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Locato V, Cimini S, De Gara L. ROS and redox balance as multifaceted players of cross-tolerance: epigenetic and retrograde control of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3373-3391. [PMID: 29722828 DOI: 10.1093/jxb/ery168] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/27/2018] [Indexed: 05/07/2023]
Abstract
Retrograde pathways occurring between chloroplasts, mitochondria, and the nucleus involve oxidative and antioxidative signals that, working in a synergistic or antagonistic mode, control the expression of specific patterns of genes following stress perception. Increasing evidence also underlines the relevance of mitochondrion-chloroplast-nucleus crosstalk in modulating the whole cellular redox metabolism by a controlled and integrated flux of information. Plants can maintain the acquired tolerance by a stress memory, also operating at the transgenerational level, via epigenetic and miRNA-based mechanisms controlling gene expression. Data discussed in this review strengthen the idea that ROS, redox signals, and shifts in cellular redox balance permeate the signalling network leading to cross-tolerance. The identification of specific ROS/antioxidative signatures leading a plant to different fates under stress is pivotal for identifying strategies to monitor and increase plant fitness in a changing environment. This review provides an update of the plant redox signalling network implicated in stress responses, in particular in cross-tolerance acquisition. The interplay between reactive oxygen species (ROS), ROS-derived signals, and antioxidative pathways is also discussed in terms of plant acclimation to stress in the short and long term.
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Affiliation(s)
- Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
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202
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Yuan P, Du L, Poovaiah BW. Ca 2+/Calmodulin-Dependent AtSR1/CAMTA3 Plays Critical Roles in Balancing Plant Growth and Immunity. Int J Mol Sci 2018; 19:ijms19061764. [PMID: 29899210 PMCID: PMC6032152 DOI: 10.3390/ijms19061764] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
During plant-pathogen interactions, plants have to relocate their resources including energy to defend invading organisms; as a result, plant growth and development are usually reduced. Arabidopsis signal responsive1 (AtSR1) has been documented as a negative regulator of plant immune responses and could serve as a positive regulator of plant growth and development. However, the mechanism by which AtSR1 balances plant growth and immunity is poorly understood. Here, we performed a global gene expression profiling using Affymetrix microarrays to study how AtSR1 regulates defense- and growth-related genes in plants with and without bacterial pathogen infection. Results revealed that AtSR1 negatively regulates most of the immune-related genes involved in molecular pattern-triggered immunity (PTI), effector-triggered immunity (ETI), and in salicylic acid (SA)- and jasmonate (JA)-mediated signaling pathways. AtSR1 may rigidly regulate several steps of the SA-mediated pathway, from the activation of SA synthesis to the perception of SA signal. Furthermore, AtSR1 may also regulate plant growth through its involvement in regulating auxin- and BRs-related pathways. Although microarray data revealed that expression levels of defense-related genes induced by pathogens are higher in wild-type (WT) plants than that in atsr1 mutant plants, WT plants are more susceptible to the infection of virulent pathogen as compared to atsr1 mutant plants. These observations indicate that the AtSR1 functions in suppressing the expression of genes induced by pathogen attack and contributes to the rapid establishment of resistance in WT background. Results of electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP)-PCR assays suggest that AtSR1 acts as transcription factor in balancing plant growth and immunity, through interaction with the “CGCG” containing CG-box in the promotors of its target genes.
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Affiliation(s)
- Peiguo Yuan
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA.
| | - Liqun Du
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA.
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - B W Poovaiah
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA.
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203
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Fard EM, Bakhshi B, Farsi M, Kakhki AM, Nikpay N, Ebrahimi MA, Mardi M, Salekdeh GH. MicroRNAs regulate the main events in rice drought stress response by manipulating the water supply to shoots. MOLECULAR BIOSYSTEMS 2018; 13:2289-2302. [PMID: 28872648 DOI: 10.1039/c7mb00298j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous regulatory RNAs that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses. miRNA profiles of rice (Oryza sativa L. cv. IR64.) leaves in a partial root zone drying (PRD) system were analysed using a high-throughput sequencing approach to identify miRNAs associated with drought signalling. The treatments performed in this study were as follows: well-watered ("wet" roots, WW), wherein both halves of the pot were watered daily; drought ("dry" roots, DD), wherein water was withheld from both halves of the pot; and well-watered/drought ("wet" and "dry" roots, WD), wherein one half of each pot was watered daily, the same as in WW, and water was withheld from the other part, the same as in DD. High-throughput sequencing enabled us to detect novel miRNAs and study the differential expression of known miRNAs. A total of 209 novel miRNAs were detected in this study. Differential miRNA profiling of the DD, WD and WW conditions showed differential expression of 159 miRNAs, among which 83, 44 and 32 miRNAs showed differential expression under both DD and WD conditions. The detection of putative targets of the differentially expressed miRNAs and investigation of their functions showed that most of these genes encode transcription factors involved in growth and development, leaf morphology, regulation of hormonal homeostasis, and stress response. The most important differences between the DD and WD conditions involved regulation of the levels of hormones such as auxin, cytokinin, abscisic acid, and jasmonic acid and also regulation of phosphor homeostasis. Overall, differentially expressed miRNAs under WD conditions were found to differ from those under DD conditions, with such differences playing a role in adaptation and inducing the normal condition. The mechanisms involved in regulating hormonal homeostasis and involved in energy production and consumption were found to be the most important regulatory pathways distinguishing the DD and WD conditions.
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Affiliation(s)
- Ehsan Mohseni Fard
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran.
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204
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Tyagi A, Nigam D, S. V. AM, Solanke AU, Singh NK, Sharma TR, Gaikwad K. Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1241-1257. [PMID: 29193664 PMCID: PMC5978871 DOI: 10.1111/pbi.12866] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 05/13/2023]
Abstract
Owing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC-936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP- D-glucose 4-epimerase) and validated as targets for three novel miRNAs, that is Ct-miR3130, Ct-miR3135 and Ct-miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan-producing species.
