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Fahad M, Tariq L, Muhammad S, Wu L. Underground communication: Long non-coding RNA signaling in the plant rhizosphere. PLANT COMMUNICATIONS 2024; 5:100927. [PMID: 38679911 PMCID: PMC11287177 DOI: 10.1016/j.xplc.2024.100927] [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: 01/31/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as integral gene-expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous and dynamic rhizosphere, plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota, as well as nutrient acquisition and heavy metal tolerance. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues. Here, we examine lncRNA biogenesis, classification, and mode of action, highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors. We then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface. A comprehensive understanding of specific lncRNAs, their regulatory targets, and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals. Looking ahead, we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere adaptation. Overcoming future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.
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Affiliation(s)
- Muhammad Fahad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Leeza Tariq
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sajid Muhammad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liang Wu
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Numan M, Sun Y, Li G. Exploring the emerging role of long non-coding RNAs (lncRNAs) in plant biology: Functions, mechanisms of action, and future directions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108797. [PMID: 38850732 DOI: 10.1016/j.plaphy.2024.108797] [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: 11/14/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA transcripts that surpass 200 nucleotides in length and lack discernible coding potential. LncRNAs that have been functionally characterized have pivotal functions in several plant processes, including the regulation of flowering, and development of lateral roots. It also plays a crucial role in the plant's response to abiotic stressors and exhibits vital activities in environmental adaptation. The progress in NGS (next-generation sequencing) and functional genomics technology has facilitated the discovery of lncRNA in plant species. This review is a brief explanation of lncRNA genomics, its molecular role, and the mechanism of action in plants. The review also addresses the challenges encountered in this field and highlights promising molecular and computational methodologies that can aid in the comparative and functional analysis of lncRNAs.
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Affiliation(s)
- Mian Numan
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Yuge Sun
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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Agho CA, Śliwka J, Nassar H, Niinemets Ü, Runno-Paurson E. Machine Learning-Based Identification of Mating Type and Metalaxyl Response in Phytophthora infestans Using SSR Markers. Microorganisms 2024; 12:982. [PMID: 38792811 PMCID: PMC11124124 DOI: 10.3390/microorganisms12050982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Phytophthora infestans is the causal agent of late blight in potato. The occurrence of P. infestans with both A1 and A2 mating types in the field may result in sexual reproduction and the generation of recombinant strains. Such strains with new combinations of traits can be highly aggressive, resistant to fungicides, and can make the disease difficult to control in the field. Metalaxyl-resistant isolates are now more prevalent in potato fields. Understanding the genetic structure and rapid identification of mating types and metalaxyl response of P. infestans in the field is a prerequisite for effective late blight disease monitoring and management. Molecular and phenotypic assays involving molecular and phenotypic markers such as mating types and metalaxyl response are typically conducted separately in the studies of the genotypic and phenotypic diversity of P. infestans. As a result, there is a pressing need to reduce the experimental workload and more efficiently assess the aggressiveness of different strains. We think that employing genetic markers to not only estimate genotypic diversity but also to identify the mating type and fungicide response using machine learning techniques can guide and speed up the decision-making process in late blight disease management, especially when the mating type and metalaxyl resistance data are not available. This technique can also be applied to determine these phenotypic traits for dead isolates. In this study, over 600 P. infestans isolates from different populations-Estonia, Pskov region, and Poland-were classified for mating types and metalaxyl response using machine learning techniques based on simple sequence repeat (SSR) markers. For both traits, random forest and the support vector machine demonstrated good accuracy of over 70%, compared to the decision tree and artificial neural network models whose accuracy was lower. There were also associations (p < 0.05) between the traits and some of the alleles detected, but machine learning prediction techniques based on multilocus SSR genotypes offered better prediction accuracy.
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Affiliation(s)
- Collins A. Agho
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, Department of Potato Genetics and Parental Lines, Platanowa Str. 19, 05-831 Młochów, Poland
| | - Helina Nassar
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia
| | - Eve Runno-Paurson
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
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Traubenik S, Charon C, Blein T. From environmental responses to adaptation: the roles of plant lncRNAs. PLANT PHYSIOLOGY 2024; 195:232-244. [PMID: 38246143 DOI: 10.1093/plphys/kiae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
As sessile organisms, plants are continuously exposed to heterogeneous and changing environments and constantly need to adapt their growth strategies. They have evolved complex mechanisms to recognize various stress factors, activate appropriate signaling pathways, and respond accordingly by reprogramming the expression of multiple genes at the transcriptional, post-transcriptional, and even epigenome levels to tolerate stressful conditions such as drought, high temperature, nutrient deficiency, and pathogenic interactions. Apart from protein-coding genes, long non-coding RNAs (lncRNAs) have emerged as key players in plant adaptation to environmental stresses. They are transcripts larger than 200 nucleotides without protein-coding potential. Still, they appear to regulate a wide range of processes, including epigenetic modifications and chromatin reorganization, as well as transcriptional and post-transcriptional modulation of gene expression, allowing plant adaptation to various environmental stresses. LncRNAs can positively or negatively modulate stress responses, affecting processes such as hormone signaling, temperature tolerance, and nutrient deficiency adaptation. Moreover, they also seem to play a role in stress memory, wherein prior exposure to mild stress enhances plant ability to adapt to subsequent stressful conditions. In this review, we summarize the contribution of lncRNAs in plant adaptation to biotic and abiotic stresses, as well as stress memory. The complex evolutionary conservation of lncRNAs is also discussed and provides insights into future research directions in this field.
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Affiliation(s)
- Soledad Traubenik
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Céline Charon
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Thomas Blein
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
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Zhao X, Li F, Ali M, Li X, Fu X, Zhang X. Emerging roles and mechanisms of lncRNAs in fruit and vegetables. HORTICULTURE RESEARCH 2024; 11:uhae046. [PMID: 38706580 PMCID: PMC11069430 DOI: 10.1093/hr/uhae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 05/07/2024]
Abstract
With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.
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Affiliation(s)
- Xiuming Zhao
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Fujun Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Maratab Ali
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xiaoan Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xiaodong Fu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xinhua Zhang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
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Cao W, Yang L, Zhuang M, Lv H, Wang Y, Zhang Y, Ji J. Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108435. [PMID: 38402798 DOI: 10.1016/j.plaphy.2024.108435] [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: 08/31/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/27/2024]
Abstract
Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.
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Affiliation(s)
- Wenxue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
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Zhang JH, Wei HB, Hong YH, Yang RR, Meng J, Luan YS. The lncRNA20718-miR6022-RLPs module regulates tomato resistance to Phytophthora infestans. PLANT CELL REPORTS 2024; 43:57. [PMID: 38319523 DOI: 10.1007/s00299-024-03161-7] [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: 11/25/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
KEY MESSAGE Sl-lncRNA20718 acts as an eTM of Sl-miR6022 regulating its expression thereby affecting SlRLP6/10 expression. SlRLP6/10 regulate PRs expression, ROS accumulation, and JA/ET content thereby affecting tomato resistance to P. infestans. Tomato (Solanum lycopersicum) is an important horticultural and cash crop whose yield and quality can be severely affected by Phytophthora infestans (P. infestans). Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are widely involved in plant defense responses against pathogens. The involvement of Sl-lncRNA20718 and Sl-miR6022 in tomato resistance to P. infestans as well as the targeting of Sl-miR6022 to receptor-like protein genes (RLPs) were predicted in our previous study. However, uncertainty exists regarding their potential interaction as well as the molecular processes regulating tomato resistance. Here, we found that Sl-lncRNA20718 and Sl-miR6022 are positive and negative regulators of tomato resistance to P. infestans by gain- and loss-of-function experiments, respectively. Overexpression of Sl-lncRNA20718 decreased the expression of Sl-miR6022, induced the expression of PRs, reduced the diameter of lesions (DOLs), thereby enhanced disease resistance. A six-point mutation in the binding region of Sl-lncRNA20718 to Sl-miR6022 disabled the interaction, indicating that Sl-lncRNA20718 acts as an endogenous target mimic (eTM) of Sl-miR6022. We demonstrated that Sl-miR6022 cleaves SlRLP6/10. Overexpression of Sl-miR6022 decreases the expression levels of SlRLP6/10, induces the accumulation of reactive oxygen species (ROS) and reduces the content of JA and ET, thus inhibiting tomato resistance to P. infestans. In conclusion, our study provides detailed information on the lncRNA20718-miR6022-RLPs module regulating tomato resistance to P. infestans by affecting the expression of disease resistance-related genes, the accumulation of ROS and the phytohormone levels, providing a new reference for tomato disease resistance breeding.
