs and CDGs remained relatively low in OsbHLH079 overexpressors, but increased sharply in osbhlh079 mutants, suggesting that OsbHLH079 negatively regulates the transcription of SAGs and CDGs under senescence conditions. Additionally, we found that OsbHLH079 delays ABA-induced senescence. Subsequent RT-qPCR and dual-luciferase reporter assays revealed that OsbHLH079 downregulates the expression of ABA signaling genes, such as OsABF2, OsABF4, OsABI5, and OsNAP. Taken together, these results demonstrate that OsbHLH079 functions in delaying leaf yellowing by attenuating the ABA responses.
Collapse
Affiliation(s)
- Suk-Hwan Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jungwon Yoon
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hanna Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sang-Ji Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|
8
|
Zhou M, Zhang Y, Yang J. Analysis of Nitrogen Dynamics and Transcriptomic Activity Revealed a Pivotal Role of Some Amino Acid Transporters in Nitrogen Remobilization in Poplar Senescing Leaves. PLANTS (BASEL, SWITZERLAND) 2023; 12:4140. [PMID: 38140467 PMCID: PMC10747403 DOI: 10.3390/plants12244140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
Leaf senescence is an important developmental process for deciduous trees during which part of leaf nitrogen is remobilized to branches, thus being beneficial for nitrogen conservation. However, the associated regulatory mechanism remains largely unknown in deciduous trees. In this study, nitrogen dynamics and transcriptomic activity in senescing leaves were measured during autumnal senescence in hybrid poplar. Both concentrations of leaf total nitrogen (N) and amine compounds were found to decline from the pre-senescence (PRE) to the middle-senescence (MS) stage. Although the total N concentration decreased further from MS to the late-senescence (LS) and leveled off to abscission (ABS) stage, amine compound concentration increased continuously from MS to ABS, suggesting that translocation of amine compounds underperformed production of amine compounds in leaves during this period. L-glutamate, L-glutamine and α-aminoadipic acid were the top three amine compounds accumulated in senescent leaves. RNA-Seq profiling identified thousands of differentially expressed genes (DEGs) with functional association with a metabolic transition towards disassimilation. Many genes encoding amino acid metabolism enzymes and amino acid transporters (AATs) were up-regulated. Comparison of expression trend with leaf N dynamics and phylogenetic analysis identified several PtAATs which exhibited down-regulation from MS to LS stage and putatively limited leaf N remobilization. This study can serve as a primary basis to further elucidate the molecular mechanisms of nitrogen remobilization in poplar senescing leaves.
Collapse
Affiliation(s)
| | | | - Jiading Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (M.Z.); (Y.Z.)
| |
Collapse
|
9
|
Zhang W, Zhang Z, Chen Q, Wang Z, Song W, Yang K, Xin M, Hu Z, Liu J, Peng H, Lai J, Guo W, Ni Z, Sun Q, Du J, Yao Y. Mutation of a highly conserved amino acid in RPM1 causes leaf yellowing and premature senescence in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:254. [PMID: 38006406 DOI: 10.1007/s00122-023-04499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/01/2023] [Indexed: 11/27/2023]
Abstract
KEY MESSAGE A point mutation of RPM1 triggers persistent immune response that induces leaf premature senescence in wheat, providing novel information of immune responses and leaf senescence. Leaf premature senescence in wheat (Triticum aestivum L.) is one of the most common factors affecting the plant's development and yield. In this study, we identified a novel wheat mutant, yellow leaf and premature senescence (ylp), which exhibits yellow leaves and premature senescence at the heading and flowering stages. Consistent with the yellow leaves phenotype, ylp had damaged and collapsed chloroplasts. Map-based cloning revealed that the phenotype of ylp was caused by a point mutation from Arg to His at amino acid 790 in a plasma membrane-localized protein resistance to Pseudomonas syringae pv. maculicola 1 (RPM1). The point mutation triggered excessive immune responses and the upregulation of senescence- and autophagy-associated genes. This work provided the information for understanding the molecular regulatory mechanism of leaf senescence, and the results would be important to analyze which mutations of RPM1 could enable plants to obtain immune activation without negative effects on plant growth.
Collapse
Affiliation(s)
- Wenjia Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoheng Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qian Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Kai Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinkun Du
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
10
|
Kumar R, Brar MS, Kunduru B, Ackerman AJ, Yang Y, Luo F, Saski CA, Bridges WC, de Leon N, McMahan C, Kaeppler SM, Sekhon RS. Genetic architecture of source-sink-regulated senescence in maize. PLANT PHYSIOLOGY 2023; 193:2459-2479. [PMID: 37595026 DOI: 10.1093/plphys/kiad460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
Source and sink interactions play a critical but mechanistically poorly understood role in the regulation of senescence. To disentangle the genetic and molecular mechanisms underlying source-sink-regulated senescence (SSRS), we performed a phenotypic, transcriptomic, and systems genetics analysis of senescence induced by the lack of a strong sink in maize (Zea mays). Comparative analysis of genotypes with contrasting SSRS phenotypes revealed that feedback inhibition of photosynthesis, a surge in reactive oxygen species, and the resulting endoplasmic reticulum (ER) stress were the earliest outcomes of weakened sink demand. Multienvironmental evaluation of a biparental population and a diversity panel identified 12 quantitative trait loci and 24 candidate genes, respectively, underlying SSRS. Combining the natural diversity and coexpression networks analyses identified 7 high-confidence candidate genes involved in proteolysis, photosynthesis, stress response, and protein folding. The role of a cathepsin B like protease 4 (ccp4), a candidate gene supported by systems genetic analysis, was validated by analysis of natural alleles in maize and heterologous analyses in Arabidopsis (Arabidopsis thaliana). Analysis of natural alleles suggested that a 700-bp polymorphic promoter region harboring multiple ABA-responsive elements is responsible for differential transcriptional regulation of ccp4 by ABA and the resulting variation in SSRS phenotype. We propose a model for SSRS wherein feedback inhibition of photosynthesis, ABA signaling, and oxidative stress converge to induce ER stress manifested as programed cell death and senescence. These findings provide a deeper understanding of signals emerging from loss of sink strength and offer opportunities to modify these signals to alter senescence program and enhance crop productivity.
Collapse
Affiliation(s)
- Rohit Kumar
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Manwinder S Brar
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Bharath Kunduru
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Arlyn J Ackerman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Yuan Yang
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC 29634, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - William C Bridges
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
| | - Christopher McMahan
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
| | - Rajandeep S Sekhon
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
11
|
Yang Q, Wang T, Cao J, Wang HL, Tan S, Zhang Y, Park S, Park H, Woo HR, Li X, Xia X, Guo H, Li Z. Histone variant HTB4 delays leaf senescence by epigenetic control of Ib bHLH transcription factor-mediated iron homeostasis. THE NEW PHYTOLOGIST 2023; 240:694-709. [PMID: 37265004 DOI: 10.1111/nph.19008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/02/2023] [Indexed: 06/03/2023]
Abstract
Leaf senescence is an orderly process regulated by multiple internal factors and diverse environmental stresses including nutrient deficiency. Histone variants are involved in regulating plant growth and development. However, their functions and underlying regulatory mechanisms in leaf senescence remain largely unclear. Here, we found that H2B histone variant HTB4 functions as a negative regulator of leaf senescence. Loss of function of HTB4 led to early leaf senescence phenotypes that were rescued by functional complementation. RNA-seq analysis revealed that several Ib subgroup basic helix-loop-helix (bHLH) transcription factors (TFs) involved in iron (Fe) homeostasis, including bHLH038, bHLH039, bHLH100, and bHLH101, were suppressed in the htb4 mutant, thereby compromising the expressions of FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER (IRT1), two important components of the Fe uptake machinery. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis revealed that HTB4 could bind to the promoter regions of Ib bHLH TFs and enhance their expression by promoting the enrichment of the active mark H3K4me3 near their transcriptional start sites. Moreover, overexpression of Ib bHLH TFs or IRT1 suppressed the premature senescence phenotype of the htb4 mutant. Our work established a signaling pathway, HTB4-bHLH TFs-FRO2/IRT1-Fe homeostasis, which regulates the onset and progression of leaf senescence.