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Affiliation(s)
- Anshika Tyagi
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | - Deepti Nigam
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | | | | | | | - Tilak R. Sharma
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
- Present address:
National Agri‐Food Biotechnology InstituteMohaliIndia
| | - Kishor Gaikwad
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
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205
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Kaleem F, Shabir G, Aslam K, Rasul S, Manzoor H, Shah SM, Khan AR. An Overview of the Genetics of Plant Response to Salt Stress: Present Status and the Way Forward. Appl Biochem Biotechnol 2018; 186:306-334. [PMID: 29611134 DOI: 10.1007/s12010-018-2738-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/15/2018] [Indexed: 01/24/2023]
Abstract
Salinity is one of the major threats faced by the modern agriculture today. It causes multidimensional effects on plants. These effects depend upon the plant growth stage, intensity, and duration of the stress. All these lead to stunted growth and reduced yield, ultimately inducing economic loss to the farming community in particular and to the country in general. The soil conditions of agricultural land are deteriorating at an alarming rate. Plants assess the stress conditions, transmit the specific stress signals, and then initiate the response against that stress. A more complete understanding of plant response mechanisms and their practical incorporation in crop improvement is an essential step towards achieving the goal of sustainable agricultural development. Literature survey shows that investigations of plant stresses response mechanism are the focus area of research for plant scientists. Although these efforts lead to reveal different plant response mechanisms against salt stress, yet many questions still need to be answered to get a clear picture of plant strategy to cope with salt stress. Moreover, these studies have indicated the presence of a complicated network of different integrated pathways. In order to work in a progressive way, a review of current knowledge is critical. Therefore, this review aims to provide an overview of our understanding of plant response to salt stress and to indicate some important yet unexplored dynamics to improve our knowledge that could ultimately lead towards crop improvement.
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Affiliation(s)
- Fawad Kaleem
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Ghulam Shabir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Kashif Aslam
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sumaira Rasul
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hamid Manzoor
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Shahid Masood Shah
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Abdul Rehman Khan
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
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206
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Zhang L, Yao L, Zhang N, Yang J, Zhu X, Tang X, Calderón-Urrea A, Si H. Lateral Root Development in Potato Is Mediated by Stu-mi164 Regulation of NAC Transcription Factor. FRONTIERS IN PLANT SCIENCE 2018; 9:383. [PMID: 29651294 PMCID: PMC5884874 DOI: 10.3389/fpls.2018.00383] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/08/2018] [Indexed: 05/23/2023]
Abstract
The NAC designation is derived from petunia (Petunia hybrida) gene NO APICAL MERISTEM (NAM) and Arabidopsis genes ATAF1/ATAF2 and CUP-SHAPED COTYLEDON2 (CUC2), which belongs to the family of plant-specific transcription factors (TFs), and plays important role in plant development processes, such as response to biotic and abiotic stress, and hormone signaling. MicroRNAs (miRNAs) are a class of small, non-coding endogenous RNAs which play versatile and significant role in plant stress response and development via negatively affecting gene expression at a post-transcriptional level. Here, we showed that Stu-mi164 had a complementary sequence in the CDS sequence of potato NAC TFs, and that NAC expression exhibited significant differences under osmotic stress. We measured expression levels of the Stu-mi164 target gene StNAC262 between control and PEG-treated plants using real-time PCR, and the results demonstrated that they had inverse relationship. We suggested that Stu-miR164 might drive overexpression of NAC gene under osmotic stress in potato. To confirm the regulation of NAC TFs by Stu-mi164, we developed transgenic plants, using Agrobacterium tumefaciens-mediated transformation, of the potato cultivars "Gannongshu 2" and "Kexin 3" overexpressing the Stu-mi164 or the TF StNAC262. Real-time PCR analysis of transgenic potato plants under osmotic (PEG) stress, showed that potato plants overexpressing Stu-mi164 had reduced expression of StNAC262 and their osmotic resistance decreased. Furthermore, these plants had low number of lateral roots although the same length as the control. Our findings support the regulatory role of Stu-miRNAs in controlling plant response to osmotic stress via StNAC262.
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Affiliation(s)
- Li Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lei Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangwei Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xi Zhu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Alejandro Calderón-Urrea
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Department of Biology, California State University, Fresno, CA, United States
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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207
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Zeng X, Xu Y, Jiang J, Zhang F, Ma L, Wu D, Wang Y, Sun W. Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing. BMC PLANT BIOLOGY 2018; 18:52. [PMID: 29587648 PMCID: PMC5870505 DOI: 10.1186/s12870-018-1242-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses. RESULTS A total of 353 cold-responsive miRNAs, 84 putative novel and 269 conserved miRNAs, were identified from the leaves and roots of two winter turnip rape varieties 'Longyou 7' (cold-tolerant) and 'Tianyou 4' (cold-sensitive), which were stressed under - 4 °C for 8 h. Eight conserved (miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u) and two novel miRNAs (Bra-novel-miR3153-5p and Bra-novel-miR3172-5p) were differentially expressed in leaves of 'Longyou 7' under cold stress. Bra-novel-miR3936-5p was up-regulated in roots of 'Longyou 7' under cold stress. Four and five conserved miRNAs were differentially expressed in leaves and roots of 'Tianyou 4' after cold stress. Besides, we found two conserved miRNAs (miR319e and miR166m-2) were down-regulated in non-stressed roots of 'Longyou 7' compared with 'Tianyou 4'. After cold stress, we found two and eight miRNAs were differentially expressed in leaves and roots of 'Longyou 7' compared with 'Tianyou 4'. The differentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR166 and miR319 families. A total of 211 target genes for 15 known miRNAs and two novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Five differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR, and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR166e, miR319, and Bra-novel-miR3936-5p) may play important roles in plant response to cold stress. CONCLUSIONS Our work indicates that miRNA and putative target genes mediated metabolic processes and stress responses are significant to cold tolerance in B. rapa.