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Affiliation(s)
- Jia-Hui Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Hong-Bo Wei
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Hui Hong
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Rui-Rui Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Shi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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Guan C, Li W, Wang G, Yang R, Zhang J, Zhang J, Wu B, Gao R, Jia C. Transcriptomic analysis of ncRNAs and mRNAs interactions during drought stress in switchgrass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111930. [PMID: 38007196 DOI: 10.1016/j.plantsci.2023.111930] [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: 09/08/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
Switchgrass (Panicum virgatum L.) plays a pivotal role as a bioenergy feedstock in the production of cellulosic ethanol and contributes significantly to enhancing ecological grasslands and soil quality. The utilization of non-coding RNAs (ncRNAs) has gained momentum in deciphering the intricate genetic responses to abiotic stress in various plant species. Nevertheless, the current research landscape lacks a comprehensive exploration of the responses of diverse ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), to drought stress in switchgrass. In this study, we employed whole transcriptome sequencing to comprehensively characterize the expression profiles of both mRNA and ncRNAs during episodes of drought stress in switchgrass. Our analysis identified a total of 12,511 mRNAs, 59 miRNAs, 38 circRNAs, and 368 lncRNAs that exhibited significant differential expression between normal and drought-treated switchgrass leaves. Notably, the majority of up-regulated mRNAs displayed pronounced enrichment within the starch and sucrose metabolism pathway, as validated through KEGG analysis. Co-expression analysis illuminated that differentially expressed (DE) lncRNAs conceivably regulated 1308 protein-coding genes in trans and 7110 protein-coding genes in cis. Furthermore, both cis- and trans-target mRNAs of DE lncRNAs exhibited enrichment in four common KEGG pathways. The intricate interplay between lncRNAs and circRNAs with miRNAs via miRNA response elements was explored within the competitive endogenous RNA (ceRNA) network framework. As a result, we constructed elaborate regulatory networks, including lncRNA-novel_miRNA480-mRNA, lncRNA-novel_miRNA304-mRNA, lncRNA/circRNA-novel_miRNA122-PvSS4, and lncRNA/circRNA-novel_miRNA14-PvSS4, and subsequently validated the functionality of the target gene, starch synthase 4 (PvSS4). Furthermore, through the overexpression of PvSS4, we ascertained its capacity to enhance drought tolerance in yeast. However, it is noteworthy that PvSS4 did not exhibit any discernible impact under salt stress conditions. These findings, as presented herein, not only contribute substantively to our understanding of ceRNA networks but also offer a basis for further investigations into their potential functions in response to drought stress in switchgrass.
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Affiliation(s)
- Cong Guan
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Wei Li
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Guoliang Wang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Ruimei Yang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Jinglei Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Jinhong Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Bo Wu
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Run Gao
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Chunlin Jia
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China.
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Chen D, Zhang Z, Chen Y, Li B, Chen T, Tian S. Transcriptional landscape of pathogen-responsive lncRNAs in tomato unveils the role of hydrolase encoding genes in response to Botrytis cinerea invasion. PLANT, CELL & ENVIRONMENT 2024; 47:651-663. [PMID: 37899711 DOI: 10.1111/pce.14757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/30/2023] [Accepted: 10/19/2023] [Indexed: 10/31/2023]
Abstract
LncRNAs have gained increasing attention owing to their important regulatory roles on growth and stress responses of plants. However, the mechanisms underlying the functions of lncRNAs in fruit-pathogen interaction are still largely unknown. In this study, a total of 273 lncRNAs responding to Botrytis cinerea infection were identified in tomato fruit, among which a higher percentage of antisense lncRNAs were targeted to the genes enriched in hydrolase activity. To ascertain the roles of these lncRNAs, seven hydrolase-related transcripts were transiently knocked-down by virus-induced gene silencing. Silencing of lncRNACXE20 reduced the expression level of a carboxylesterase gene, further enhancing the resistance of tomato to B. cinerea. In contrast, silencing of lncRNACHI, lncRNAMMP, lncRNASBT1.9 and lncRNAPME1.9 impaired the resistance to B. cinerea, respectively. Further RT-qPCR assay and enzymatic activity detection displayed that the attenuated resistance of lncRNAMMP and lncRNASBT1.9-silenced plants was associated with the inhibition on the expression of JA-related genes, while the decreased resistance of lncRNACHI-silenced plants resulted in reduced chitinase activity. Collectively, these results may provide references for deciphering the mechanisms underlying specific lncRNAs to interfere with B. cinerea infection by regulating the expression of defence-related genes or affecting hydrolase activity.
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Affiliation(s)
- Daoguo Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhanquan Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Boqiang Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Tong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Shiping Tian
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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10
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Cui C, Wan H, Li Z, Ai N, Zhou B. Long noncoding RNA TRABA suppresses β-glucosidase-encoding BGLU24 to promote salt tolerance in cotton. PLANT PHYSIOLOGY 2024; 194:1120-1138. [PMID: 37801620 DOI: 10.1093/plphys/kiad530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/23/2023] [Accepted: 09/04/2023] [Indexed: 10/08/2023]
Abstract
Salt stress severely damages the growth and yield of crops. Recently, long noncoding RNAs (lncRNAs) were demonstrated to regulate various biological processes and responses to environmental stresses. However, the regulatory mechanisms of lncRNAs in cotton (Gossypium hirsutum) response to salt stress are still poorly understood. Here, we observed that a lncRNA, trans acting of BGLU24 by lncRNA (TRABA), was highly expressed while GhBGLU24-A was weakly expressed in a salt-tolerant cotton accession (DM37) compared to a salt-sensitive accession (TM-1). Using TRABA as an effector and proGhBGLU24-A-driven GUS as a reporter, we showed that TRABA suppressed GhBGLU24-A promoter activity in double transgenic Arabidopsis (Arabidopsis thaliana), which explained why GhBGLU24-A was weakly expressed in the salt-tolerant accession compared to the salt-sensitive accession. GhBGLU24-A encodes an endoplasmic reticulum (ER)-localized β-glucosidase that responds to salt stress. Further investigation revealed that GhBGLU24-A interacted with RING-type E3 ubiquitin ligase (GhRUBL). Virus-induced gene silencing (VIGS) and transgenic Arabidopsis studies revealed that both GhBGLU24-A and GhRUBL diminish plant tolerance to salt stress and ER stress. Based on its substantial effect on ER-related degradation (ERAD)-associated gene expression, GhBGLU24-A mediates ER stress likely through the ERAD pathway. These findings provide insights into the regulatory role of the lncRNA TRABA in modulating salt and ER stresses in cotton and have potential implications for developing more resilient crops.
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Affiliation(s)
- Changjiang Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Zhu Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, 832000 Xinjiang, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
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Ren J, Chen L, Liu J, Zhou B, Sha Y, Hu G, Peng J. Transcriptomic insights into the molecular mechanism for response of wild emmer wheat to stripe rust fungus. FRONTIERS IN PLANT SCIENCE 2024; 14:1320976. [PMID: 38235210 PMCID: PMC10791934 DOI: 10.3389/fpls.2023.1320976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024]
Abstract
Introduction Continuous identification and application of novel resistance genes against stripe rust are of great importance for wheat breeding. Wild emmer wheat, Triticum dicoccoides, has adapted to a broad range of environments and is a valuable genetic resource that harbors important beneficial traits, including resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). However, there has been a lack of systematic exploration of genes against Pst races in wild emmer wheat. Methods Genome-wide transcriptome profiles were conducted on two wild emmer wheat genotypes with different levels of resistance to (Pst (DR3 exhibiting moderate (Pst resistance, and D7 displaying high (Pst resistance). qRT-PCR was performed to verify findings by RNA-seq. Results A higher number of DEGs were identified in the moderately (Pst-resistant genotype, while the highly (Pst-resistant genotype exhibited a greater enrichment of pathways. Nonetheless, there were consistent patterns in the enrichment of pathways between the two genotypes at the same time of inoculation. At 24 hpi, a majority of pathways such as the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, phenylalanine metabolism, and alpha-Linolenic acid metabolism exhibited significant enrichment in both genotypes. At 72 hpi, the biosynthesis of secondary metabolites and circadian rhythm-plant pathways were notably and consistently enriched in both genotypes. The majority of (WRKY, MADs , and AP2-ERF families were found to be involved in the initial stage of response to Pst invasion (24 hpi), while the MYB, NAC, TCP, and b-ZIP families played a role in defense during the later stage of Pst infection (72 hpi). Discussion In this present study, we identified numerous crucial genes, transcription factors, and pathways associated with the response and regulation of wild emmer wheat to Pst infection. Our findings offer valuable information for understanding the function of crucial Pst-responsive genes, and will deepen the understanding of the complex resistance mechanisms against Pst in wheat.