Collapse
Affiliation(s)
- Qi Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jie Cao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuan Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Sanghoon Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea
| | - Hyunsoo Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea
| | - Xiaojuan Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Department of Biology, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
12
|
Gao Y, Shi X, Chang Y, Li Y, Xiong X, Liu H, Li M, Li W, Zhang X, Fu Z, Xue Y, Tang J. Mapping the gene of a maize leaf senescence mutant and understanding the senescence pathways by expression analysis. PLANT CELL REPORTS 2023; 42:1651-1663. [PMID: 37498331 DOI: 10.1007/s00299-023-03051-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
KEY MESSAGES Narrowing down to a single putative target gene behind a leaf senescence mutant and constructing the regulation network by proteomic method. Leaf senescence mutant is an important resource for exploring molecular mechanism of aging. To dig for potential modulation networks during maize leaf aging process, we delimited the gene responsible for a premature leaf senescence mutant els5 to a 1.1 Mb interval in the B73 reference genome using a BC1F1 population with 40,000 plants, and analyzed the leaf proteomics of the mutant and its near-isogenic wild type line. A total of 1355 differentially accumulated proteins (DAP) were mainly enriched in regulation pathways such as "photosynthesis", "ribosome", and "porphyrin and chlorophyll metabolism" by the KEGG pathway analysis. The interaction networks constructed by incorporation of transcriptome data showed that ZmELS5 likely repaired several key factors in the photosynthesis system. The putative candidate proteins for els5 were proposed based on DAPs in the fined QTL mapping interval. These results provide fundamental basis for cloning and functional research of the els5 gene, and new insights into the molecular mechanism of leaf senescence in maize.
Collapse
Affiliation(s)
- Yong Gao
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xia Shi
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongyuan Chang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingbo Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehang Xiong
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongmei Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengyuan Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehai Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yadong Xue
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
13
|
Lei P, Yu F, Liu X. Recent advances in cellular degradation and nuclear control of leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5472-5486. [PMID: 37453102 DOI: 10.1093/jxb/erad273] [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: 04/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Senescence is the final stage of plant growth and development, and is a highly regulated process at the molecular, cellular, and organismal levels. When triggered by age, hormonal, or environmental cues, plants actively adjust their metabolism and gene expression to execute the progression of senescence. Regulation of senescence is vital for the reallocation of nutrients to sink organs, to ensure reproductive success and adaptations to stresses. Identification and characterization of hallmarks of leaf senescence are of great importance for understanding the molecular regulatory mechanisms of plant senescence, and breeding future crops with more desirable senescence traits. Tremendous progress has been made in elucidating the genetic network underpinning the metabolic and cellular changes in leaf senescence. In this review, we focus on three hallmarks of leaf senescence - chlorophyll and chloroplast degradation, loss of proteostasis, and activation of senescence-associated genes (SAGs), and discuss recent findings of the molecular players and the crosstalk of senescence pathways.
Collapse
Affiliation(s)
- Pei Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
14
|
Ren Y, Sun X, Nie J, Guo P, Wu X, Zhang Y, Gao M, Niaz M, Yang X, Sun C, Zhang N, Chen F. Mapping QTL conferring flag leaf senescence in durum wheat cultivars. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:66. [PMID: 37564974 PMCID: PMC10409934 DOI: 10.1007/s11032-023-01410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023]
Abstract
Flag leaf senescence is a critical factor affecting the yield and quality of wheat. The aim of this study was to identify QTLs associated with flag leaf senescence in an F10 recombinant inbred line population derived from durum wheats UC1113 and Kofa. Bulked segregant analysis using the wheat 660K SNP array identified 3225 SNPs between extreme-phenotype bulks, and the differential SNPs were mainly clustered on chromosomes 1A, 1B, 3B, 5A, 5B, and 7A. BSR-Seq indicated that the significant SNPs were mainly located in two intervals of 354.0-389.0 Mb and 8.0-15.0 Mb on 1B and 3B, respectively. Based on the distribution of significant SNPs on chromosomes 1B and 3B, a total of 109 insertion/deletion (InDel) markers were developed, and 8 of them were finally used to map QTL in UC1113/Kofa population for flag leaf senescence. Inclusive composite interval mapping identified two major QTL in marker intervals Mar2005-Mar2116 and Mar207-Mar289, explaining 14.2-15.4% and 31.4-68.6% of the phenotypic variances across environments, respectively. Using BSR-Seq, gene expression and sequence analysis, the TraesCS1B02G211600 and TraesCS3B02G023000 were identified as candidate senescence-associated genes. This study has potential to be used in cloning key genes for flag leaf senescence and provides available molecular markers for genotyping and marker-assisted selection breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01410-3.
Collapse
Affiliation(s)
- Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaonan Sun
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Jingyun Nie
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Peng Guo
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaohui Wu
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Yixiao Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Mengjuan Gao
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Mohsin Niaz
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xia Yang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Congwei Sun
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| |
Collapse
|
15
|
Tan S, Sha Y, Sun L, Li Z. Abiotic Stress-Induced Leaf Senescence: Regulatory Mechanisms and Application. Int J Mol Sci 2023; 24:11996. [PMID: 37569371 PMCID: PMC10418887 DOI: 10.3390/ijms241511996] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Leaf senescence is a natural phenomenon that occurs during the aging process of plants and is influenced by various internal and external factors. These factors encompass plant hormones, as well as environmental pressures such as inadequate nutrients, drought, darkness, high salinity, and extreme temperatures. Abiotic stresses accelerate leaf senescence, resulting in reduced photosynthetic efficiency, yield, and quality. Gaining a comprehensive understanding of the molecular mechanisms underlying leaf senescence in response to abiotic stresses is imperative to enhance the resilience and productivity of crops in unfavorable environments. In recent years, substantial advancements have been made in the study of leaf senescence, particularly regarding the identification of pivotal genes and transcription factors involved in this process. Nevertheless, challenges remain, including the necessity for further exploration of the intricate regulatory network governing leaf senescence and the development of effective strategies for manipulating genes in crops. This manuscript provides an overview of the molecular mechanisms that trigger leaf senescence under abiotic stresses, along with strategies to enhance stress tolerance and improve crop yield and quality by delaying leaf senescence. Furthermore, this review also highlighted the challenges associated with leaf senescence research and proposes potential solutions.
Collapse
Affiliation(s)
| | | | - Liwei Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
16
|
Lihavainen J, Šimura J, Bag P, Fataftah N, Robinson KM, Delhomme N, Novák O, Ljung K, Jansson S. Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature. Nat Commun 2023; 14:4288. [PMID: 37463905 DOI: 10.1038/s41467-023-39564-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive "switches"; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.
Collapse
Affiliation(s)
- Jenna Lihavainen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90189, Umeå, Sweden
| | - Jan Šimura
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Pushan Bag
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90189, Umeå, Sweden
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, UK
| | - Nazeer Fataftah
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90189, Umeå, Sweden
| | - Kathryn Megan Robinson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90189, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90189, Umeå, Sweden.
| |
Collapse
|
17
|
Jiang L, Liu K, Zhang T, Chen J, Zhao S, Cui Y, Zhou W, Yu Y, Chen S, Wang C, Zhang C. The RhWRKY33a-RhPLATZ9 regulatory module delays petal senescence by suppressing rapid reactive oxygen species accumulation in rose flowers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1425-1442. [PMID: 36951178 DOI: 10.1111/tpj.16202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/12/2023] [Accepted: 03/10/2023] [Indexed: 06/17/2023]
Abstract
Redox homeostasis in plant cells is critical for maintaining normal growth and development because reactive oxygen species (ROS) can function as signaling molecules or toxic compounds. However, how plants fine-tune redox homeostasis during natural or stress-induced senescence remains unclear. Cut roses (Rosa hybrida), an economically important ornamental product worldwide, often undergo stress-induced precocious senescence at the post-harvest bud stage. Here, we identified RhPLATZ9, an age- and dehydration-induced PLATZ (plant AT-rich sequence and zinc-binding) protein, and determined that it functions as a transcriptional repressor in rose flowers during senescence. We also showed that RhWRKY33a regulates RhPLATZ9 expression during flower senescence. RhPLATZ9-silenced flowers and RhWRKY33a-silenced flowers showed accelerated senescence, with higher ROS contents than the control. By contrast, overexpression of RhWRKY33a or RhPLATZ9 delayed flower senescence, and overexpression in rose calli showed lower ROS accumulation than the control. RNA-sequencing analysis revealed that apoplastic NADPH oxidase genes (RhRbohs) were enriched among the upregulated differentially expressed genes in RhPLATZ9-silenced flowers compared to wild-type flowers. Yeast one-hybrid assays, electrophoretic mobility shift assays, dual luciferase assays and chromatin immunoprecipitation quantitative PCR confirmed that the RhRbohD gene is a direct target of RhPLATZ9. These findings suggest that the RhWRKY33a-RhPLATZ9-RhRbohD regulatory module acts as a brake to help maintain ROS homeostasis in petals and thus antagonize age- and stress-induced precocious senescence in rose flowers.