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Affiliation(s)
- Xiucun Zeng
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Yaozhao Xu
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Fenqin Zhang
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Li Ma
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Dewei Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Wancang Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
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209
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Ren W, Wang H, Bai J, Wu F, He Y. Association of microRNAs with Types of Leaf Curvature in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2018; 9:73. [PMID: 29467771 PMCID: PMC5808167 DOI: 10.3389/fpls.2018.00073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/15/2018] [Indexed: 05/29/2023]
Abstract
Many vegetable crops of Brassica rapa are characterized by their typical types of leaf curvature. Leaf curvature in the right direction and to the proper degree is important for the yield and quality of green vegetable products, when cultivated under stress conditions. Recent research has unveiled some of the roles of miRNAs in Brassica crops such as how they regulate the timing of leafy head initiation and shape of the leafy head. However, the molecular mechanism underlying the variability in leaf curvature in B. rapa remains unclear. We tested the hypothesis that the leaf curvature of B. rapa is affected by miRNA levels. On the basis of leaf phenotyping, 56 B. rapa accessions were classified into five leaf curvature types, some of which were comparable to miRNA mutants of Arabidopsis thaliana in phenotype. Higher levels of miR166 and miR319a expression were associated with downward curvature and wavy margins, respectively. Overexpression of the Brp-MIR166g-1 gene caused rosette leaves to change from flat to downward curving and folding leaves to change from upward curving to flat, leading to the decrease in the number of incurved leaves and size of the leafy head. Our results reveal that miRNAs affect the types of leaf curvature in B. rapa. These findings provide insight into the relationship between miRNAs and variation in leaf curvature.
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Affiliation(s)
- Wenqing Ren
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Han Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing, China
| | - Jinjuan Bai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Feijie Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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210
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Mondal TK, Panda AK, Rawal HC, Sharma TR. Discovery of microRNA-target modules of African rice (Oryza glaberrima) under salinity stress. Sci Rep 2018; 8:570. [PMID: 29330361 PMCID: PMC5766505 DOI: 10.1038/s41598-017-18206-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/22/2017] [Indexed: 11/09/2022] Open
Abstract
Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs. We also used smallRNAseq data of NCBI of O. glaberrima to discover additional 246 known miRNAs. Totally, 29 known and 32 novel miRNAs were differentially regulated under salinity stress. Gene ontology and KEGG analysis indicated several targets were involved in vital biological pathways of salinity stress tolerance. Expression of selected miRNAs as indicated by Illumina data were found to be coherent with real time-PCR analysis. However, target gene expression was inversely correlated with their corresponding miRNAs. Finally based upon present results as well as existing knowledge of literature, we proposed the miRNA-target modules that were induced by salinity stress. Therefore, the present findings provide valuable information about miRNA-target networks in salinity adaption of O. glaberrima.
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Affiliation(s)
- Tapan Kumar Mondal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India.
| | - Alok Kumar Panda
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India
| | - Hukam C Rawal
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India
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Tian X, Song L, Wang Y, Jin W, Tong F, Wu F. miR394 Acts as a Negative Regulator of Arabidopsis Resistance to B. cinerea Infection by Targeting LCR. FRONTIERS IN PLANT SCIENCE 2018; 9:903. [PMID: 30018624 PMCID: PMC6037856 DOI: 10.3389/fpls.2018.00903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/07/2018] [Indexed: 05/11/2023]
Abstract
Gray mold of tomato is caused by the pathogen Botrytis cinerea. MicroRNAs play a crucial role in the biotic and abiotic stress responses of plants and regulate their targets by gene silencing. miR394 is an ancient and conserved miRNA in plants, and it participates in the regulation of plant development and stress responses. In our previous study, miR394 was found to respond to B. cinerea infection in tomato, but the roles and regulatory mechanisms of miR394 in B. cinerea-infected tomato remain unclear. miR394 was down-regulated in tomato in response to B. cinerea infection, showing an expression pattern opposite to the previous finding that miR394 was up-regulated in tomato cv. Jinpeng 1 infected by B. cinerea. We obtained transgenic Arabidopsis overexpressing miR394, which resulted in low expression levels of its target LEAF CURLING RESPONSIVENESS (LCR). Leaf lesion size and trypan blue staining showed that miR394 overexpression led to increased sensitivity of transgenic Arabidopsis to B. cinerea compared to wild type. We also detected changes in the expression levels of stress-related miRNAs, including miR159, miR156, miR168, and miR172. In the transgenic plants, it indicated potential cross talk between these miRNAs and miR394, except for miR159. miR394 also enhanced the expression of ARGONAUTE 1 (AGO1), DSRNA-BINDING PROTEIN 4 (DRB4) and the RNA-binding protein gene DAWDLE (DDL), which are involved in the pathways of miRNA biosynthesis and regulation, suggesting that miR394 overexpression has a feedback effect on these genes. Our data indicate that overexpression of miR394 in Arabidopsis increased the susceptibility of plants to B. cinerea by affecting the expression of its target gene LCR along with a number of key genes involved in plant miRNA metabolism (AGO1). Thus, miR394 is a negative regulator of Arabidopsis resistance to B. cinerea infection by targeting LCR.
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Affiliation(s)
| | | | | | - Weibo Jin
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fudan Tong
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fangli Wu
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
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212
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Megha S, Basu U, Kav NNV. Regulation of low temperature stress in plants by microRNAs. PLANT, CELL & ENVIRONMENT 2018; 41:1-15. [PMID: 28346818 DOI: 10.1111/pce.12956] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 05/22/2023]
Abstract
Low temperature is one of the most common environmental stresses that seriously affect the growth and development of plants. However, plants have the plasticity in their defence mechanisms enabling them to tolerate and, sometimes, even survive adverse environmental conditions. MicroRNAs (miRNAs) are small non-coding RNAs, approximately 18-24 nucleotides in length, and are being increasingly recognized as regulators of gene expression at the post-transcriptional level and have the ability to influence a broad range of biological processes. There is growing evidence in the literature that reprogramming of gene expression mediated through miRNAs is a major defence mechanism in plants enabling them to respond to stresses. To date, numerous studies have established the importance of miRNA-based regulation of gene expression under low temperature stress. Individual miRNAs can modulate the expression of multiple mRNA targets, and, therefore, the manipulation of a single miRNA has the potential to affect multiple biological processes. Numerous functional studies have attempted to identify the miRNA-target interactions and have elaborated the role of several miRNAs in cold-stress regulation. This review summarizes the current understanding of miRNA-mediated modulation of the expression of key genes as well as genetic and regulatory pathways, involved in low temperature stress responses in plants.