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Affiliation(s)
- Jing Ren
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jian Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Bailing Zhou
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yujie Sha
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Junhua Peng
- Spring Valley Agriscience Co., Ltd, Jinan, China
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12
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Si X, Liu H, Cheng X, Xu C, Han Z, Dai Z, Wang R, Pan C, Lu G. Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum. Int J Biol Macromol 2023; 253:126891. [PMID: 37709224 DOI: 10.1016/j.ijbiomac.2023.126891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.
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Affiliation(s)
- Xiuyang Si
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongyan Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi Cheng
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chengcui Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanghui Han
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhongren Dai
- Branch Academy of Horticultural Research, Harbin Academy of Agricultural Sciences, Harbin 150029, China
| | - Rongqing Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Changtian Pan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China
| | - Gang Lu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China.
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13
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Yuan C, He RR, Zhao WL, Chen YQ, Zhang YC. Insights into the roles of long noncoding RNAs in the communication between plants and the environment. THE PLANT GENOME 2023; 16:e20277. [PMID: 36345558 DOI: 10.1002/tpg2.20277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant biological processes has markedly increased. These lncRNA roles involve plant vegetative and reproductive growth and responses to biotic and abiotic stresses. In this review, we examine the classification, mechanisms, and functions of lncRNAs and then emphasize the roles played by these lncRNAs in the communication between plants and the environment mainly with respect to the following environmental factors: temperature, light, water, salt stress, and nutrient deficiencies. We also discuss the consensus among researchers and the remaining challenges and underscore the exciting ways lncRNAs may affect the biology of plants.
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Affiliation(s)
- Chao Yuan
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
| | - Wen-Long Zhao
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen Univ., Guangzhou, 510275, China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen Univ., Guangzhou, 510275, China
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14
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Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Guo W, Wu F, Feng X, Wang Q, Lu Y, Xu J. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. Int J Mol Sci 2023; 24:15039. [PMID: 37894720 PMCID: PMC10606207 DOI: 10.3390/ijms242015039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m6A), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.
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Affiliation(s)
- Xin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qimeng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoju Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiu Zhong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Mao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wubin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianhong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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Hazra S, Moulick D, Mukherjee A, Sahib S, Chowardhara B, Majumdar A, Upadhyay MK, Yadav P, Roy P, Santra SC, Mandal S, Nandy S, Dey A. Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107940. [PMID: 37738864 DOI: 10.1016/j.plaphy.2023.107940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.
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Affiliation(s)
- Swati Hazra
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | | | - Synudeen Sahib
- S. S. Cottage, Njarackal, P.O.: Perinad, Kollam, 691601, Kerala, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies, Arunachal Pradesh 792103, India.
| | - Arnab Majumdar
- Department of Earth Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, West Bengal 741246, India.
| | - Munish Kumar Upadhyay
- Department of Civil Engineering, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
| | - Priyabrata Roy
- Department of Molecular Biology and Biotechnology, University of Kalyani, West Bengal 741235, India.
| | - Subhas Chandra Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | - Sayanti Mandal
- Department of Biotechnology, Dr. D. Y. Patil Arts, Commerce & Science College (affiliated to Savitribai Phule Pune University), Sant Tukaram Nagar, Pimpri, Pune, Maharashtra-411018, India.
| | - Samapika Nandy
- School of Pharmacy, Graphic Era Hill University, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India; Department of Botany, Vedanta College, 33A Shiv Krishna Daw Lane, Kolkata-700054, India.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal 700073, India.
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Su C, Wang Z, Cui J, Wang Z, Wang R, Meng J, Luan Y. Sl-lncRNA47980, a positive regulator affects tomato resistance to Phytophthora infestans. Int J Biol Macromol 2023; 248:125824. [PMID: 37453642 DOI: 10.1016/j.ijbiomac.2023.125824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) involve in defense respond against pathogen attack and show great potentials to improve plant resistance. Tomato late blight, a destructive plant disease, is caused by the oomycete pathogen Phytophthora infestans, which seriously affects the yield and quality of tomato. Our previous research has shown that Sl-lncRNA47980 is involved in response to P. infestans infection, but its molecular mechanism is unknown. Gain- and loss-of-function experiments revealed that Sl-lncRNA47980 as a positive regulator, played a crucial role in enhancing tomato resistance to P. infestans. The Sl-lncRNA47980-overexpressing transgenic plants exhibited an improved ability to scavenge reactive oxygen species (ROS), decreased contents of endogenous gibberellin (GA) and salicylic acid (SA), and increased contents of jasmonic acid (JA), while silencing of Sl-lncRNA47980 showed an opposite trend in the levels of these hormones. Furthermore, it was found that Sl-lncRNA47980 could upregulate the expression of SlGA2ox4 gene through activation of the promoter of SlGA2ox4 to affect GA content. The increased expression of the tomato GA signaling repressor SlDELLA could activate JA-related genes and inhibit SA-related genes to varying degrees respectively. In addition, exogenous application of GA3 and GA synthesis inhibitor uniconazole could increase disease susceptibility of Sl-lncRNA47980-overexpressing plants and the resistance of Sl-lncRNA47980-silenced plants, respectively, to P. infestans. From thus, it was speculated that Sl-lncRNA47980 conferred tomato resistance to P. infestans, which was related to the decrease in endogenous GA content. Our study provided information to link Sl-lncRNA47980 with changes in ROS accumulation and phytohormone levels in plant immunity, thus providing a new candidate gene for tomato breeding.
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Affiliation(s)
- Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhengjie Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
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Yang R, Wang Z, Zhao L, Liu J, Meng J, Luan Y. Secreted Peptide SpPIP1 Modulates Disease Resistance and Salt Tolerance in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12264-12279. [PMID: 37535837 DOI: 10.1021/acs.jafc.3c03412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Tomato is a globally important horticultural and economic crop, but its productivity is severely affected by various stresses. Plant small secretory peptides have been identified as crucial mediators in plant resistance. Here, we conducted a comparative transcriptome analysis and identified the prePIP1 gene from Solanum pimpinellifolium (SpprePIP1), as an ortholog of Arabidopsis prePIP1 encoding the precursor protein of PAMP-induced SSP 1. The expression level of SpprePIP1 is transcriptionally induced in tomato upon infection with Phytophthora infestans (P. infestans), the pathogen responsible for late blight. Overexpression of SpprePIP1 resulted in enhanced tomato resistance to P. infestans. In addition, exogenous application of SpPIP1, whether through spraying or irrigation, improved tomato resistance by enhancing the transcript accumulations of pathogenesis-related proteins, as well as reactive oxygen species and the jasmonic acid (JA) levels. Integrated analysis of transcriptomics and metabolomics revealed the potential contributions of JA and phenylpropanoid biosynthesis to SpPIP1-induced tomato immunity. Additionally, SpPIP1 may strengthen tomato resistance to salt stress through the ABA signaling pathway. Overall, our findings demonstrate that SpPIP1 positively regulates tomato tolerance to P. infestans and salt stress, making it a potential plant elicitor for crop protection in an environmentally friendly way.
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Affiliation(s)
- Ruirui Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jie Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
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18
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Li X, Xu B, Xu J, Li Z, Jiang C, Zhou Y, Yang Z, Deng M, Lv J, Zhao K. Tomato-Thaumatin-like Protein Genes Solyc08g080660 and Solyc08g080670 Confer Resistance to Five Soil-Borne Diseases by Enhancing β-1,3-Glucanase Activity. Genes (Basel) 2023; 14:1622. [PMID: 37628673 PMCID: PMC10454901 DOI: 10.3390/genes14081622] [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: 07/14/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Although thaumatin-like proteins (TLPs) are involved in resistance to a variety of fungal diseases, whether the TLP5 and TLP6 genes in tomato plants (Solanum lycopersicum) confer resistance to the pathogenesis of soil-borne diseases has not been demonstrated. In this study, five soil-borne diseases (fungal pathogens: Fusarium solani, Fusarium oxysporum, and Verticillium dahliae; bacterial pathogens: Clavibacter michiganense subsp. michiganense and Ralstonia solanacearum) were used to infect susceptible "No. 5" and disease-resistant "S-55" tomato cultivars. We found that SlTLP5 and SlTLP6 transcript levels were higher in susceptible cultivars treated with the three fungal pathogens than in those treated with the two bacterial pathogens and that transcript levels varied depending on the pathogen. Moreover, the SlTLP5 and SlTLP6 transcript levels were much higher in disease-resistant cultivars than in disease-susceptible cultivars, and the SlTLP5 and SlTLP6 transcript levels were higher in cultivars treated with the same fungal pathogen than in those treated with bacterial pathogens. SlTLP6 transcript levels were higher than SlTLP5. SlTLP5 and SlTLP6 overexpression and gene-edited transgenic mutants were generated in both susceptible and resistant cultivars. Overexpression and knockout increased and decreased resistance to the five diseases, respectively. Transgenic plants overexpressing SlTLP5 and SlTLP6 inhibited the activities of peroxidase (POD), superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT) after inoculation with fungal pathogens, and the activities of POD, SOD, and APX were similar to those of fungi after infection with bacterial pathogens. The activities of CAT were increased, and the activity of β-1,3-glucanase was increased in both the fungal and bacterial treatments. Overexpressed plants were more resistant than the control plants. After SlTLP5 and SlTLP6 knockout plants were inoculated, POD, SOD, and APX had no significant changes, but CAT activity increased and decreased significantly after the fungal and bacterial treatments, contrary to overexpression. The activity of β-1,3-glucanase decreased in the treatment of the five pathogens, and the knocked-out plants were more susceptible to disease than the control. In summary, this study contributes to the further understanding of TLP disease resistance mechanisms in tomato plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Kai Zhao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China; (X.L.); (Z.Y.); (M.D.); (J.L.)