Collapse
Affiliation(s)
- Liwei Jiang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Kun Liu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Tao Zhang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jin Chen
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Siqi Zhao
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yusen Cui
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wentong Zhou
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Yu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Siyu Chen
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Caiyuan Wang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Changqing Zhang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
18
|
Wang L, Doan PPT, Chuong NN, Lee HY, Kim JH, Kim J. Comprehensive transcriptomic analysis of age-, dark-, and salt-induced senescence reveals underlying mechanisms and key regulators of leaf senescence in Zoysia japonica. FRONTIERS IN PLANT SCIENCE 2023; 14:1170808. [PMID: 37324695 PMCID: PMC10265201 DOI: 10.3389/fpls.2023.1170808] [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: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 06/17/2023]
Abstract
The lawn grass Zoysia japonica is widely cultivated for its ornamental and recreational value. However, its green period is subject to shortening, which significantly decreases the economic value of Z. japonica, especially for large cultivations. Leaf senescence is a crucial biological and developmental process that significantly influences the lifespan of plants. Moreover, manipulation of this process can improve the economic value of Z. japonica by extending its greening period. In this study, we conducted a comparative transcriptomic analysis using high-throughput RNA sequencing (RNA-seq) to investigate early senescence responses triggered by age, dark, and salt. Gene set enrichment analysis results indicated that while distinct biological processes were involved in each type of senescence response, common processes were also enriched across all senescence responses. The identification and validation of differentially expressed genes (DEGs) via RNA-seq and quantitative real-time PCR provided up- and down-regulated senescence markers for each senescence and putative senescence regulators that trigger common senescence pathways. Our findings revealed that the NAC, WRKY, bHLH, and ARF transcription factor (TF) groups are major senescence-associated TF families that may be required for the transcriptional regulation of DEGs during leaf senescence. In addition, we experimentally validated the senescence regulatory function of seven TFs including ZjNAP, ZjWRKY75, ZjARF2, ZjNAC1, ZjNAC083, ZjARF1, and ZjPIL5 using a protoplast-based senescence assay. This study provides new insight into the molecular mechanisms underlying Z. japonica leaf senescence and identifies potential genetic resources for enhancing its economic value by prolonging its green period.
Collapse
Affiliation(s)
- Lanshuo Wang
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, Republic of Korea
| | - Phan Phuong Thao Doan
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, Republic of Korea
| | - Nguyen Nguyen Chuong
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, Republic of Korea
| | - Hyo-Yeon Lee
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
- Department of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Jeongsik Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, Republic of Korea
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea
| |
Collapse
|
19
|
Wen B, Zhao X, Gong X, Zhao W, Sun M, Chen X, Li D, Li L, Xiao W. The NAC transcription factor MdNAC4 positively regulates nitrogen deficiency-induced leaf senescence by enhancing ABA biosynthesis in apple. MOLECULAR HORTICULTURE 2023; 3:5. [PMID: 37789499 PMCID: PMC10514974 DOI: 10.1186/s43897-023-00053-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/22/2023] [Indexed: 10/05/2023]
Abstract
Although it is well established that nitrogen (N) deficiency induces leaf senescence, the molecular mechanism of N deficiency-induced leaf senescence remains largely unknown. Here, we show that an abscisic acid (ABA)-responsive NAC transcription factor (TF) is involved in N deficiency-induced leaf senescence. The overexpression of MdNAC4 led to increased ABA levels in apple calli by directly activating the transcription of the ABA biosynthesis gene MdNCED2. In addition, MdNAC4 overexpression promoted N deficiency-induced leaf senescence. Further investigation showed that MdNAC4 directly bound the promoter of the senescence-associated gene (SAG) MdSAG39 and upregulated its expression. Interestingly, the function of MdNAC4 in promoting N deficiency-induced leaf senescence was enhanced in the presence of ABA. Furthermore, we identified an interaction between the ABA receptor protein MdPYL4 and the MdNAC4 protein. Moreover, MdPYL4 showed a function similar to that of MdNAC4 in ABA-mediated N deficiency-induced leaf senescence. These findings suggest that ABA plays a central role in N deficiency-induced leaf senescence and that MdPYL4 interacts with MdNAC4 to enhance the response of the latter to N deficiency, thus promoting N deficiency-induced leaf senescence. In conclusion, our results provide new insight into how MdNAC4 regulates N deficiency-induced leaf senescence.
Collapse
Affiliation(s)
- Binbin Wen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xuehui Zhao
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, 261061, Shandong, China
| | - Xingyao Gong
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Wenzhe Zhao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Mingyue Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xiude Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Dongmei Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Ling Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China.
| | - Wei Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China.
| |
Collapse
|
20
|
Wang HL, Yin W, Xia X, Li Z. Orthologs of Human-Disease-Associated Genes in Plants Are Involved in Regulating Leaf Senescence. Life (Basel) 2023; 13:559. [PMID: 36836919 PMCID: PMC9965218 DOI: 10.3390/life13020559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
As eukaryotes, plants and animals have many commonalities on the genetic level, although they differ greatly in appearance and physiological habits. The primary goal of current plant research is to improve the crop yield and quality. However, plant research has a wider aim, exploiting the evolutionary conservatism similarities between plants and animals, and applying discoveries in the field of botany to promote zoological research that will ultimately serve human health, although very few studies have addressed this aspect. Here, we analyzed 35 human-disease-related gene orthologs in plants and characterized the genes in depth. Thirty-four homologous genes were found to be present in the herbaceous annual plant Arabidopsis thaliana and the woody perennial plant Populus trichocarpa, with most of the genes having more than two exons, including the ATM gene with 78 exons. More surprisingly, 27 (79.4%) of the 34 homologous genes in Arabidopsis were found to be senescence-associated genes (SAGs), further suggesting a close relationship between human diseases and cellular senescence. Protein-protein interaction network analysis revealed that the 34 genes formed two main subnetworks, and genes in the first subnetwork interacted with 15 SAGs. In conclusion, our results show that most of the 34 homologs of human-disease-associated genes in plants are involved in the leaf senescence process, suggesting that leaf senescence may offer a means to study the pathogenesis of human diseases and to screen drugs for the treat of diseases.
Collapse
Affiliation(s)
| | | | - Xinli Xia
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhonghai Li
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
21
|
Kim JY, Lee J, Kang MH, Trang TTM, Lee J, Lee H, Jeong H, Lim PO. Dynamic landscape of long noncoding RNAs during leaf aging in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1068163. [PMID: 36531391 PMCID: PMC9753222 DOI: 10.3389/fpls.2022.1068163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Leaf senescence, the last stage of leaf development, is essential for whole-plant fitness as it marks the relocation of nutrients from senescing leaves to reproductive or other developing organs. Temporally coordinated physiological and functional changes along leaf aging are fine-tuned by a highly regulated genetic program involving multi-layered regulatory mechanisms. Long noncoding RNAs (lncRNAs) are newly emerging as hidden players in many biological processes; however, their contribution to leaf senescence has been largely unknown. Here, we performed comprehensive analyses of RNA-seq data representing all developmental stages of leaves to determine the genome-wide lncRNA landscape along leaf aging. A total of 771 lncRNAs, including 232 unannotated lncRNAs, were identified. Time-course analysis revealed 446 among 771 developmental age-related lncRNAs (AR-lncRNAs). Intriguingly, the expression of AR-lncRNAs was regulated more dynamically in senescing leaves than in growing leaves, revealing the relevant contribution of these lncRNAs to leaf senescence. Further analyses enabled us to infer the function of lncRNAs, based on their interacting miRNA or mRNA partners. We considered functionally diverse lncRNAs including antisense lncRNAs (which regulate overlapping protein-coding genes), competitive endogenous RNAs (ceRNAs; which regulate paired mRNAs using miRNAs as anchors), and mRNA-interacting lncRNAs (which affect the stability of mRNAs). Furthermore, we experimentally validated the senescence regulatory function of three novel AR-lncRNAs including one antisense lncRNA and two mRNA-interacting lncRNAs through molecular and phenotypic analyses. Our study provides a valuable resource of AR-lncRNAs and potential regulatory networks that link the function of coding mRNA and AR-lncRNAs. Together, our results reveal AR-lncRNAs as important elements in the leaf senescence process.