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Affiliation(s)
- Swati Megha
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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Kumar V, Khare T, Shriram V, Wani SH. Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. PLANT CELL REPORTS 2018; 37:61-75. [PMID: 28951953 DOI: 10.1007/s00299-017-2210-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/12/2017] [Indexed: 05/07/2023]
Abstract
Saline environment cues distort the plant growth, development and crop yield. Epigenetics has emerged as one of the prime themes in plant functional genomics for molecular-stress-physiology research, as copious studies have provided new visions into the epigenetic control of stress adaptations. The epigenetic control is associated with the regulation of the expression of stress-related genes which also comprises many steady alterations inherited in next cellular generation as stress memory. These epigenetic amendments also implicate induction of small RNA (sRNA)-mediated fine-tuning of transcriptional and post-transcriptional regulations of gene expression. These tiny (19-24 nt) RNA species, particularly microRNAs (miRNAs) besides endogenous small interfering RNA (siRNA) have emerged as important responsive entities for epigenetic modulation of salt-stress effects on plants. There is a recent upsurge in development of tools and databases useful for prediction, identification and validation of small RNAs (sRNAs) and their target messenger RNAs (mRNAs). Therefore, these small but key regulatory molecules have received a wide attention in post-genomic era as potential targets for engineering stress tolerance in major glycophytic crops, though it is yet to be explored optimally. This review aims to provide critical updates on plant sRNAs as key epigenetic regulators of plant salt-stress responses, their target prediction and validation, computational tools and databases available for plant small RNAs, besides discussing their roles in salt-stress regulatory networks and adaptive mechanisms in plants, with special emphasis on their exploration for engineering salinity tolerance in plants.
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Affiliation(s)
- Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016, India.
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016, India
| | - Varsha Shriram
- Department of Botany, Prof. Ramkrishna More College (Savitribai Phule Pune University), Akurdi, Pune, 411044, India
| | - Shabir H Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192101, India.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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Baxter HL, Mazarei M, Dumitrache A, Natzke JM, Rodriguez M, Gou J, Fu C, Sykes RW, Turner GB, Davis MF, Brown SD, Davison BH, Wang Z, Stewart CN. Transgenic miR156 switchgrass in the field: growth, recalcitrance and rust susceptibility. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:39-49. [PMID: 28436149 PMCID: PMC5785337 DOI: 10.1111/pbi.12747] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 03/16/2017] [Accepted: 04/10/2017] [Indexed: 05/02/2023]
Abstract
Sustainable utilization of lignocellulosic perennial grass feedstocks will be enabled by high biomass production and optimized cell wall chemistry for efficient conversion into biofuels. MicroRNAs are regulatory elements that modulate the expression of genes involved in various biological functions in plants, including growth and development. In greenhouse studies, overexpressing a microRNA (miR156) gene in switchgrass had dramatic effects on plant architecture and flowering, which appeared to be driven by transgene expression levels. High expressing lines were extremely dwarfed, whereas low and moderate-expressing lines had higher biomass yields, improved sugar release and delayed flowering. Four lines with moderate or low miR156 overexpression from the prior greenhouse study were selected for a field experiment to assess the relationship between miR156 expression and biomass production over three years. We also analysed important bioenergy feedstock traits such as flowering, disease resistance, cell wall chemistry and biofuel production. Phenotypes of the transgenic lines were inconsistent between the greenhouse and the field as well as among different field growing seasons. One low expressing transgenic line consistently produced more biomass (25%-56%) than the control across all three seasons, which translated to the production of 30% more biofuel per plant during the final season. The other three transgenic lines produced less biomass than the control by the final season, and the two lines with moderate expression levels also exhibited altered disease susceptibilities. Results of this study emphasize the importance of performing multiyear field studies for plants with altered regulatory transgenes that target plant growth and development.
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Affiliation(s)
- Holly L. Baxter
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
| | - Mitra Mazarei
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
| | - Alexandru Dumitrache
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jace M. Natzke
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Miguel Rodriguez
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jiqing Gou
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Samuel Roberts Noble FoundationArdmoreOKUSA
| | - Chunxiang Fu
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Samuel Roberts Noble FoundationArdmoreOKUSA
| | - Robert W. Sykes
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Geoffrey B. Turner
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Mark F. Davis
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Steven D. Brown
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Brian H. Davison
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Zeng‐Yu Wang
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Samuel Roberts Noble FoundationArdmoreOKUSA
| | - C. Neal Stewart
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
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215
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Augstein F, Carlsbecker A. Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:1410. [PMID: 30319672 PMCID: PMC6167918 DOI: 10.3389/fpls.2018.01410] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.