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19
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Sun N, Bu Y, Wu X, Ma X, Yang H, Du L, Li X, Xiao J, Lin J, Jing Y. Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154055. [PMID: 37506405 DOI: 10.1016/j.jplph.2023.154055] [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: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in numerous biological processes in plants, such as regulating the gene expression. However, only a few studies have looked into their potential functions in xylem development. High-throughput sequencing of P. euramericana 'Zhonglin46' developing and mature xylem was performed in this study. Through sequencing analysis, 14,028 putative lncRNA transcripts were identified, including 4525 differentially expressed lncRNAs (DELs). Additional research revealed that in mature xylem, a total of 2320 DELs were upregulated and 2205 were downregulated compared to developing xylem. Meanwhile, there were a total of 8122 differentially expressed mRNAs (DEMs) that were upregulated and 16,424 that were downregulated in mature xylem compared with developing xylem. The cis- and trans-target genes of DELs were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, which indicated that these DELs participate in controlling the phenylpropanoid and lignin biosynthesis pathway as well as the starch and sucrose metabolism pathway. Among the cis-regulated DELs, LNC_006291, LNC_006292, and LNC_006532 all participate in regulating multiple HCT gene family membranes. As targets, POPTR_001G045900v3 (CCR2) and POPTR_018G063500v3 (SUS) both have only one cis-regulatory lncRNA, referred to as LNC_000057 and LNC_006212, respectively. Moreover, LNC_004484 and two DELs named LNC_008014 and LNC_010781 were revealed to be important nodes in the co-expression network of trans-lncRNAs and mRNAs associated to the lignin biosynthesis pathway and cellulose and xylan biosynthetic pathways, respectively. Finally, quantitative real-time PCR (qRT-PCR) was used to confirme 34 pairs of lncRNA-mRNA. Taken together, these findings may help to clarify the regulatory role that lncRNAs play in xylem development and wood formation.
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Affiliation(s)
- Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaojuan Li
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jianwei Xiao
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jinxing Lin
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
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20
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Sharma S, Sett S, Das T, Prasad A, Prasad M. Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107852. [PMID: 37356385 DOI: 10.1016/j.plaphy.2023.107852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
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Affiliation(s)
| | - Susmita Sett
- National Institute of Plant Genome Research, New Delhi, India.
| | - Tuhin Das
- National Institute of Plant Genome Research, New Delhi, India.
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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21
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Yi K, Yan W, Li X, Yang S, Li J, Yin Y, Yuan F, Wang H, Kang Z, Han D, Zeng Q. Identification of Long Intergenic Noncoding RNAs in Rhizoctonia cerealis following Inoculation of Wheat. Microbiol Spectr 2023; 11:e0344922. [PMID: 37036374 PMCID: PMC10269763 DOI: 10.1128/spectrum.03449-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/12/2023] [Indexed: 04/11/2023] Open
Abstract
Wheat sharp eyespot caused by Rhizoctonia cerealis is primarily a severe threat to worldwide wheat production. Currently, there are no resistant wheat cultivars, and the use of fungicides is the primary method for controlling this disease. Elucidating the mechanisms of R. cerealis pathogenicity can accelerate the pace of the control of this disease. Long intergenic noncoding RNAs (lincRNAs) that function in plant-pathogen interactions might provide a new perspective. We systematically analyzed lincRNAs and identified a total of 1,319 lincRNAs in R. cerealis. We found that lincRNAs are involved in various biological processes, as shown by differential expression analysis and weighted correlation network analysis (WGCNA). Next, one of nine hub lincRNAs in the blue module that was related to infection and growth processes, MSTRG.4380.1, was verified to reduce R. cerealis virulence on wheat by a host-induced gene silencing (HIGS) assay. Following that, RNA sequencing (RNA-Seq) analysis revealed that the significantly downregulated genes in the MSTRG.4380.1 knockdown lines were associated mainly with infection-related processes, including hydrolase, transmembrane transporter, and energy metabolism activities. Additionally, 23 novel microRNAs (miRNAs) were discovered during small RNA (sRNA) sequencing (sRNA-Seq) analysis of MSTRG.4380.1 knockdown, and target prediction of miRNAs suggested that MSTRG.4380.1 does not act as a competitive endogenous RNA (ceRNA). This study performed the first genome-wide identification of R. cerealis lincRNAs and miRNAs. It confirmed the involvement of a lincRNA in the infection process, providing new insights into the mechanism of R. cerealis infection and offering a new approach for protecting wheat from R. cerealis. IMPORTANCE Rhizoctonia cerealis, the primary causal agent of wheat sharp eyespot, has caused significant losses in worldwide wheat production. Since no resistant wheat cultivars exist, chemical control is the primary method. However, this approach is environmentally unfriendly and costly. RNA interference (RNAi)-mediated pathogenicity gene silencing has been proven to reduce the growth of Rhizoctonia and provides a new perspective for disease control. Recent studies have shown that lincRNAs are involved in various biological processes across species, such as biotic and abiotic stresses. Therefore, verifying the function of lincRNAs in R. cerealis is beneficial for understanding the infection mechanism. In this study, we reveal that lincRNAs could contribute to the virulence of R. cerealis, which provides new insights into controlling this pathogen.
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Affiliation(s)
- Ke Yi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Weiyi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuqing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiaqi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Yifan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
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22
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Li C, Lai X, Yu X, Xiong Z, Chen J, Lang X, Feng H, Wan X, Liu K. Plant long noncoding RNAs: Recent progress in understanding their roles in growth, development, and stress responses. Biochem Biophys Res Commun 2023; 671:270-277. [PMID: 37311264 DOI: 10.1016/j.bbrc.2023.05.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023]
Abstract
Long noncoding RNA (lncRNA) transcripts are longer than 200 nt and are not translated into proteins. LncRNAs function in a wide variety of processes in plants and animals, but, perhaps because of their lower expression and conservation levels, plant lncRNAs had attracted less attention than protein-coding mRNAs. Now, recent studies have made remarkable progress in identifying lncRNAs and understanding their functions. In this review, we discuss a number of lncRNAs that have important functions in growth, development, reproduction, responses to abiotic stresses, and regulation of disease and insect resistance in plants. Additionally, we describe the known mechanisms of action of plant lncRNAs according to their origins within the genome. This review thus provides a guide for identifying and functionally characterizing new lncRNAs in plants.
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Affiliation(s)
- Chunmei Li
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xuanyue Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Zhiwen Xiong
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jie Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xingxuan Lang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Haotian Feng
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaorong Wan
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Kai Liu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
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23
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Zhou R, Dong Y, Wang C, Liu J, Liang Q, Meng X, Lang X, Xu S, Liu W, Zhang S, Wang N, Yang KQ, Fang H. LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by Colletotrichum gloeosporioides. HORTICULTURE RESEARCH 2023; 10:uhad086. [PMID: 37786525 PMCID: PMC10541558 DOI: 10.1093/hr/uhad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/20/2023] [Indexed: 10/04/2023]
Abstract
Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a C. gloeosporioides-induced lncRNA, lncRNA109897, located upstream from the target gene JrCCR4, upregulated the expression of JrCCR4. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of lncRNA109897 to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of Arabidopsis thaliana further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of C. gloeosporioides. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.