Collapse
Affiliation(s)
- Jung Yeon Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Juhyeon Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Myeong Hoon Kang
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Tran Thi My Trang
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Jusung Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Heeho Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg, Germany
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| |
Collapse
|
22
|
Yang T, Zhang M, Yang Q, Liu K, Cui J, Chen J, Ren Y, Shao Y, Wang R, Li G. The S40 family members delay leaf senescence by promoting cytokinin synthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 191:99-109. [PMID: 36201884 DOI: 10.1016/j.plaphy.2022.09.017] [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: 07/16/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Leaf senescence is regulated by both endogenous hormones and environmental stimuli in a programmed and concerted way. The members of the S40 family have been reported to play roles in leaf senescence. Here we identified an S40 family member, CiS40-11, from Caragana intermedia. Phylogenetic analysis revealed that the CiS40-11 protein had the highest identity with AtS40-5 (AT1G11700) and AtS40-6 (AT1G61930) of Arabidopsis thaliana. CiS40-11 was highly expressed in leaves and was down-regulated after dark treatment. The subcellular localization analysis showed that CiS40-11 was a cytoplasm-nucleus dual-localized protein. Leaf senescence was delayed in both the CiS40-11 overexpressed A. thaliana and its transiently expressed C. intermedia. Transcriptomic analysis and endogenous hormones assay revealed that CiS40-11 inhibited leaf senescence via promoting the biosynthesis of cytokinins by blocking AtMYB2 expression in the CiS40-11 overexpression lines. Furthermore, overexpression of either AtS40-5 or AtS40-6 showed similar phenotype as the CiS40-11 overexpressing lines, while in the ats40-5a or ats40-6a mutants, the AtMYB2 expression was increased and their leaves exhibited a premature senescence phenotype. These results provide a new molecular mechanism of the S40 family in leaf senescence regulation of plants.
Collapse
Affiliation(s)
- Tianrui Yang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Minna Zhang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Qi Yang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Kun Liu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Jiaming Cui
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Jia Chen
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Yufan Ren
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Yunjie Shao
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China; Inner Mongolia Enterprise Key Laboratory of Tree Breeding, Mengshu Ecological Construction Group Co., Ltd., Hohhot, 011517, PR China
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China; Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010021, PR China; Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010021, PR China.
| |
Collapse
|
23
|
Genome-Wide Identification and Expression Analysis of Senescence-Associated Genes in Grapevine ( Vitis vinifera L.) Reveal Their Potential Functions in Leaf Senescence Order. Int J Mol Sci 2022; 23:ijms232112731. [PMID: 36361520 PMCID: PMC9656468 DOI: 10.3390/ijms232112731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 01/25/2023] Open
Abstract
Natural leaf senescence is an acclimation strategy that enables plants to reallocate nutrients. In the present study, interestingly, we found that the basal mature leaves of grapevine primary shoots (P) exhibited the earliest senescence, followed by the apical young leaves of secondary shoots (ST), and then the basal mature leaves of secondary shoots (S). The Chl level decreased with the extent of leaf senescence. According to the genome-wide identification and expression analysis, sixteen senescence-associated genes (SAGs) involved in Chl breakdown were identified in the grapevine genome. Their expression patterns showed that the transcript changes in VvSGR, VvPPH2, and VvFtsH6-2 corresponded to the changes in Chl content among P, S, and ST. The changes in the transcription of VvNYC1, VvSGR, VvPAO1, VvPAO2, VvPAO4, VvPPH1, VvPPH3, and VvFtsH6-1 only contributed to low Chl levels in P. The cis-element analysis indicated that these SAGs possessed several light- and hormone-responsive elements in their promoters. Among them, ABA-responsive elements were found in twelve of the sixteen promoters of SAGs. Correspondingly, ABA-signaling components presented various changes in transcription among P, S, and ST. The transcription changes in VvbZIP45 and VvSnRK2.1 were similar to those in VvSGR, VvPPH2, and VvFtsH6-2. The other nine ABA-signaling components, which included VvRCAR2, VvRCAR4, VvRCAR6, VvRCAR7, VvRCAR2, VvPP2C4, VvPP2C9, VvbZIP25, and VvSnRK2.3, were highly expressed in P but there was no difference between S and ST, with similar expression patterns for VvNYC1, VvSGR, VvPAO1, VvPAO2, VvPAO4, VvPPH1, VvPPH3, and VvFtsH6-1. These results suggested that the senescence of P and ST could be regulated by different members of Chl breakdown-related SAGs and ABA-signaling components. These findings provide us with important candidate genes to further study the regulation mechanism of leaf senescence order in grapevine.
Collapse
|
24
|
Cao J, Zhang Y, Tan S, Yang Q, Wang HL, Xia X, Luo J, Guo H, Zhang Z, Li Z. LSD 4.0: an improved database for comparative studies of leaf senescence. MOLECULAR HORTICULTURE 2022; 2:24. [PMID: 37789481 PMCID: PMC10515038 DOI: 10.1186/s43897-022-00045-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/22/2022] [Indexed: 10/05/2023]
Affiliation(s)
- Jie Cao
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yang Zhang
- National Genomics Data Center, Beijing, 100101, China
- China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuya Tan
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qi Yang
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hou-Ling Wang
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jingchu Luo
- College of Life Sciences, Peking University, Beijing, 100871, China
- Center for Bioinformatics, Peking University, Beijing, 100871, China
| | - Hongwei Guo
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, Guangdong, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing, 100101, China.
- China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhonghai Li
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
25
|
Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
Collapse
Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
26
|
LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071095. [PMID: 35888183 PMCID: PMC9316258 DOI: 10.3390/life12071095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/16/2022]
Abstract
Plant leaves, which convert light energy into chemical energy, serve as a major food source on Earth. The decrease in crop yield and quality is caused by plant leaf premature senescence. It is important to detect senescence-associated genes. In this study, we collected 5853 genes from a leaf senescence database and developed a leaf-senescence-associated genes (SAGs) prediction model using the support vector machine (SVM) and XGBoost algorithms. This is the first computational approach for predicting SAGs with the sequence dataset. The SVM-PCA-Kmer-PC-PseAAC model achieved the best performance (F1score = 0.866, accuracy = 0.862 and receiver operating characteristic = 0.922), and based on this model, we developed a SAGs prediction tool called “SAGs_Anno”. We identified a total of 1,398,277 SAGs from 3,165,746 gene sequences from 83 species, including 12 lower plants and 71 higher plants. Interestingly, leafy species showed a higher percentage of SAGs, while leafless species showed a lower percentage of SAGs. Finally, we constructed the Leaf SAGs Annotation Platform using these available datasets and the SAGs_Anno tool, which helps users to easily predict, download, and search for plant leaf SAGs of all species. Our study will provide rich resources for plant leaf-senescence-associated genes research.
Collapse
|
27
|
Zhang Y, Tan S, Gao Y, Kan C, Wang HL, Yang Q, Xia X, Ishida T, Sawa S, Guo H, Li Z. CLE42 delays leaf senescence by antagonizing ethylene pathway in Arabidopsis. THE NEW PHYTOLOGIST 2022; 235:550-562. [PMID: 35396726 DOI: 10.1111/nph.18154] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Leaf senescence is the final stage of leaf development and is influenced by numerous internal and environmental factors. CLE family peptides are plant-specific peptide hormones that regulate various developmental processes. However, the role of CLE in regulating Arabidopsis leaf senescence remains unclear. Here, we found that CLE42 is a negative regulator of leaf senescence by using a CRISPR/Cas9-produced CLE mutant collection. The cle42 mutant displayed earlier senescence phenotypes, while overexpression of CLE42 delayed age-dependent and dark-induced leaf senescence. Moreover, application of the synthesized 12-amino-acid peptide (CLE42p) also delayed leaf senescence under natural and dark conditions. CLE42 and CLE41/44 displayed functional redundancy in leaf senescence, and the cle41 cle42 cle44 triple mutant displayed more pronounced earlier senescence phenotypes than any single mutant. Analysis of differentially expressed genes obtained by RNA-Seq methodology revealed that the ethylene pathway was suppressed by overexpressing CLE42. Moreover, CLE42 suppressed ethylene biosynthesis and thus promoted the protein accumulation of EBF, which in turn decreased the function of EIN3. Accordingly, mutation of EIN3/EIL1 or overexpression of EBF1 suppressed the earlier senescence phenotypes of the cle42 mutant. Together, our results reveal that the CLE peptide hormone regulates leaf senescence by communicating with the ethylene pathway.