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216
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Yang X, Liu F, Zhang Y, Wang L, Cheng YF. Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum. BMC Genomics 2017; 18:1000. [PMID: 29287583 PMCID: PMC5747154 DOI: 10.1186/s12864-017-4341-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance. Results Here, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association. Conclusions In summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12864-017-4341-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Fei Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Lu Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu-Fu Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
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Saroha M, Singroha G, Sharma M, Mehta G, Gupta OP, Sharma P. sRNA and epigenetic mediated abiotic stress tolerance in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0330-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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222
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Leaf wax trait in crops for drought and biotic stress tolerance: regulators of epicuticular wax synthesis and role of small RNAs. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0333-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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223
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Sahito ZA, Wang L, Sun Z, Yan Q, Zhang X, Jiang Q, Ullah I, Tong Y, Li X. The miR172c-NNC1 module modulates root plastic development in response to salt in soybean. BMC PLANT BIOLOGY 2017; 17:229. [PMID: 29191158 PMCID: PMC5709930 DOI: 10.1186/s12870-017-1161-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 11/08/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant roots are highly plastic to high salinity. However, the molecular mechanism by which root developmental plasticity is regulated remains largely unknown. Previously we reported that miR172c-NNC1 module plays a key role in soybean-rhizobial symbiosis. The fact that the miR172c promoter contains several stress-related cis elements indicates that miR172c may have a role in root response to abiotic stress. RESULTS Here we showed that miR172c is greatly induced by salt stress in soybean. Overexpression of miR172c and knockdown of miR172c activity resulted in substantially increased and reduced root sensitivity to salt stress, respectively. Furthermore, we show that the target gene NNC1 (Nodule Number Control 1) of miR172c was downregulated by salt stress. The transgenic roots overexpressing or knocking down NNC1 expression also exhibited the altered root sensitivity to salt stress. CONCLUSION The study reveals the crucial role of miR172c-NNC1 module in root stress tolerance to salt stress in soybean.
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Affiliation(s)
- Zulfiqar Ali Sahito
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Zhengxi Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qiqi Yan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xingke Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Qiong Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Ihteram Ullah
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Dong Z, Zhang J, Zhu Q, Zhao L, Sui S, Li Z, Zhang Y, Wang H, Tian D, Zhao Y. Identification of microRNAs involved in drought stress responses in early-maturing cotton by high-throughput sequencing. Genes Genomics 2017; 40:305-314. [PMID: 29892798 DOI: 10.1007/s13258-017-0637-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 01/19/2023]
Abstract
Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants. However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencing of small RNAs to identify known and novel miRNAs involved in the regulation of drought stress and understand the expression profile of miRNAs in early-maturing cotton. Three cotton small RNA libraries: non-stressed Shizao1 (early-maturing cotton variety) library (NSS), drought-stressed Shizao1 library (DSS) and non-stressed Jimian958 (medium-maturing cotton variety) library (NSJ) were constructed for deep sequencing. As a result, we identified a total of 64 known and 67 novel miRNAs in the 3 libraries and 88 of them were dramatically differentially expressed (greater than twofold) during drought stress. In addition, we found the expression of 41 miRNAs increased or reduced more than twofold in early-maturing cotton variety compared with that in medium-maturing cotton variety. Our results significantly increased the number of miRNAs in cotton and revealed for the first time the expression profile of miRNAs for early-maturing cotton.
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Affiliation(s)
- Zhanghui Dong
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 598 Heping Road, Shijiazhuang, 050051, Hebei, China
| | - Qingzhu Zhu
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Lifen Zhao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Shuxiang Sui
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Zengshu Li
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Yanli Zhang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Hu Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Dongliang Tian
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Yankun Zhao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
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Guo Y, Zhao S, Zhu C, Chang X, Yue C, Wang Z, Lin Y, Lai Z. Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress. BMC PLANT BIOLOGY 2017; 17:211. [PMID: 29157225 PMCID: PMC5696764 DOI: 10.1186/s12870-017-1172-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/10/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Drought stress is one of the major natural challenges in the main tea-producing regions of China. The tea plant (Camellia sinensis) is a traditional beverage plant whose growth status directly affects tea quality. Recent studies have revealed that microRNAs (miRNAs) play key functions in plant growth and development. Although some miRNAs have been identified in C. sinensis, little is known about their roles in the drought stress response of tea plants. RESULTS Physiological characterization of Camellia sinensis 'Tieguanyin' under drought stress showed that the malondialdehyde concentration and electrical conductivity of leaves of drought-stressed plants increased when the chlorophyll concentration decreased under severe drought stress. We sequenced four small-RNA (sRNA) libraries constructed from leaves of plants subjected to four different treatments, normal water supply (CK); mild drought stress (T1); moderate drought stress (T2) and severe drought stress (T3). A total of 299 known mature miRNA sequences and 46 novel miRNAs were identified. Gene Ontology enrichment analysis revealed that most of the differentially expressed-miRNA target genes were related to regulation of transcription. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the most highly enriched pathways under drought stress were D-alanine metabolism, sulfur metabolism, and mineral absorption pathways. Real-time quantitative PCR (qPCR) was used to validate the expression patterns of 21 miRNAs (2 up-regulated and 19 down-regulated under drought stress). The observed co-regulation of the miR166 family and their targets ATHB-14-like and ATHB-15-like indicate the presence of negative feedback regulation in miRNA pathways. CONCLUSIONS Analyses of drought-responsive miRNAs in tea plants showed that most of differentially expressed-miRNA target genes were related to regulation of transcription. The results of study revealed that the expressions of phase-specific miRNAs vary with morphological, physiological, and biochemical changes. These findings will be useful for research on drought resistance and provide insights into the mechanisms of drought adaptation and resistance in C. sinensis.
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Affiliation(s)
- Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shanshan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaojun Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chuan Yue
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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İlhan E, Büyük İ, İnal B. Transcriptome - Scale characterization of salt responsive bean TCP transcription factors. Gene 2017; 642:64-73. [PMID: 29129811 DOI: 10.1016/j.gene.2017.11.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/22/2017] [Accepted: 11/07/2017] [Indexed: 11/26/2022]
Abstract
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) proteins are important regulators of growth and developmental processes including branching, floral organ morphogenesis and leaf growth as well as stress response. This study identified 27 TCP genes of Phaseolus vulgaris (common bean), which were divided into three clusters based on phylogenetic relationship. In addition, this study showed that some of TCP genes such as Pvul-TCP-4 and Pvul-TCP-15 located on chromosomes 3 and 7, Pvul-TCP-7 and Pvul-TCP-20 located on chromosome 7 and 9, were segmentally duplicated. On the other hand, a total of 20 Pvul-TCP genes have predicted to be targeted by microRNAs (miRNA). Most of the miRNA-target genes were Pvul-TCP-1, -11, -13 and -27, which were targeted by 13, 17, 22 and 13 plant miRNAs, respectively. miR319 was one of the highly represented regulatory miRNAs to target TCP transcripts. Promoter region analysis of TCP genes resulted that the GT-1 motif, which was related to salt stress, was found in 14 different Pvul-TCP genes. Expression profiling of 10 Pvul-TCP genes based on RNA-sequencing data further confirmed with quantitative real-time RT-PCR measurements identified that Pvul-TCP genes under salt stress are expressed in a cultivar- and tissue-specific manner.