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Affiliation(s)
- Rui Zhou
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Yuhui Dong
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Changxi Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Jianning Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Qiang Liang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Xiaoye Meng
- Department of Natural Resources Of Shandong Province, Forestry Protection and Development Service Center, Jinan, Shandong, China, 250000
| | - Xinya Lang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Shengyi Xu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Shuhui Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Ke Qiang Yang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Hongcheng Fang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
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24
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Wang Z, Cui Q, Su C, Zhao S, Wang R, Wang Z, Meng J, Luan Y. Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress. Int J Biol Macromol 2023:124952. [PMID: 37257526 DOI: 10.1016/j.ijbiomac.2023.124952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.
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Affiliation(s)
- Zhengjie Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qi Cui
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
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25
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Abstract
Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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26
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Saxena S, Das A, Kaila T, Ramakrishna G, Sharma S, Gaikwad K. Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea. Genes Genomics 2023; 45:783-811. [PMID: 37115379 DOI: 10.1007/s13258-023-01383-9] [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: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 04/29/2023]
Abstract
BACKGROUND Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea. OBJECTIVE Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines. METHODS We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data. RESULTS We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration. CONCLUSION Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.
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Affiliation(s)
- Swati Saxena
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Antara Das
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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Wu M, Luo Z, Cao S. Promoter Variation of the Key Apple Fruit Texture Related Gene MdPG1 and the Upstream Regulation Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1452. [PMID: 37050079 PMCID: PMC10096972 DOI: 10.3390/plants12071452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
MdPG1 encoding polygalacturonase in apple (Malus × domestica) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of MdPG1 are still not known. In this study, we identified a SNPA/C variant within an ERF-binding element located in the promoter region of MdPG1. The promoter containing the ERF-binding element with SNPA, rather than the SNPC, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, lncRNAPG1, in the promoter of MdPG1 was a causative variant. lncRNAPG1 was specifically expressed in fruit tissues postharvest. lncRNAPG1 could reduce promoter activity when it was fused to the promoter of MdPG1 and a tobacco gene encoding Mg-chelatase H subunit (NtCHLH) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a cis-regulatory effect. Our results provide new insights into genetic regulation of MdPG1 allele expression and are also useful for the development of elite apple cultivars.
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Affiliation(s)
- Mengmeng Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengrong Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
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Wang Z, Wang S, Fan X, Zhang K, Zhang J, Zhao H, Gao X, Zhang Y, Guo S, Zhou D, Li Q, Na Z, Chen D, Guo R. Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation. Int J Mol Sci 2023; 24:ijms24065886. [PMID: 36982959 PMCID: PMC10058195 DOI: 10.3390/ijms24065886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are pivotal regulators in gene expression and diverse biological processes, such as immune defense and host-pathogen interactions. However, little is known about the roles of lncRNAs in the response of the Asian honey bee (Apis cerana) to microsporidian infestation. Based on our previously obtained high-quality transcriptome datasets from the midgut tissues of Apis cerana cerana workers at 7 days post inoculation (dpi) and 10 dpi with Nosema ceranae (AcT7 and AcT10 groups) and the corresponding un-inoculated midgut tissues (AcCK7 and AcCK10 groups), the transcriptome-wide identification and structural characterization of lncRNAs were conducted, and the differential expression pattern of lncRNAs was then analyzed, followed by investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in host response. Here, 2365, 2322, 2487, and 1986 lncRNAs were, respectively, identified in the AcCK7, AcT7, AcCK7, and AcT10 groups. After removing redundant ones, a total of 3496 A. c. cerana lncRNAs were identified, which shared similar structural characteristics with those discovered in other animals and plants, such as shorter exons and introns than mRNAs. Additionally, 79 and 73 DElncRNAs were screened from the workers' midguts at 7 dpi and 10 dpi, respectively, indicating the alteration of the overall expression pattern of lncRNAs in host midguts after N. ceranae infestation. These DElncRNAs could, respectively, regulate 87 and 73 upstream and downstream genes, involving a suite of functional terms and pathways, such as metabolic process and Hippo signaling pathway. Additionally, 235 and 209 genes co-expressed with DElncRNAs were found to enrich in 29 and 27 terms, as well as 112 and 123 pathways, such as ABC transporters and the cAMP signaling pathway. Further, it was detected that 79 (73) DElncRNAs in the host midguts at 7 (10) dpi could target 321 (313) DEmiRNAs and further target 3631 (3130) DEmRNAs. TCONS_00024312 and XR_001765805.1 were potential precursors for ame-miR-315 and ame-miR-927, while TCONS_00006120 was the putative precursor for both ame-miR-87-1 and ame-miR-87-2. These results together suggested that DElncRNAs are likely to play regulatory roles in the host response to N. ceranae infestation through the regulation of neighboring genes via a cis-acting effect, modulation of co-expressed mRNAs via trans-acting effect, and control of downstream target genes' expression via competing endogenous RNA networks. Our findings provide a basis for disclosing the mechanism underlying DElncRNA-mediated host N. ceranae response and a new perspective into the interaction between A. c. cerana and N. ceranae.
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Affiliation(s)
- Zixin Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyi Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kaiyao Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiaxin Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haodong Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingding Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiming Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhihao Na
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Zhang C, Dong Y, Ren Y, Wang S, Yang M. Conjoint Analysis of Genome-Wide lncRNA and mRNA Expression during the Salicylic Acid Response in Populus × euramericana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1377. [PMID: 36987064 PMCID: PMC10058947 DOI: 10.3390/plants12061377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. To explore the molecular mechanism of the response of poplar to salicylic acid (SA), the changes in protective enzymes, which are closely related to plant resistance induced by exogenous SA, were studied, and the expression of mRNA and lncRNA were determined by high-throughput RNA sequencing. The results showed that the activities of phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), in the leaves of Populus × euramericana, were significantly increased by exogenous SA application. High-throughput RNA sequencing showed that 26,366 genes and 5690 lncRNAs were detected under the different treatment conditions: SA and H2O application. Among these, 606 genes and 49 lncRNAs were differentially expressed. According to target prediction, lncRNAs and target genes involved in light response, stress response, plant disease resistance, and growth and development, were differentially expressed in SA-treated leaves. Interaction analysis showed that lncRNA-mRNA interactions, following exogenous SA, were involved in the response of poplar leaves to the external environment. Our study provides a comprehensive view of Populus × euramericana lncRNAs and offers insights into the potential functions and regulatory interactions of SA-responsive lncRNAs, thus forming the foundation for future functional analysis of SA-responsive lncRNAs in Populus × euramericana.
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Affiliation(s)
- Chao Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yachao Ren
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
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30
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Guan Y, Wei Z, Song P, Zhou L, Hu H, Hu P, Li C. MicroRNA Expression Profiles in Response to Phytophthora infestans and Oidium neolycopersici and Functional Identification of sly-miR397 in Tomato. PHYTOPATHOLOGY 2023; 113:497-507. [PMID: 36346372 DOI: 10.1094/phyto-04-22-0117-r] [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] [Indexed: 06/16/2023]
Abstract
Late blight and powdery mildew are two widespread tomato diseases caused by Phytophthora infestans and Oidium neolycopersici, respectively, which reduce the quantity and quality of tomato. MicroRNAs (miRNAs) play critical roles in tomato resistance to various pathogens. Investigating the function of miRNAs is of great significance in controlling tomato diseases. To identify potential miRNAs involved in the interaction of tomato with P. infestans or O. neolycopersici, we analyzed the expression profiles of small RNAs in tomato leaves infected with these two pathogens using RNA-seq technology. A total of 330 and 288 miRNAs exhibited differences in expression levels after exposure to P. infestans and O. neolycopersici, respectively. One hundred and forty-six commonly differentially expressed (DE) miRNAs responsive to P. infestans and O. neolycopersici infestation were detected, including 10 commonly known conserved DE miRNAs and 136 novel miRNAs. Among these known DE miRNAs, sly-miR397 was strongly downregulated in response to P. infestans or O. neolycopersici infection. Silencing of sly-miR397 resulted in enhanced tolerance to the pathogens, whereas overexpression of sly-miR397 showed increased susceptibility. Furthermore, changes in sly-miR397 expression could also affect expression levels of pathogenesis-related genes and reactive oxygen species-scavenging genes, leading to altered necrotic cells and H2O2 levels. In addition, the number of lateral branches significantly changed in transgenic plants. Taken together, our results provide potential miRNA resources for further research of miRNA-disease associations and indicates that sly-miR397 acts as a negative regulator of disease resistance and influences lateral branch development in tomato.