Collapse
Affiliation(s)
- Yi Zhang
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, Guangdong, China
| | - Shuya Tan
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yuhan Gao
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chengcheng Kan
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Hou-Ling Wang
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Qi Yang
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Takashi Ishida
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, 860-8555, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Hongwei Guo
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, Guangdong, China
| | - Zhonghai Li
- National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
28
|
Xu J, Ji Z, Wang C, Xu F, Wang F, Zheng Y, Tang Y, Wei Z, Zhao T, Zhao K. WATER-SOAKED SPOT1 Controls Chloroplast Development and Leaf Senescence via Regulating Reactive Oxygen Species Homeostasis in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:918673. [PMID: 35693165 PMCID: PMC9178249 DOI: 10.3389/fpls.2022.918673] [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: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Transmembrane kinases (TMKs) play important roles in plant growth and signaling cascades of phytohormones. However, its function in the regulation of early leaf senescence (ELS) of plants remains unknown. Here, we report the molecular cloning and functional characterization of the WATER-SOAKED SPOT1 gene which encodes a protein belongs to the TMK family and controls chloroplast development and leaf senescence in rice (Oryza sativa L.). The water-soaked spot1 (oswss1) mutant displays water-soaked spots which subsequently developed into necrotic symptoms at the tillering stage. Moreover, oswss1 exhibits slightly rolled leaves with irregular epidermal cells, decreased chlorophyll contents, and defective stomata and chloroplasts as compared with the wild type. Map-based cloning revealed that OsWSS1 encodes transmembrane kinase TMK1. Genetic complementary experiments verified that a Leu396Pro amino acid substitution, residing in the highly conserved region of leucine-rich repeat (LRR) domain, was responsible for the phenotypes of oswss1. OsWSS1 was constitutively expressed in all tissues and its encoded protein is localized to the plasma membrane. Mutation of OsWSS1 led to hyper-accumulation of reactive oxygen species (ROS), more severe DNA fragmentation, and cell death than that of the wild-type control. In addition, we found that the expression of senescence-associated genes (SAGs) was significantly higher, while the expression of genes associated with chloroplast development and photosynthesis was significantly downregulated in oswss1 as compared with the wild type. Taken together, our results demonstrated that OsWSS1, a member of TMKs, plays a vital role in the regulation of ROS homeostasis, chloroplast development, and leaf senescence in rice.
Collapse
Affiliation(s)
- Jiangmin Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunlian Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feifei Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fujun Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuhan Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongchao Tang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheng Wei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyong Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
29
|
Yang F, Miao Y, Liu Y, Botella JR, Li W, Li K, Song CP. Function of Protein Kinases in Leaf Senescence of Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:864215. [PMID: 35548290 PMCID: PMC9083415 DOI: 10.3389/fpls.2022.864215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence is an evolutionarily acquired process and it is critical for plant fitness. During senescence, macromolecules and nutrients are disassembled and relocated to actively growing organs. Plant leaf senescence process can be triggered by developmental cues and environmental factors, proper regulation of this process is essential to improve crop yield. Protein kinases are enzymes that modify their substrates activities by changing the conformation, stability, and localization of those proteins, to play a crucial role in the leaf senescence process. Impressive progress has been made in understanding the role of different protein kinases in leaf senescence recently. This review focuses on the recent progresses in plant leaf senescence-related kinases. We summarize the current understanding of the function of kinases on senescence signal perception and transduction, to help us better understand how the orderly senescence degeneration process is regulated by kinases, and how the kinase functions in the intricate integration of environmental signals and leaf age information.
Collapse
Affiliation(s)
- Fengbo Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Yuyue Liu
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Jose R. Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Kun Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| |
Collapse
|
30
|
Zhang Y, Gao Y, Wang HL, Kan C, Li Z, Yang X, Yin W, Xia X, Nam HG, Li Z, Guo H. Verticillium dahliae secretory effector PevD1 induces leaf senescence by promoting ORE1-mediated ethylene biosynthesis. MOLECULAR PLANT 2021; 14:1901-1917. [PMID: 34303024 DOI: 10.1016/j.molp.2021.07.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/01/2021] [Accepted: 07/20/2021] [Indexed: 05/16/2023]
Abstract
Leaf senescence, the final stage of leaf development, is influenced by numerous internal and environmental signals. However, how biotic stresses such as pathogen infection regulate leaf senescence remains largely unclear. In this study, we found that the premature leaf senescence in Arabidopsis caused by the soil-borne vascular fungus Verticillium dahliae was impaired by disruption of a protein elicitor from V. dahliae 1 named PevD1. Constitutive or inducible overexpression of PevD1 accelerated Arabidopsis leaf senescence. Interestingly, a senescence-associated NAC transcription factor, ORE1, was targeted by PevD1. PevD1 could interact with and stabilize ORE1 protein by disrupting its interaction with the RING-type ubiquitin E3 ligase NLA. Mutation of ORE1 suppressed the premature senescence caused by overexpressing PevD1, whereas overexpression of ORE1 or PevD1 led to enhanced ethylene production and thereby leaf senescence. We showed that ORE1 directly binds the promoter of ACS6 and promotes its expression for mediating PevD1-induced ethylene biosynthesis. Loss-of-function of ACSs could suppress V. dahliae-induced leaf senescence in ORE1-overexpressing plants. Furthermore, we found thatPevD1 also interacts with Gossypium hirsutum ORE1 (GhORE1) and that virus-induced gene silencing of GhORE1 delays V. dahliae-triggered leaf senescence in cotton, indicating a possibly conserved mechanism in plants. Taken together, these results suggest that V. dahliae induces leaf senescence by secreting the effector PevD1 to manipulate the ORE1-ACS6 cascade, providing new insights into biotic stress-induced senescence in plants.
Collapse
Affiliation(s)
- Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yuhan Gao
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Chengcheng Kan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ze Li
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiufen Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weilun Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu 42988, Republic of Korea; New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.
| |
Collapse
|
31
|
Fraga OT, de Melo BP, Quadros IPS, Reis PAB, Fontes EPB. Senescence-Associated Glycine max ( Gm) NAC Genes: Integration of Natural and Stress-Induced Leaf Senescence. Int J Mol Sci 2021; 22:8287. [PMID: 34361053 PMCID: PMC8348617 DOI: 10.3390/ijms22158287] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/20/2021] [Accepted: 07/24/2021] [Indexed: 11/30/2022] Open
Abstract
Leaf senescence is a genetically regulated developmental process that can be triggered by a variety of internal and external signals, including hormones and environmental stimuli. Among the senescence-associated genes controlling leaf senescence, the transcriptional factors (TFs) comprise a functional class that is highly active at the onset and during the progression of leaf senescence. The plant-specific NAC (NAM, ATAF, and CUC) TFs are essential for controlling leaf senescence. Several members of Arabidopsis AtNAC-SAGs are well characterized as players in elucidated regulatory networks. However, only a few soybean members of this class display well-known functions; knowledge about their regulatory circuits is still rudimentary. Here, we describe the expression profile of soybean GmNAC-SAGs upregulated by natural senescence and their functional correlation with putative AtNAC-SAGs orthologs. The mechanisms and the regulatory gene networks underlying GmNAC081- and GmNAC030-positive regulation in leaf senescence are discussed. Furthermore, new insights into the role of GmNAC065 as a negative senescence regulator are presented, demonstrating extraordinary functional conservation with the Arabidopsis counterpart. Finally, we describe a regulatory circuit which integrates a stress-induced cell death program with developmental leaf senescence via the NRP-NAC-VPE signaling module.
Collapse
Affiliation(s)
- Otto Teixeira Fraga
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Bruno Paes de Melo
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- Embrapa Genetic Resources and Biotechnology, Brasília 70770.917, DF, Brazil
| | - Iana Pedro Silva Quadros
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Pedro Augusto Braga Reis
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Elizabeth Pacheco Batista Fontes
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| |
Collapse
|
32
|
Wang HL, Zhang Y, Wang T, Yang Q, Yang Y, Li Z, Li B, Wen X, Li W, Yin W, Xia X, Guo H, Li Z. An alternative splicing variant of PtRD26 delays leaf senescence by regulating multiple NAC transcription factors in Populus. THE PLANT CELL 2021; 33:1594-1614. [PMID: 33793897 PMCID: PMC8254505 DOI: 10.1093/plcell/koab046] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/01/2021] [Indexed: 05/05/2023]
Abstract
During leaf senescence, the final stage of leaf development, nutrients are recycled from leaves to other organs, and therefore proper control of senescence is thus critical for plant fitness. Although substantial progress has been achieved in understanding leaf senescence in annual plants, the molecular factors that control leaf senescence in perennial woody plants are largely unknown. Using RNA sequencing, we obtained a high-resolution temporal profile of gene expression during autumn leaf senescence in poplar (Populus tomentosa). Identification of hub transcription factors (TFs) by co-expression network analysis of genes revealed that senescence-associated NAC family TFs (Sen-NAC TFs) regulate autumn leaf senescence. Age-dependent alternative splicing (AS) caused an intron retention (IR) event in the pre-mRNA encoding PtRD26, a NAC-TF. This produced a truncated protein PtRD26IR, which functions as a dominant-negative regulator of senescence by interacting with multiple hub Sen-NAC TFs, thereby repressing their DNA-binding activities. Functional analysis of senescence-associated splicing factors identified two U2 auxiliary factors that are involved in AS of PtRD26IR. Correspondingly, silencing of these factors decreased PtRD26IR transcript abundance and induced early senescence. We propose that an age-dependent increase of IR splice variants derived from Sen-NAC TFs is a regulatory program to fine tune the molecular mechanisms that regulate leaf senescence in trees.
Collapse
Affiliation(s)
- Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Ting Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qi Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanli Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ze Li
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bosheng Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Xing Wen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Wenyang Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Weilun Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
- Author for correspondence: (Z.L.), (H.G.)