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Affiliation(s)
- Emre İlhan
- Depart. of Molecular Bio. and Genetics, Erzurum Technical University, Erzurum, Turkey.
| | - İlker Büyük
- Depart. of Biology, Ankara University, Ankara, Turkey; Depart. of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Behcet İnal
- Depart. of Agricultural Biotechnology, Siirt University, Siirt, Turkey
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Liu Q, Yan S, Yang T, Zhang S, Chen YQ, Liu B. Small RNAs in regulating temperature stress response in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:774-791. [PMID: 28731217 DOI: 10.1111/jipb.12571] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 05/21/2023]
Abstract
Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered microRNAs (miRNAs) and endogenous small-interfering RNAs (siRN As) have also been demonstrated as important players in plant temperature stress response. Using high-throughput sequencing, many small RNAs, especially miRNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of miRNAs and siRNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.
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Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Li L, Yi H, Xue M, Yi M. miR398 and miR395 are involved in response to SO 2 stress in Arabidopsis thaliana. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:1181-1187. [PMID: 28819808 DOI: 10.1007/s10646-017-1843-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/05/2017] [Indexed: 05/21/2023]
Abstract
Sulfur dioxide (SO2) is a common air pollutant that has adverse effects on plants. MicroRNAs (miRNAs) are small noncoding RNA that play critical roles in plant development and stress response. In this study, we found that two miRNAs, miR398 and miR395, were differentially expressed in Arabidopsis shoots under SO2 stress. The expression of miR398 was down-regulated, and the transcript levels of its target genes, Cu/Zn superoxide dismutases (CSD1 and CSD2), were increased during SO2 exposure. The activity of superoxide dismutase (SOD), one of the major antioxidant enzymes, was enhanced with the increase in the CSD transcript level, suggesting an important role of miR398 in response to SO2-induced oxidative stress. Meanwhile, the expression of miR395 was increased, and the transcript levels of its target genes, ATP sulfurylases (APS3 and APS4) and a low-affinity sulfate transporter (SULTR2;1), were decreased in Arabidopsis shoots, showing that miR395 played important roles in the regulation of sulfate assimilation and translocation during SO2 exposure. The content of glutathione (GSH), an important sulfur-containing antioxidant, was enhanced with the changes in sulfur metabolism in Arabidopsis shoots under SO2 stress. These results showed that both miR398 and miR395 were involved in protecting plants from oxidative damage during SO2 exposure. Many stress-responsive cis-elements were found in the promoter regions of MIR398 and MIR395, suggesting that these miRNAs might respond to various environmental conditions, including SO2 stress. Overall, our study provides an insight into the regulatory roles of miRNAs in response to SO2 stress in plants, and highlights the molecular mechanisms of plant adaptation to environmental stress.
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Affiliation(s)
- Lihong Li
- School of Life Science, Shanxi University, Taiyuan, 030006, China
- Fisheries Research Institute of Shanxi Province, Taiyuan, 030006, China
| | - Huilan Yi
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| | - Meizhao Xue
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Min Yi
- Department of Statistics, University of Missouri-Columbia, Columbia, 65211, USA
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229
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Yang Y, Zhang X, Su Y, Zou J, Wang Z, Xu L, Que Y. miRNA alteration is an important mechanism in sugarcane response to low-temperature environment. BMC Genomics 2017; 18:833. [PMID: 29084515 PMCID: PMC5661916 DOI: 10.1186/s12864-017-4231-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/22/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cold is a major abiotic stress limiting the production of tropical and subtropical crops in new production areas. Sugarcane (Saccharum spp.) originates from the tropics but is cultivated primarily in the sub-tropics where it frequently encounters cold stress. Besides regulating plant growth, miRNAs play an important role in environmental adaption. RESULTS In this study, a total of 412 sugarcane miRNAs, including 261 known and 151 novel miRNAs, were obtained from 4 small RNA libraries through the Illumina sequencing method. Among them, 62 exhibited significant differential expression under cold stress, with 34 being upregulated and 28 being downregulated. The expression of 13 miRNAs and 12 corresponding targets was validated by RT-qPCR, with the majority being consistent with the sequencing data. GO and KEGG analysis indicated that these miRNAs were involved in stress-related biological pathways. To further investigate the involvement of these miRNAs in tolerance to abiotic stresses, sugarcane miR156 was selected for functional analysis. RT-qPCR revealed that miR156 levels increased in sugarcane during cold, salt and drought stress treatments. Nicotiana benthamiana plants transiently overexpressing miR156 exhibited better growth status, lower ROS levels, higher anthocyanin contents as well as the induction of some cold-responsive genes, suggesting its positive role in the plant cold stress response. CONCLUSIONS This study provides a global view of the association of miRNA expression with the sugarcane response to cold stress. The findings have enriched the present miRNA resource and have made an attempt to verify the involvement of miR156 in plant response to cold stress.