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Affiliation(s)
- Yuanyuan Guan
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Zhiyuan Wei
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Puwen Song
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Luyi Zhou
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Haiyan Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Ping Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Chengwei Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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31
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Zhuo X, Yu Q, Russo R, Zhang Y, Wei X, Wang YZ, Holden PM, Gmitter FG. Role of long non-coding RNA in regulatory network response to Candidatus Liberibacter asiaticus in citrus. FRONTIERS IN PLANT SCIENCE 2023; 14:1090711. [PMID: 36890903 PMCID: PMC9986497 DOI: 10.3389/fpls.2023.1090711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) serve as crucial regulators in plant response to various diseases, while none have been systematically identified and characterized in response to citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) bacteria. Here, we comprehensively investigated the transcriptional and regulatory dynamics of the lncRNAs in response to CLas. Samples were collected from leaf midribs of CLas- and mock-inoculated HLB-tolerant rough lemon (Citrus jambhiri) and HLB-sensitive sweet orange (C. sinensis) at week 0, 7, 17, and 34 following inoculation using CLas+ budwood of three biological replicates in the greenhouse. A total of 8,742 lncRNAs, including 2,529 novel lncRNAs, were identified from RNA-seq data with rRNA-removed from strand-specific libraries. Genomic variation analyses of conserved lncRNAs from 38 citrus accessions showed that 26 single nucleotide polymorphisms (SNPs) were significantly correlated with HLB. In addition, lncRNA-mRNA weighted gene co-expression network analysis (WGCNA) showed a significant module correlated with CLas-inoculation in rough lemon. Notably, the most significant LNC_28805 and multiple co-expressed genes related to plant defense in the module were targeted by miRNA5021, suggesting that LNC28805 might compete with endogenous miR5021 to maintain the homeostasis of immune gene expression levels. Candidate WRKY33 and SYP121 genes targeted by miRNA5021 were identified as two key hub genes interacting with bacteria pathogen response genes based on the prediction of protein-protein interaction (PPI) network. These two genes were also found within HLB-associated QTL in linkage group 6. Overall, our findings provide a reference for a better understanding of the role of lncRNAs involved in citrus HLB regulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Fred G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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Xue Y, Muhammad S, Yang J, Wang X, Zhao N, Qin B, Qiu Y, Du Z, Ulhassan Z, Zhou W, Liu F, Li R. Comparative transcriptome-wide identification and differential expression of genes and lncRNAs in rice near-isogenic line (KW- Bph36-NIL) in response to BPH feeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1095602. [PMID: 36874914 PMCID: PMC9981640 DOI: 10.3389/fpls.2022.1095602] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Brown planthopper (BPH) is the most devastating pest of rice in Asia, causing substantial yield losses and has become a challenging task to be controlled under field conditions. Although extensive measures have been taken over the past decades, which resulted in the evolution of new resistant BPH strains. Therefore, besides other possible approaches, equipping host plants with resistant genes is the most effective and environment-friendly technique for BPH control. Here, we systematically analyzed transcriptome changes in the susceptible rice variety Kangwenqingzhan (KW) and the resistant near-isogenic line (NIL) KW-Bph36-NIL, through RNA-seq, depicting the differential expression profiles of mRNAs and long non-coding RNAs (lncRNAs) in rice before and after BPH feeding. We observed a proportion of genes (1.48%) and (2.74%) were altered in KW and NIL, respectively, indicating different responses of rice strains against BPH feeding. Nevertheless, we characterized 384 differentially expressed long non-coding RNAs (DELs) that can be impacted by the two strains by alternatively changing the expression patterns of the respective coding genes, suggesting their certain involvement in response to BPH feeding. In BPH invasion, KW and NIL responded differently by modifying the synthesis, storage, and transformation of intracellular substances, adjusting the nutrient accumulation and utilization inside and outside the cells. In addition, NIL expressed stronger resistance by acutely up-regulating genes and other transcription factors related to stress resistance and plant immunity. Altogether, our study elaborates valuable insights into the genome-wide DEGs and DELs expression profiles of rice under BPH invasion by high throughput sequencing and further suggests that NILs can be utilized in BPH resistance breeding programs in developing high-resistance rice lines.
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Affiliation(s)
- Yanxia Xue
- School of Electrical and Control Engineering, North University of China, Taiyuan, China
| | - Sajid Muhammad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xuan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yongfu Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimin Du
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zaid Ulhassan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Weijun Zhou
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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Meena SK, Heidecker M, Engelmann S, Jaber A, de Vries T, Triller S, Baumann-Kaschig K, Abel S, Behrens SE, Gago-Zachert S. Altered expression levels of long non-coding natural antisense transcripts overlapping the UGT73C6 gene affect rosette size in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:460-477. [PMID: 36495314 DOI: 10.1111/tpj.16058] [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: 12/03/2021] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Natural antisense long non-coding RNAs (lncNATs) are involved in the regulation of gene expression in plants, modulating different relevant developmental processes and responses to various stimuli. We have identified and characterized two lncNATs (NAT1UGT73C6 and NAT2UGT73C6 , collectively NATsUGT73C6 ) from Arabidopsis thaliana that are transcribed from a gene fully overlapping UGT73C6, a member of the UGT73C subfamily of genes encoding UDP-glycosyltransferases (UGTs). Expression of both NATsUGT73C6 is developmentally controlled and occurs independently of the transcription of UGT73C6 in cis. Downregulation of NATsUGT73C6 levels through artificial microRNAs results in a reduction of the rosette area, while constitutive overexpression of NAT1UGT73C6 or NAT2UGT73C6 leads to the opposite phenotype, an increase in rosette size. This activity of NATsUGT73C6 relies on its RNA sequence and, although modulation of UGT73C6 in cis cannot be excluded, the observed phenotypes are not a consequence of the regulation of UGT73C6 in trans. The NATsUGT73C6 levels were shown to affect cell proliferation and thus individual leaf size. Consistent with this concept, our data suggest that the NATsUGT73C6 influence the expression levels of key transcription factors involved in regulating leaf growth by modulating cell proliferation. These findings thus reveal an additional regulatory layer on the process of leaf growth. In this work, we characterized at the molecular level two long non-coding RNAs (NATsUGT73C6 ) that are transcribed in the opposite direction to UGT73C6, a gene encoding a glucosyltransferase involved in brassinosteroid homeostasis in A. thaliana. Our results indicate that NATsUGT73C6 expression influences leaf growth by acting in trans and by modulating the levels of transcription factors that are involved in the regulation of cell proliferation.
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Affiliation(s)
- Shiv Kumar Meena
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Michel Heidecker
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Susanne Engelmann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Ammar Jaber
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Tebbe de Vries
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Saskia Triller
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Katja Baumann-Kaschig
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Sven-Erik Behrens
- Section Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, D-06120, Germany
| | - Selma Gago-Zachert
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
- Section Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, D-06120, Germany
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Chen Z, Meng J, Zhao S, Yin C, Luan Y. sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs. Interdiscip Sci 2023; 15:189-201. [PMID: 36705893 DOI: 10.1007/s12539-023-00552-4] [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: 07/22/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators of biological processes. It has recently been shown that some lncRNAs include small open reading frames (sORFs) that can encode small peptides of no more than 100 amino acids. However, existing methods are commonly applied to human and animal datasets and still suffer from low feature representation capability. Thus, accurate and credible prediction of sORFs with coding ability in plant lncRNAs is imperative. This paper proposes a new method termed sORFPred, in which we design a model named MCSEN by combining multi-scale convolution and Squeeze-and-Excitation Networks to fully mine distinct information embedded in sORFs, integrate and optimize multiple sequence-based and physicochemical feature descriptors, and built a two-layer prediction classifier based on Bayesian optimization algorithm and Extra Trees. sORFPred has been evaluated on sORFs datasets of three species and experimentally validated sORFs dataset. Results indicate that sORFPred outperforms existing methods and achieves 97.28% accuracy, 97.06% precision, 97.52% recall, and 97.29% F1-score on Arabidopsis thaliana, which shows a significant improvement in prediction performance compared to various conventional shallow machine learning and deep learning models.
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Affiliation(s)
- Ziwei Chen
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China. .,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China.