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Author for correspondence: (Z.L.), (H.G.)
| |
Collapse
|
33
|
Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
Collapse
Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
| |
Collapse
|
34
|
Yi SY, Rameneni JJ, Lee M, Song SG, Choi Y, Lu L, Lee H, Lim YP. Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa. Int J Mol Sci 2021; 22:ijms22116017. [PMID: 34199515 PMCID: PMC8199657 DOI: 10.3390/ijms22116017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/16/2022] Open
Abstract
Leaf senescence is a developmental process induced by various molecular and environmental stimuli that may affect crop yield. The dark-induced leaf senescence-91 (DLS-91) plants displayed rapid leaf senescence, dramatically decreased chlorophyll contents, low photochemical efficiencies, and upregulation of the senescence-associated marker gene BrSAG12-1. To understand DLS molecular mechanism, we examined transcriptomic changes in DLS-91 and control line DLS-42 following 0, 1, and 4 days of dark treatment (DDT) stages. We identified 501, 446, and 456 DEGs, of which 16.7%, 17.2%, and 14.4% encoded TFs, in samples from the three stages. qRT-PCR validation of 16 genes, namely, 7 MADS, 6 NAC, and 3 WRKY, suggested that BrAGL8-1, BrAGL15-1, and BrWRKY70-1 contribute to the rapid leaf senescence of DLS-91 before (0 DDT) and after (1 and 4 DDT) dark treatment, whereas BrNAC046-2, BrNAC029-2/BrNAP, and BrNAC092-1/ORE1 TFs may regulate this process at a later stage (4 DDT). In-silico analysis of cis-acting regulatory elements of BrAGL8-1, BrAGL42-1, BrNAC029-2, BrNAC092-1, and BrWRKY70-3 of B. rapa provides insight into the regulation of these genes. Our study has uncovered several AGL-MADS, WRKY, and NAC TFs potentially worthy of further study to understand the underlying mechanism of rapid DLS in DLS-91.
Collapse
Affiliation(s)
- So Young Yi
- Institute of Agricultural Science, Chungnam National University, Daejeon 34134, Korea; (S.Y.Y.); (J.J.R.); (M.L.)
| | - Jana Jeevan Rameneni
- Institute of Agricultural Science, Chungnam National University, Daejeon 34134, Korea; (S.Y.Y.); (J.J.R.); (M.L.)
| | - Myungjin Lee
- Institute of Agricultural Science, Chungnam National University, Daejeon 34134, Korea; (S.Y.Y.); (J.J.R.); (M.L.)
| | - Seul Gi Song
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.G.S.); (Y.C.); (L.L.); (H.L.)
| | - Yuri Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.G.S.); (Y.C.); (L.L.); (H.L.)
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.G.S.); (Y.C.); (L.L.); (H.L.)
| | - Hyeokgeun Lee
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.G.S.); (Y.C.); (L.L.); (H.L.)
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.G.S.); (Y.C.); (L.L.); (H.L.)
- Correspondence: ; Tel.: +82-42-821-5739; Fax: +82-42-821-8847
| |
Collapse
|
35
|
Chen D, Qiu Z, He L, Hou L, Li M, Zhang G, Wang X, Chen G, Hu J, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Guo L, Qian Q, Zeng D, Zhu L. The rice LRR-like1 protein YELLOW AND PREMATURE DWARF 1 is involved in leaf senescence induced by high light. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1589-1605. [PMID: 33200773 DOI: 10.1093/jxb/eraa532] [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: 05/02/2020] [Accepted: 11/10/2020] [Indexed: 06/11/2023]
Abstract
Senescence in plants is induced by endogenous physiological changes and exogenous stresses. In this study, we isolated two alleles of a novel rice (Oryza sativa) mutant, yellow and premature dwarf 1 (ypd1). The ypd1 mutants exhibited a yellow and dwarf phenotype from germination, and premature senescence starting at tillering. Moreover, the ypd1 mutants were sensitive to high light, which accelerated cell death and senescence. Consistent with their yellow phenotype, the ypd1 mutants had abnormal chloroplasts and lower levels of photosynthetic pigments. TUNEL assays together with histochemical staining demonstrated that ypd1 mutants showed cell death and that they accumulated reactive oxygen species. The ypd1 mutants also showed increased expression of genes associated with senescence. Map-based cloning revealed a G→A substitution in exon 6 (ypd1-1) and exon 13 (ypd1-2) of LOC_Os06g13050 that affected splicing and caused premature termination of the encoded protein. YPD1 was found to be preferentially expressed in the leaf and it encodes a LRR-like1 protein. Complementation, overexpression, and targeted deletion confirmed that the mutations in YPD1 caused the ypd1 phenotype. YPD1 was localized on the chloroplast membrane. Our results thus demonstrate that the novel rice LRR-like1 protein YPD1 affects chloroplast development and leaf senescence.
Collapse
Affiliation(s)
- Dongdong Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhennan Qiu
- College of Life Science, Dezhou University, Dezhou, China
| | - Lei He
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Linlin Hou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Man Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoqi Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| |
Collapse
|
36
|
Kan C, Zhang Y, Wang HL, Shen Y, Xia X, Guo H, Li Z. Transcription Factor NAC075 Delays Leaf Senescence by Deterring Reactive Oxygen Species Accumulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:634040. [PMID: 33719309 PMCID: PMC7943619 DOI: 10.3389/fpls.2021.634040] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/22/2021] [Indexed: 05/23/2023]
Abstract
Leaf senescence is a highly complex genetic process that is finely tuned by multiple layers of regulation. Among them, transcriptional regulation plays a critical role in controlling the initiation and progression of leaf senescence. Here, we found that the NAC transcription factor NAC075 functions as a novel negative regulator of leaf senescence. Loss of function of NAC075 promotes leaf senescence in an age-dependent manner, whereas constitutive overexpression of NAC075 delays senescence in Arabidopsis. Transcriptome analysis revealed that transcript levels of antioxidant enzymes such as catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD) are significantly suppressed in nac075 mutants compared with wild-type plants. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analyses revealed that NAC075 directly binds the promoter of catalase 2 (CAT2). Moreover, genetic analysis showed that overexpression of CAT2 suppresses the overproduction of reactive oxygen species (ROS) and the early senescence phenotypes of nac075 mutants, suggesting that CAT2 acts downstream of NAC075 to delay leaf senescence by repressing ROS accumulation. Collectively, our findings provide a new regulatory module involving NAC075-CAT2-ROS in controlling leaf senescence in Arabidopsis.
Collapse
Affiliation(s)
- Chengcheng Kan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yingbai Shen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| |
Collapse
|
37
|
Miryeganeh M. Senescence: The Compromised Time of Death That Plants May Call on Themselves. Genes (Basel) 2021; 12:143. [PMID: 33499161 PMCID: PMC7912376 DOI: 10.3390/genes12020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/03/2023] Open
Abstract
Plants synchronize their life history events with proper seasonal conditions, and as the fitness consequences of each life stage depend on previous and/or subsequent one, changes in environmental cues create cascading effects throughout their whole life cycle. For monocarpic plants, proper senescence timing is very important as the final production of plants depends on it. Citing available literatures, this review discusses how plants not only may delay senescence until after they reproduce successfully, but they may also bring senescence time forward, in order to reproduce in favored conditions. It demonstrates that even though senescence is part of aging, it does not necessarily mean plants have to reach a certain age to senesce. Experiments using different aged plants have suggested that in interest of their final outcome and fitness, plants carefully weigh out environmental cues and transit to next developmental phase at proper time, even if that means transiting to terminal senescence phase earlier and shortening their lifespan. How much plants have control over senescence timing and how they balance internal and external signals for that is not well understood. Future studies are needed to identify processes that trigger senescence timing in response to environment and investigate genetic/epigenetic mechanisms behind it.