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Affiliation(s)
- Yuting Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jiake Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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230
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Jeyaraj A, Liu S, Zhang X, Zhang R, Shangguan M, Wei C. Genome-wide identification of microRNAs responsive to Ectropis oblique feeding in tea plant (Camellia sinensis L.). Sci Rep 2017; 7:13634. [PMID: 29051614 PMCID: PMC5648755 DOI: 10.1038/s41598-017-13692-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/29/2017] [Indexed: 12/02/2022] Open
Abstract
The tea plant (Camellia sinensis L.) is vulnerable to the geometrid Ectropis oblique; although microRNAs (miRNAs) are important for plant growth, development and stress response, the function of miRNAs in the response of C. sinensis to stress from E. oblique is unclear. To identify E. oblique stress-responsive miRNAs and their target genes in tea plant, three small RNA libraries were constructed from leaves subjected to mechanical wounding (MW), geometrid attack (GA) and from healthy control (CK) leaves. Using high-throughput sequencing, 130 known miRNAs and 512 novel miRNAs were identified; of these, differential expression under GA stress was observed for 36 known and 139 novel miRNAs. Furthermore, 169 GA-responsive and 173 MW-responsive miRNAs were detected by miRNA microarray. The expression patterns of six GA-responsive miRNAs were validated by qRT-PCR. Several target genes for these miRNAs encode various transcription factors, including ethylene-responsive transcription factors and squamosa promoter-binding-like proteins, which suggests that these miRNAs may regulate stress-responsive transcriptional processes in tea plant. The present findings provide novel insights into miRNA-mediated regulatory mechanisms underlying the response to GA stress, and also offer valuable information for development of pest resistance using RNA interference-based strategies in tea plants.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Ran Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Mingzhu Shangguan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China.
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231
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Smith O, Palmer SA, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG. Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment. Mol Biol Evol 2017; 34:2555-2562. [PMID: 28655202 PMCID: PMC5850308 DOI: 10.1093/molbev/msx175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The recovery of ancient RNA from archeological material could enable the direct study of microevolutionary processes. Small RNAs are a rich source of information because their small size is compatible with biomolecular preservation, and their roles in gene regulation make them likely foci of evolutionary change. We present here the small RNA fraction from a sample of archeological barley generated using high-throughput sequencing that has previously been associated with localized adaptation to drought. Its microRNA profile is broadly similar to 19 globally distributed modern barley samples with the exception of three microRNAs (miRNA159, miRNA319, and miR396), all of which are known to have variable expression under stress conditions. We also found retrotransposon activity to be significantly reduced in the archeological barley compared with the controls, where one would expect the opposite under stress conditions. We suggest that the archeological barley's conflicting stress signals could be the result of long-term adaptation to its local environment.
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Affiliation(s)
- Oliver Smith
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Sarah A. Palmer
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Alan J. Clapham
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Pamela Rose
- The Austrian Archaeological Institute, Cairo Branch, Zamalek, Cairo, Egypt
| | - Yuan Liu
- BGI-Europe-UK, London, United Kingdom
| | | | - Robin G. Allaby
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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232
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Shen LM, Song ZW, Hua Y, Chao X, Liu JB. miR-181d-5p promotes neurite outgrowth in PC12 Cells via PI3K/Akt pathway. CNS Neurosci Ther 2017; 23:894-906. [PMID: 28961370 DOI: 10.1111/cns.12761] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/04/2017] [Accepted: 09/07/2017] [Indexed: 02/01/2023] Open
Abstract
INTRODUCTION miRNAs dysregulate in spinal cord injury (SCI) and have been demonstrated to play a crucial role in neurite outgrowth. However, the underlying mechanism remains elusive. In this study, we constructed a mouse model of SCI, extracted RNA from injured spinal cord tissue for the use of microarray assay. miR-181d-5p which is one of the most significantly expressed miRNAs in miRNA-mRNA network, abundantly expressed in center system and highly conserved across different spices, was chosen for our further study. AIMS To demonstrate whether miR-181d-5p can promote neurite outgrowth in PC12 cells via PI3K/Akt signaling pathway, we performed function analysis of miR-181d-5p with LV-miR-181d-5p and LV-sh-GFP to infect PC12 cells. RESULTS Through microarray assay analysis, we totally found 262 significantly expressed miRNAs and 2973 target genes in SCI and observed that their expression dynamically changed postinjury. Here, we provided enough evidences that the overexpression of miR181d-5p significantly decreased the expression of PTEN, upregulated p-Akt expression, increased neurite outgrowth-related proteins (GAP-43 and NF-200) and synaptic vesicle-related proteins (Synapsin and PSD95), and then promoted neurite outgrowth in PC12 cells. Furthermore, we confirmed that miR-181d-5p could directly target to the 3'-UTR of PTEN mRNA through dual-luciferase report assay. CONCLUSIONS Our study supports that aberrant expression of miRNAs is involved in the pathogenesis of SCI, miR-181d-5p plays an important role in neurite growth in PC12 cells via PI3K/Akt signaling pathway and may be a candidate target for the treatment of SCI in the future.
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Affiliation(s)
- Li-Ming Shen
- Department of Orthopedics, the Third Affiliated Hospital, Soochow University, Changzhou, Jiangsu, China.,Department of Orthopedic Surgery, Liyang People's Hospital, Liyang City, Jiang Su, China
| | - Zhi-Wen Song
- Department of Orthopedics, the Third Affiliated Hospital, Soochow University, Changzhou, Jiangsu, China
| | - Yin Hua
- Department of Orthopedics, the Third Affiliated Hospital, Soochow University, Changzhou, Jiangsu, China
| | - Xu Chao
- Department of Orthopedics, the Third Affiliated Hospital, Soochow University, Changzhou, Jiangsu, China
| | - Jin-Bo Liu
- Department of Orthopedics, the Third Affiliated Hospital, Soochow University, Changzhou, Jiangsu, China
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233
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Liu M, Yu H, Zhao G, Huang Q, Lu Y, Ouyang B. Identification of drought-responsive microRNAs in tomato using high-throughput sequencing. Funct Integr Genomics 2017; 18:67-78. [PMID: 28956210 DOI: 10.1007/s10142-017-0575-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/12/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022]
Abstract
Drought is a major abiotic stress affecting crop productivity and quality. As a class of noncoding RNA, microRNA (miRNA) plays important roles in plant growth, development, and stress response. However, their response and roles in tomato drought stress is largely unknown. Here, by using high-throughput sequencing, we compared the miRNA profiles before and after drought treatment in two tomato genotypes: M82, a drought-sensitive cultivated tomato (Solanum lycopersicum), and IL2-5, a drought-tolerant introgression line derived from M82 and the tomato wild species S. pennellii (LA0716). A total of 108 conserved and 208 novel miRNAs were identified, among them, 32 and 68 were significantly changed in expression after stress. Further, 1936 putative target genes were predicted for those differentially-expressed miRNAs. Gene ontology and pathway analysis showed that many of the target genes were involved in stress resistance, such as genes in GO terms including response to stress, defense response, response to stimulus, phosphorylation, and signal transduction. Our results suggested that miRNAs play an essential role in the drought response of tomato. This work will help to further characterize specific miRNAs functioning in drought tolerance.