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Chao Yin
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Yushi Luan
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
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Li Q, Shen H, Yuan S, Dai X, Yang C. miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1094459. [PMID: 36714724 PMCID: PMC9875070 DOI: 10.3389/fpls.2022.1094459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
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Affiliation(s)
- Qian Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Heng Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shoujuan Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xigang Dai
- School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Ai G, Li T, Zhu H, Dong X, Fu X, Xia C, Pan W, Jing M, Shen D, Xia A, Tyler BM, Dou D. BPL3 binds the long non-coding RNA nalncFL7 to suppress FORKED-LIKE7 and modulate HAI1-mediated MPK3/6 dephosphorylation in plant immunity. THE PLANT CELL 2023; 35:598-616. [PMID: 36269178 PMCID: PMC9806616 DOI: 10.1093/plcell/koac311] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
RNA-binding proteins (RBPs) participate in a diverse set of biological processes in plants, but their functions and underlying mechanisms in plant-pathogen interactions are largely unknown. We previously showed that Arabidopsis thaliana BPA1-LIKE PROTEIN3 (BPL3) belongs to a conserved plant RBP family and negatively regulates reactive oxygen species (ROS) accumulation and cell death under biotic stress. In this study, we demonstrate that BPL3 suppresses FORKED-LIKE7 (FL7) transcript accumulation and raises levels of the cis-natural antisense long non-coding RNA (lncRNA) of FL7 (nalncFL7). FL7 positively regulated plant immunity to Phytophthora capsici while nalncFL7 negatively regulated resistance. We also showed that BPL3 directly binds to and stabilizes nalncFL7. Moreover, nalncFL7 suppressed accumulation of FL7 transcripts. Furthermore, FL7 interacted with HIGHLY ABA-INDUCED PP2C1 (HAI1), a type 2C protein phosphatase, and inhibited HAI1 phosphatase activity. By suppressing HAI1 activity, FL7 increased the phosphorylation levels of MITOGEN-ACTIVATED PROTEIN KINASE 3 (MPK3) and MPK6, thus enhancing immunity responses. BPL3 and FL7 are conserved in all plant species tested, but the BPL3-nalncFL7-FL7 cascade was specific to the Brassicaceae. Thus, we identified a conserved BPL3-nalncFL7-FL7 cascade that coordinates plant immunity.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohua Dong
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowei Fu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuyan Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiye Pan
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Brett M Tyler
- Center for Quantitative Life Sciences and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Daolong Dou
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Ding LN, Li YT, Wu YZ, Li T, Geng R, Cao J, Zhang W, Tan XL. Plant Disease Resistance-Related Signaling Pathways: Recent Progress and Future Prospects. Int J Mol Sci 2022; 23:ijms232416200. [PMID: 36555841 PMCID: PMC9785534 DOI: 10.3390/ijms232416200] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Plant-pathogen interactions induce a signal transmission series that stimulates the plant's host defense system against pathogens and this, in turn, leads to disease resistance responses. Plant innate immunity mainly includes two lines of the defense system, called pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). There is extensive signal exchange and recognition in the process of triggering the plant immune signaling network. Plant messenger signaling molecules, such as calcium ions, reactive oxygen species, and nitric oxide, and plant hormone signaling molecules, such as salicylic acid, jasmonic acid, and ethylene, play key roles in inducing plant defense responses. In addition, heterotrimeric G proteins, the mitogen-activated protein kinase cascade, and non-coding RNAs (ncRNAs) play important roles in regulating disease resistance and the defense signal transduction network. This paper summarizes the status and progress in plant disease resistance and disease resistance signal transduction pathway research in recent years; discusses the complexities of, and interactions among, defense signal pathways; and forecasts future research prospects to provide new ideas for the prevention and control of plant diseases.
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38
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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Cloning and Characterization of Two Novel PR4 Genes from Picea asperata. Int J Mol Sci 2022; 23:ijms232314906. [PMID: 36499235 PMCID: PMC9737788 DOI: 10.3390/ijms232314906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
Pathogenesis-related (PR) proteins are important in plant pathogenic resistance and comprise 17 families, including the PR4 family, with antifungal and anti-pathogenic functions. PR4 proteins contain a C-terminal Barwin domain and are divided into Classes I and II based on the presence of an N-terminal chitin-binding domain (CBD). This study is the first to isolate two PR4 genes, PaPR4-a and PaPR4-b, from Picea asperata, encoding PaPR4-a and PaPR4-b, respectively. Sequence analyses suggested that they were Class II proteins, owing to the presence of an N-terminal signal peptide and a C-terminal Barwin domain, but no CBD. Tertiary structure analyses using the Barwin-like protein of papaya as a template revealed structural similarity, and therefore, functional similarity between the proteins. Predictive results revealed an N-terminal transmembrane domain, and subcellular localization studies confirmed its location on cell membrane and nuclei. Real-time quantitative PCR (RT-qPCR) demonstrated that PaPR4-a and PaPR4-b expression levels were upregulated following infection with Lophodermium piceae. Additionally, PaPR4-a and PaPR4-b were induced in Escherichia coli, where the recombinant proteins existed in inclusion bodies. The renatured purified proteins showed antifungal activity. Furthermore, transgenic tobacco overexpressing PaPR4-a and PaPR4-b exhibited improved resistance to fungal infection. The study can provide a basis for further molecular mechanistic insights into PR4-induced defense responses.
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Jing J, Yang P, Wang Y, Qu Q, An J, Fu B, Hu X, Zhou Y, Hu T, Cao Y. Identification of Competing Endogenous RNAs (ceRNAs) Network Associated with Drought Tolerance in Medicago truncatula with Rhizobium Symbiosis. Int J Mol Sci 2022; 23:14237. [PMID: 36430715 PMCID: PMC9696283 DOI: 10.3390/ijms232214237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Abstract
Drought, bringing the risks of agricultural production losses, is becoming a globally environmental stress. Previous results suggested that legumes with nodules exhibited superior drought tolerance compared with the non-nodule group. To investigate the molecular mechanism of rhizobium symbiosis impacting drought tolerance, transcriptome and sRNAome sequencing were performed to identify the potential mRNA-miRNA-ncRNA dynamic network. Our results revealed that seedlings with active nodules exhibited enhanced drought tolerance by reserving energy, synthesizing N-glycans, and medicating systemic acquired resistance due to the early effects of symbiotic nitrogen fixation (SNF) triggered in contrast to the drought susceptible with inactive nodules. The improved drought tolerance might be involved in the decreased expression levels of miRNA such as mtr_miR169l-5p, mtr_miR398b, and mtr_miR398c and its target genes in seedlings with active nodules. Based on the negative expression pattern between miRNA and its target genes, we constructed an mRNA-miR169l-ncRNA ceRNA network. During severe drought stress, the lncRNA alternative splicings TCONS_00049507 and TCONS_00049510 competitively interacted with mtr_miR169l-5p, which upregulated the expression of NUCLEAR FACTOR-Y (NF-Y) transcription factor subfamily NF-YA genes MtNF-YA2 and MtNF-YA3 to regulate their downstream drought-response genes. Our results emphasized the importance of SNF plants affecting drought tolerance. In conclusion, our work provides insight into ceRNA involvement in rhizobium symbiosis contributing to drought tolerance and provides molecular evidence for future study.
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Affiliation(s)
- Jiaxian Jing
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yue Wang
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Qihao Qu
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Jie An
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory of Agrobiotechnology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100083, China
| | - Bingzhe Fu
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xiaoning Hu
- Shaanxi Academy of Forestry, Xi’an 710082, China
| | - Yi Zhou
- School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yuman Cao
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
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41
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Liao L, Xie B, Guan P, Jiang N, Cui J. New insight into the molecular mechanism of miR482/2118 during plant resistance to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:1026762. [PMID: 36388487 PMCID: PMC9650292 DOI: 10.3389/fpls.2022.1026762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
MicroRNAs (miRNAs), a group of small noncoding RNAs (approximately 20-24 nucleotides), act as essential regulators affecting endogenous gene expression in plants. MiR482/2118 is a unique miRNA superfamily in plants and represses NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT (NBS-LRR) genes to function in plant resistance to pathogens. In addition, over the past several years, it has been found that miR482/2118 not only targets NBS-LRRs but also acts on other molecular mechanisms to affect plant resistance. miR482/2118-5ps, phased small interfering RNAs (phasiRNAs) and long noncoding RNAs (lncRNAs) play important roles in plant disease resistance. This review summarizes the current knowledge of the interactions and links between miR482/2118 and its new interacting molecules, miR482/2118-5p, phasiRNAs and lncRNAs, in plant disease resistance. Here, we aim to provide a comprehensive view describing the new molecular mechanism associated with miR482/2118 in the plant immune system.
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Affiliation(s)
- Lijuan Liao
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, Changsha, China
| | - Biao Xie
- College of Life Science, Hunan Normal University, Changsha, China
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, Changsha, China
| | - Peipei Guan
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, Changsha, China
| | - Ning Jiang
- Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jun Cui
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, Changsha, China
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42
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Li M, Si X, Liu Y, Liu Y, Cheng X, Dai Z, Yu X, Ali M, Lu G. Transcriptomic analysis of ncRNA and mRNA interactions during leaf senescence in tomato. Int J Biol Macromol 2022; 222:2556-2570. [DOI: 10.1016/j.ijbiomac.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/27/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022]
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Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane. Int J Mol Sci 2022; 23:ijms231911603. [PMID: 36232906 PMCID: PMC9569758 DOI: 10.3390/ijms231911603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.