Collapse
Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
| |
Collapse
|
38
|
Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R, Song S, Ma L, Zou D, Tian D, Li C, Zhu J, Gong Z, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z, Zhao W, Xue Y, Bao Y, Zhang T, Kang W, Yang F, Qu J, Zhang W, Bao Y, Liu GH, Liu L, Zhang Y, Niu G, Zhu T, Feng C, Liu X, Zhang Y, Li Z, Chen R, Li Q, Teng X, Ma L, Hua Z, Tian D, Jiang C, Chen Z, He F, Zhao Y, Jin Y, Zhang Z, Huang L, Song S, Yuan Y, Zhou C, Xu Q, He S, Ye W, Cao R, Wang P, Ling Y, Yan X, Wang Q, Zhang G, Li Z, Liu L, Jiang S, Li Q, Feng C, Du Q, Ma L, Zong W, Kang H, Zhang M, Xiong Z, Li R, Huan W, Ling Y, Zhang S, Xia Q, Cao R, Fan X, Wang Z, Zhang G, Chen X, Chen T, Zhang S, Tang B, Zhu J, Dong L, Zhang Z, Wang Z, Kang H, Wang Y, Ma Y, Wu S, Kang H, Chen M, Li C, Tian D, Tang B, Liu X, Teng X, Song S, Tian D, Liu X, Li C, Teng X, Song S, Zhang Y, Zou D, Zhu T, Chen M, Niu G, Liu C, Xiong Y, Hao L, Niu G, Zou D, Zhu T, Shao X, Hao L, Li Y, Zhou H, Chen X, Zheng Y, Kang Q, Hao D, Zhang L, Luo H, Hao Y, Chen R, Zhang P, He S, Zou D, Zhang M, Xiong Z, Nie Z, Yu S, Li R, Li M, Li R, Bao Y, Xiong Z, Li M, Yang F, Ma Y, Sang J, Li Z, Li R, Tang B, Zhang X, Dong L, Zhou Q, Cui Y, Zhai S, Zhang Y, Wang G, Zhao W, Wang Z, Zhu Q, Li X, Zhu J, Tian D, Kang H, Li C, Zhang S, Song S, Li M, Zhao W, Yan J, Sang J, Zou D, Li C, Wang Z, Zhang Y, Zhu T, Song S, Wang X, Hao L, Liu Y, Wang Z, Luo H, Zhu J, Wu X, Tian D, Li C, Zhao W, Jing HC, Chen M, Zou D, Hao L, Zhao L, Wang J, Li Y, Song T, Zheng Y, Chen R, Zhao Y, He S, Zou D, Mehmood F, Ali S, Ali A, Saleem S, Hussain I, Abbasi AA, Ma L, Zou D, Zou D, Jiang S, Zhang Z, Jiang S, Zhao W, Xiao J, Bao Y, Zhang Z, Zuo Z, Ren J, Zhang X, Xiao Y, Li X, Zhang X, Xiao Y, Li X, Tu Y, Xue Y, Wu W, Ji P, Zhao F, Meng X, Chen M, Peng D, Xue Y, Luo H, Gao F, Zhang X, Xiao Y, Li X, Ning W, Xue Y, Lin S, Xue Y, Liu T, Guo AY, Yuan H, Zhang YE, Tan X, Xue Y, Zhang W, Xue Y, Xie Y, Ren J, Wang C, Xue Y, Liu CJ, Guo AY, Yang DC, Tian F, Gao G, Tang D, Xue Y, Yao L, Xue Y, Cui Q, An NA, Li CY, Luo X, Ren J, Zhang X, Xiao Y, Li X. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res 2021; 49:D18-D28. [PMID: 33175170 PMCID: PMC7779035 DOI: 10.1093/nar/gkaa1022] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.
Collapse
|
39
|
Liu Q, Li L, Feng Z, Yu S. Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:809522. [PMID: 35069667 PMCID: PMC8766411 DOI: 10.3389/fpls.2021.809522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/10/2021] [Indexed: 05/06/2023]
Abstract
Senescence in plants is a complex trait, which is controlled by both genetic and environmental factors and can affect the yield and quality of cotton. However, the genetic basis of cotton senescence remains relatively unknown. In this study, we reported genome-wide association studies (GWAS) based on 185 accessions of upland cotton and 26,999 high-quality single-nucleotide polymorphisms (SNPs) to reveal the genetic basis of cotton senescence. To determine cotton senescence, we evaluated eight traits/indices. Our results revealed a high positive correlation (r>0.5) among SPAD value 20 days after topping (SPAD20d), relative difference of SPAD (RSPAD), nodes above white flower on topping day (NAWF0d), nodes above white flower 7 days after topping (NAWF7d), and number of open bolls on the upper four branches (NB), and genetic analysis revealed that all traits had medium or high heritability ranging from 0.53 to 0.86. Based on a multi-locus method (FASTmrMLM), a total of 63 stable and significant quantitative trait nucleotides (QTNs) were detected, which represented 50 genomic regions (GWAS risk loci) associated with cotton senescence. We observed three reliable loci located on chromosomes A02 (A02_105891088_107196428), D03 (D03_37952328_38393621) and D13 (D13_59408561_60730103) because of their high repeatability. One candidate gene (Ghir_D03G011060) was found in the locus D03_37952328_38393621, and its Arabidopsis thaliana homologous gene (AT5G23040) encodes a cell growth defect factor-like protein (CDF1), which might be involved in chlorophyll synthesis and cell death. Moreover, qRT-PCR showed that the transcript level of Ghir_D03G011060 was down-regulated in old cotton leaves, and virus-induced gene silencing (VIGS) indicated that silencing of Ghir_D03G011060 resulted in leaf chlorosis and promoted leaf senescence. In addition, two candidate genes (Ghir_A02G017660 and Ghir_D13G021720) were identified in loci A02_105891088_107196428 and D13_59408561_60730103, respectively. These results provide new insights into the genetic basis of cotton senescence and will serve as an important reference for the development and implementation of strategies to prevent premature senescence in cotton breeding programs.
Collapse
Affiliation(s)
- Qibao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Libei Li
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Zhen Feng
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Zhen Feng
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
- Shuxun Yu
| |
Collapse
|
40
|
Zhang YM, Guo P, Xia X, Guo H, Li Z. Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives. FRONTIERS IN PLANT SCIENCE 2021; 12:788996. [PMID: 34938309 PMCID: PMC8685244 DOI: 10.3389/fpls.2021.788996] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 05/22/2023]
Abstract
Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.
Collapse
Affiliation(s)
- Yue-Mei Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pengru Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhonghai Li,
| |
Collapse
|
41
|
Zhao Z, Zhang JW, Lu SH, Zhang H, Liu F, Fu B, Zhao MQ, Liu H. Transcriptome divergence between developmental senescence and premature senescence in Nicotiana tabacum L. Sci Rep 2020; 10:20556. [PMID: 33239739 PMCID: PMC7688636 DOI: 10.1038/s41598-020-77395-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/05/2020] [Indexed: 12/02/2022] Open
Abstract
Senescence is a degenerative process triggered by intricate and coordinated regulatory networks, and the mechanisms of age-dependent senescence and stress-induced premature senescence still remain largely elusive. Thus we selected leaf samples of developmental senescence (DS) and premature senescence (PS) to reveal the regulatory divergence. Senescent leaves were confirmed by yellowing symptom and physiological measurement. A total of 1171 and 309 genes (DEGs) were significantly expressed respectively in the whole process of DS and PS. Up-regulated DEGs in PS were mostly related to ion transport, while the down-regulated DEGs were mainly associated with oxidoreductase activity and sesquiterpenoid and triterpenoid biosynthesis. In DS, photosynthesis, precursor metabolites and energy, protein processing in endoplasmic reticulum, flavonoid biosynthesis were notable. Moreover, we found the vital pathways shared by DS and PS, of which the DEGs were analyzed further via protein-protein interaction (PPI) network analysis to explore the alteration responding to two types of senescence. In addition, plant hormone transduction pathway was mapped by related DEGs, suggesting that ABA and ethylene signaling played pivotal roles in formulating the distinction of DS and PS. Finally, we conducted a model containing oxidative stress and ABA signaling as two hub points, which highlighted the major difference and predicted the possible mechanism under DS and PS. This work gained new insight into molecular divergence of developmental senescence and premature senescence and would provide reference on potential mechanism initiating and motivating senescence for further study.
Collapse
Affiliation(s)
- Zhe Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Jia-Wen Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Shao-Hao Lu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Fang Liu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Bo Fu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Ming-Qin Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.
| | - Hui Liu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| |
Collapse
|
42
|
Hinckley WE, Brusslan JA. Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis. PLANT DIRECT 2020; 4:e00279. [PMID: 33204935 PMCID: PMC7649007 DOI: 10.1002/pld3.279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/13/2020] [Accepted: 09/30/2020] [Indexed: 05/29/2023]
Abstract
In plants, the vegetative to reproductive phase transition (termed bolting in Arabidopsis) generally precedes age-dependent leaf senescence (LS). Many studies describe a temporal link between bolting time and LS, as plants that bolt early, senesce early, and plants that bolt late, senesce late. The molecular mechanisms underlying this relationship are unknown and are potentially agriculturally important, as they may allow for the development of crops that can overcome early LS caused by stress-related early-phase transition. We hypothesized that leaf gene expression changes occurring in synchrony with bolting were regulating LS. ARABIDOPSIS TRITHORAX (ATX) enzymes are general methyltransferases that regulate the adult vegetative to reproductive phase transition. We generated an atx1, atx3, and atx4 (atx1,3,4) triple T-DNA insertion mutant that displays both early bolting and early LS. This mutant was used in an RNA-seq time-series experiment to identify gene expression changes in rosette leaves that are likely associated with bolting. By comparing the early bolting mutant to vegetative WT plants of the same age, we were able to generate a list of differentially expressed genes (DEGs) that change expression with bolting as the plants age. We trimmed the list by intersection with publicly available WT datasets, which removed genes from our DEG list that were atx1,3,4 specific. The resulting 398 bolting-associated genes (BAGs) are differentially expressed in a mature rosette leaf at bolting. The BAG list contains many well-characterized LS regulators (ORE1, WRKY45, NAP, WRKY28), and GO analysis revealed enrichment for LS and LS-related processes. These bolting-associated LS regulators may contribute to the temporal coupling of bolting time to LS.