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44
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Reactive oxygen species in plants: an invincible fulcrum for biotic stress mitigation. Appl Microbiol Biotechnol 2022; 106:5945-5955. [PMID: 36063177 DOI: 10.1007/s00253-022-12138-z] [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: 04/13/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Climate change-associated environmental vagaries have amplified the incidence of pests and pathogens on plants, thus imparting the increased quest for management strategies. Plants respond to stresses through intricate signaling networks that regulate diverse cellular mechanisms. Reactive oxygen species (ROS) are cardinal towards the maintenance of normal plant activities as well as improving stress management. Plants that exhibit a fine balance between ROS levels and its management apparently mitigate stresses better. There have been very many compendiums on signaling and management of ROS during several abiotic stresses. However, expansion of knowledge related to ROS induction and homeostasis during biotic stresses is pertinent. Hence, considering its importance, we provide insights in this review on how plants signal and manage ROS upon an oxidative burst during their interaction with pathogens and herbivores. Substantial degree of molecular changes and pivotal roles of ROS have been detected during phyto-pathogen/herbivore interactions, opening novel platforms to understand signaling/management of events under varied biotic stresses. It is interesting to know that, though plants react to biotic stresses through oxidative burst, receptors and elicitors involved in the signal transduction differ across stresses. The review provides explicit details about the specific signaling of ROS production in plants under pathogen and herbivore attack. Furthermore, we also provide an update about tackling the accumulated ROS under biotic stresses as another pivotal step. ROS signaling and homeostasis can be exploited as critical players and a fulcrum to tackle biotic stresses, thus paving the way for futuristic combinatorial stress management strategies. KEY POINTS: • The review is a comprehension of redox signaling and management in plants during herbivory and pathogen infection • Reactive oxygen species (ROS) is an important factor during normal plant activities as well as in their response to stresses. Diverse modes of ROS signaling and management have been observed during both biotic stresses independently • Exploration of plant biology in multi-stress resistant plants like the crop wild relatives could pave the way for combinatorial management of stress for a better tomorrow.
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45
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Corona-Gomez JA, Coss-Navarrete EL, Garcia-Lopez IJ, Klapproth C, Pérez-Patiño JA, Fernandez-Valverde SL. Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana. Sci Rep 2022; 12:14063. [PMID: 35982083 PMCID: PMC9388643 DOI: 10.1038/s41598-022-18254-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.
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Affiliation(s)
| | | | | | - Christopher Klapproth
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.,ScaDS.AI Leipzig (Center for Scalable Data Analytics and Artificial Intelligence), Humboldstrasse 25, 04105, Leipzig, Germany
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46
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Zhao Z, Zang S, Zou W, Pan YB, Yao W, You C, Que Y. Long Non-Coding RNAs: New Players in Plants. Int J Mol Sci 2022; 23:ijms23169301. [PMID: 36012566 PMCID: PMC9409372 DOI: 10.3390/ijms23169301] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China
| | - Cuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
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47
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Liu N, Xu Y, Li Q, Cao Y, Yang D, Liu S, Wang X, Mi Y, Liu Y, Ding C, Liu Y, Li Y, Yuan YW, Gao G, Chen J, Qian W, Zhang X. A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. Cell Host Microbe 2022; 30:1124-1138.e8. [DOI: 10.1016/j.chom.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/07/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022]
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48
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Tian J, Zhang G, Zhang F, Ma J, Wen C, Li H. Genome-Wide Identification of Powdery Mildew Responsive Long Non-Coding RNAs in Cucurbita pepo. Front Genet 2022; 13:933022. [PMID: 35846119 PMCID: PMC9283782 DOI: 10.3389/fgene.2022.933022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Cucurbita pepo L. is an essential economic vegetable crop worldwide, and its production is severely affected by powdery mildew (PM). However, our understanding of the molecular mechanism of PM resistance in C. pepo is very limited. Long non-coding RNAs (lncRNAs) play an important role in regulating plant responses to biotic stress. Here, we systematically identified 2,363 reliably expressed lncRNAs from the leaves of PM-susceptible (PS) and PM-resistant (PR) C. pepo. The C. pepo lncRNAs are shorter in length and expressed at a lower level than the protein-coding transcripts. Among the 2,363 lncRNAs, a total of 113 and 146 PM-responsive lncRNAs were identified in PS and PR, respectively. Six PM-responsive lncRNAs were predicted as potential precursors of microRNAs (miRNAs). In addition, 58 PM-responsive lncRNAs were predicted as targets of miRNAs and one PM-responsive lncRNA was predicted as an endogenous target mimic (eTM). Furthermore, a total of 5,200 potential cis target genes and 5,625 potential trans target genes were predicted for PM-responsive lncRNAs. Functional enrichment analysis showed that these potential target genes are involved in different biological processes, such as the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway. Taken together, this study provides a comprehensive view of C. pepo lncRNAs and explores the putative functions of PM-responsive lncRNAs, thus laying the foundation for further study of the regulatory mechanisms of lncRNAs responding to PM.
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Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jian Ma
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
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Zhang Y, Li H, Yang X, Chen J, Shi T. Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes. Comput Struct Biotechnol J 2022; 20:2848-2860. [PMID: 35765649 PMCID: PMC9193371 DOI: 10.1016/j.csbj.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022] Open
Abstract
Non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, emerge as crucial components for gene regulation. Nelumbo nucifera (lotus), a horticulturally important plant, differentiates into a temperate ecotype of enlarged rhizomes and a tropical ecotype of thin rhizomes. Nevertheless, whether and how ncRNAs can be rewired in expression and differentially methylated contributing to adaptive divergence of this storage organ in lotus ecotypes is unclear. Herein, we study the expression behaviors and DNA methylation patterns of ncRNAs in temperate and tropical lotus rhizomes. By whole transcriptome sequencing, we found both mRNAs and lncRNAs have divergent expression patterns between ecotypes, whereas miRNAs and circRNAs tended to be accession-specific or noisier in expression. The differentially expressed ncRNAs are involved in phenotypic differentiation of lotus rhizome between ecotypes, as the genes that interacted with them in the competing endogenous RNA network are enriched in functions including carbohydrate metabolism and plant hormone signaling, being critical to rhizome enlargement. Intriguingly, ncRNA-targeted genes are less prone to show positive selection or differential expression during ecotypic divergence due to constraints from ncRNA-mRNA interactions. The methylation levels of ncRNAs generally tend to be higher in temperate lotus than in tropical lotus, and differential methylation of lncRNAs also tends to have expression changes. Overall, our study of ncRNAs and their targets highlights the role of ncRNAs in rhizome growth variation between lotus ecotypes through expression rewiring and methylation modification.
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Zhu Y, Chen L, Hong X, Shi H, Li X. Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species. BMC Genomics 2022; 23:381. [PMID: 35590257 PMCID: PMC9118565 DOI: 10.1186/s12864-022-08602-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioinformatics pipelines, etc. For example, the sequencing of RNAs with poly(A) tails excluded a large portion of lncRNAs without poly(A), and use of regular RNA-sequencing technique did not distinguish transcripts’ direction for lncRNAs. The current study was designed to systematically discover and analyze lncRNAs across eight evolutionarily representative plant species, using strand-specific (directional) and whole transcriptome sequencing (RiboMinus) technique. Results A total of 39,945 lncRNAs (25,350 lincRNAs and 14,595 lncNATs) were identified, which showed molecular features of lncRNAs that are consistent across divergent plant species but different from those of mRNA. Further, transposable elements (TEs) were found to play key roles in the origination of lncRNA, as significantly large number of lncRNAs were found to contain TEs in gene body and promoter region, and transcription of many lncRNAs was driven by TE promoters. The lncRNA sequences were divergent even in closely related species, and most plant lncRNAs were genus/species-specific, amid rapid turnover in evolution. Evaluated with PhastCons scores, plant lncRNAs showed similar conservation level to that of intergenic sequences, suggesting that most lincRNAs were young and with short evolutionary age. INDUCED BY PHOSPHATE STARVATION (IPS) was found so far to be the only plant lncRNA group with conserved motifs, which may play important roles in the adaptation of terrestrial life during migration from aquatic to terrestrial. Most highly and specially expressed lncRNAs formed co-expression network with coding genes, and their functions were believed to be closely related to their co-expression genes. Conclusion The study revealed novel features and complexity of lncRNAs in plants through systematic analysis, providing important insights into the origination and evolution of plant lncRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08602-9.
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Affiliation(s)
- Yan Zhu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Longxian Chen
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangna Hong
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Henan University, Kaifeng, China
| | - Han Shi
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
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