Collapse
Affiliation(s)
| | - Judy A. Brusslan
- Department of Biological SciencesCalifornia State UniversityLong Beach, Long BeachCAUSA
| |
Collapse
|
43
|
Physiological Characterization and Transcriptome Analysis of Camellia oleifera Abel. during Leaf Senescence. FORESTS 2020. [DOI: 10.3390/f11080812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Camellia (C.) oleifera Abel. is an evergreen small arbor with high economic value for producing edible oil that is well known for its high level of unsaturated fatty acids. The yield formation of tea oil extracted from fruit originates from the leaves, so leaf senescence, the final stage of leaf development, is an important agronomic trait affecting the production and quality of tea oil. However, the physiological characteristics and molecular mechanism underlying leaf senescence of C. oleifera are poorly understood. In this study, we performed physiological observation and de novo transcriptome assembly for annual leaves and biennial leaves of C. oleifera. The physiological assays showed that the content of chlorophyll (Chl), soluble protein, and antioxidant enzymes including superoxide dismutase, peroxide dismutase, and catalase in senescing leaves decreased significantly, while the proline and malondialdehyde concentration increased. By analyzing RNA-Seq data, we identified 4645 significantly differentially expressed unigenes (DEGs) in biennial leaves with most associated with flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism pathways. Among these DEGs, 77 senescence-associated genes (SAGs) including NOL, ATAF1, MDAR, and SAG12 were classified to be related to Chl degradation, plant hormone, and oxidation pathways. The further analysis of the 77 SAGs based on the Spearman correlation algorithm showed that there was a significant expression correlation between these SAGs, suggesting the potential connections between SAGs in jointly regulating leaf senescence. A total of 162 differentially expressed transcription factors (TFs) identified during leaf senescence were mostly distributed in MYB (myeloblastosis), ERF (Ethylene-responsive factor), WRKY, and NAC (NAM, ATAF1/2 and CUCU2) families. In addition, qRT-PCR analysis of 19 putative SAGs were in accordance with the RNA-Seq data, further confirming the reliability and accuracy of the RNA-Seq. Collectively, we provide the first report of the transcriptome analysis of C. oleifera leaves of two kinds of age and a basis for understanding the molecular mechanism of leaf senescence.
Collapse
|
44
|
Genetic Network between Leaf Senescence and Plant Immunity: Crucial Regulatory Nodes and New Insights. PLANTS 2020; 9:plants9040495. [PMID: 32294898 PMCID: PMC7238237 DOI: 10.3390/plants9040495] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/30/2022]
Abstract
Leaf senescence is an essential physiological process that is accompanied by the remobilization of nutrients from senescent leaves to young leaves or other developing organs. Although leaf senescence is a genetically programmed process, it can be induced by a wide variety of biotic and abiotic factors. Accumulating studies demonstrate that senescence-associated transcription factors (Sen-TFs) play key regulatory roles in controlling the initiation and progression of leaf senescence process. Interestingly, recent functional studies also reveal that a number of Sen-TFs function as positive or negative regulators of plant immunity. Moreover, the plant hormone salicylic acid (SA) and reactive oxygen species (ROS) have been demonstrated to be key signaling molecules in regulating leaf senescence and plant immunity, suggesting that these two processes share similar or common regulatory networks. However, the interactions between leaf senescence and plant immunity did not attract sufficient attention to plant scientists. Here, we review the regulatory roles of SA and ROS in biotic and abiotic stresses, as well as the cross-talks between SA/ROS and other hormones in leaf senescence and plant immunity, summarize the transcriptional controls of Sen-TFs on SA and ROS signal pathways, and analyze the cross-regulation between senescence and immunity through a broad literature survey. In-depth understandings of the cross-regulatory mechanisms between leaf senescence and plant immunity will facilitate the cultivation of high-yield and disease-resistant crops through a molecular breeding strategy.
Collapse
|
45
|
Zhang Z, Zhao W, Xiao J, Bao Y, He S, Zhang G, Li Y, Zhao G, Chen R, Gao Y, Zhang C, Yuan L, Zhang G, Xu S, Zhang C, Gao Y, Ning Z, Lu Y, Xu S, Zeng J, Yuan N, Zhu J, Pan M, Zhang H, Wang Q, Shi S, Jiang M, Lu M, Qian Q, Gao Q, Shang Y, Wang J, Du Z, Xiao J, Tian D, Wang P, Tang B, Li C, Teng X, Liu X, Zou D, Song S, Xiong Z, Li M, Yang F, Ma Y, Sang J, Li Z, Li R, Wang Z, Zhu Q, Zhu J, Li X, Zhang S, Tian D, Kang H, Li C, Dong L, Ying C, Duan G, Song S, Li M, Zhao W, Zhi X, Ling Y, Cao R, Jiang Z, Zhou H, Lv D, Liu W, Klenk HP, Zhao G, Zhang G, Zhang Y, Zhang Z, Zhang H, Xiao J, Chen T, Zhang S, Chen X, Zhu J, Wang Z, Kang H, Dong L, Wang Y, Ma Y, Wu S, Li Z, Gong Z, Chen M, Li C, Tian D, Teng X, Wang P, Tang B, Liu X, Zou D, Song S, Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X, Sun L, Chen R, Zhao Y, Wang J, Zhang P, Li Y, Zheng Y, Chen R, He S, Teng X, Chen X, Xue H, Teng Y, Zhang P, Kang Q, Hao Y, Zhao Y, Chen R, He S, Cao J, Liu L, Li Z, Li Q, Zou D, Du Q, Abbasi AA, Shireen H, Pervaiz N, Batool F, Raza RZ, Ma L, Niu G, Zhang Y, Zou D, Zhu T, Sang J, Li M, Hao L, Zou D, Wang G, Li M, Li R, Li M, Li R, Bao Y, Yan J, Sang J, Zou D, Li C, Wang Z, Zhang Y, Zhu T, Song S, Wang X, Hao L, Li Z, Zhang Y, Zou D, Zhao Y, Wang H, Zhang Y, Xia X, Guo H, Zhang Z, Zou D, Ma L, Dong L, Tang B, Zhu J, Zhou Q, Wang Z, Kang H, Chen X, Lan L, Bao Y, Zhao W, Zou D, Zhu J, Tang B, Bao Y, Lan L, Zhang X, Ma Y, Xue Y, Sun Y, Zhai S, Yu L, Sun M, Chen H, Zhang Z, Zhao W, Xiao J, Bao Y, Hao L, Hu H, Guo AY, Lin S, Xue Y, Wang C, Xue Y, Ning W, Xue Y, Zhang X, Xiao Y, Li X, Tu Y, Xue Y, Wu W, Ji P, Zhao F, Luo H, Gao F, Guo Y, Xue Y, Yuan H, Zhang YE, Zhang Q, Guo AY, Zhou J, Xue Y, Huang Z, Cui Q, Miao YR, Guo AY, Ruan C, Xue Y, Yuan C, Chen M, Jin JP, Tian F, Gao G, Shi Y, Xue Y, Yao L, Xue Y, Cui Q, Li X, Li CY, Tang Q, Guo AY, Peng D, Xue Y. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 2020; 48:D24-D33. [PMID: 31702008 PMCID: PMC7145560 DOI: 10.1093/nar/gkz913] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022] Open
Abstract
The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. With the rapid advancements in higher-throughput and lower-cost sequencing technologies and accordingly the huge volume of multi-omics data generated at exponential scales and rates, NGDC is continually expanding, updating and enriching its core database resources through big data integration and value-added curation. In the past year, efforts for update have been mainly devoted to BioProject, BioSample, GSA, GWH, GVM, NONCODE, LncBook, EWAS Atlas and IC4R. Newly released resources include three human genome databases (PGG.SNV, PGG.Han and CGVD), eLMSG, EWAS Data Hub, GWAS Atlas, iSheep and PADS Arsenal. In addition, four web services, namely, eGPS Cloud, BIG Search, BIG Submission and BIG SSO, have been significantly improved and enhanced. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.
Collapse
|