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Affiliation(s)
- Minmin Liu
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gangjun Zhao
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiufeng Huang
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China.
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234
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Yang C, Gao Q, Liu C, Wang L, Zhou Z, Gong C, Zhang A, Zhang H, Qiu L, Song L. The transcriptional response of the Pacific oyster Crassostrea gigas against acute heat stress. FISH & SHELLFISH IMMUNOLOGY 2017; 68:132-143. [PMID: 28698121 DOI: 10.1016/j.fsi.2017.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/05/2017] [Accepted: 07/08/2017] [Indexed: 06/07/2023]
Abstract
The Pacific oyster, Crassostrea gigas, has evolved sophisticated mechanisms to adapt the changing ambient conditions, and protect themselves from stress-induced injuries. In the present study, the expression profiles of mRNA transcripts in the haemocytes of oysters under heat stress were examined to reveal the possible mechanism of heat stress response. There were 23,315, 23,904, 23,123 and 23,672 transcripts identified in the haemocytes of oysters cultured at 25 °C for 0, 6, 12, and 24 h (designed as B, H6, H12, H24), respectively. And 22,330 differentially expressed transcripts (DTs) were yielded in the pairwise comparisons between the above four samples, which corresponded to 8074 genes. There were 9, 12 and 22 Gene Ontology (GO) terms identified in the DT pairwise comparison groups of H6_B, H12_H6 and H24_H12, respectively, and the richest GO terms in biological process category were cellular catabolic process, translational initiation and apoptotic process, respectively. There were 108, 102 and 102 KEGG pathways successfully retrieved from DTs comparison groups DTH6_B, DTH12_H6 and DTH24_H12, respectively, among which 93 pathways were shared by all three comparison groups, and most of them were related to metabolism of protein, carbohydrate and fat. The expression patterns of 12 representative heat stress response-relevant genes detected by quantitative real-time PCR (qRT-PCR) were similar to those obtained from transcriptome analysis. By flow cytometric analysis, the apoptosis rate of haemocytes increased significantly after oysters were treated at 25 °C for 24 h and recovered at 4 °C for 12 h (p < 0.05) and 36 h (p < 0.01), and it also increased significantly when the heat treatment lasted to 60 h (p < 0.01). The present results indicated that, when oysters encountered short term heat stress, the expression of genes related to energy metabolism, as well as unfolded protein response (UPR) and anti-apoptotic system, were firstly regulated to maintain basic life activities, and then a large number of genes involved in stabilizing protein conformation and facilitating further protein refolding were activated to repair the stress injury. However, the stress injury gradually became irreparable with the stress persisting, and apoptosis was activated when the heat treatment prolonged to 24 h. The information was useful to better understand the molecular mechanism of heat stress response and develop strategies for the improvement of oyster survival rate during summer high-temperature period.
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Affiliation(s)
- Chuanyan Yang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Qiang Gao
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zhi Zhou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Changhao Gong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Anguo Zhang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Huan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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Banerjee S, Sirohi A, Ansari AA, Gill SS. Role of small RNAs in abiotic stress responses in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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236
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Fast I, Hewel C, Wester L, Schumacher J, Gebert D, Zischler H, Berger C, Rosenkranz D. Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures. RNA (NEW YORK, N.Y.) 2017; 23:1352-1364. [PMID: 28630141 PMCID: PMC5558905 DOI: 10.1261/rna.061119.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/06/2017] [Indexed: 06/14/2023]
Abstract
The majority of Drosophila genes are expressed in a temperature-dependent manner, but the way in which small RNAs may contribute to this effect is completely unknown as we currently lack an idea of how small RNA transcriptomes change as a function of temperature. Applying high-throughput sequencing techniques complemented by quantitative real-time PCR experiments, we demonstrate that altered ambient temperature induces drastic but reversible changes in sequence composition and total abundance of both miRNA and piRNA populations. Further, mRNA sequencing reveals that the expression of miRNAs and their predicted target transcripts correlates inversely, suggesting that temperature-responsive miRNAs drive adaptation to different ambient temperatures on the transcriptome level. Finally, we demonstrate that shifts in temperature affect both primary and secondary piRNA pools, and the observed aberrations are consistent with altered expression levels of the involved Piwi-pathway factors. We further reason that enhanced ping-pong processing at 29°C is driven by dissolved RNA secondary structures at higher temperatures, uncovering target sites that are not accessible at low temperatures. Together, our results show that small RNAs are an important part of epigenetic regulatory mechanisms that ensure homeostasis and adaptation under fluctuating environmental conditions.
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Affiliation(s)
- Isabel Fast
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Laura Wester
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Julia Schumacher
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Hans Zischler
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Christian Berger
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
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237
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Yu X, Hou Y, Chen W, Wang S, Wang P, Qu S. Malus hupehensis miR168 Targets to ARGONAUTE1 and Contributes to the Resistance against Botryosphaeria dothidea Infection by Altering Defense Responses. PLANT & CELL PHYSIOLOGY 2017; 58:1541-1557. [PMID: 28633325 DOI: 10.1093/pcp/pcx080] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 05/29/2017] [Indexed: 05/23/2023]
Abstract
MicroRNA (miRNA)-mediated post-transcriptional regulation plays a fundamental role in various plant physiological processes, including responses to pathogens. MicroRNA168 has been implicated as an essential factor of miRNA pathways by targeting ARGONAUTE1 (AGO1), the core component of the RNA-induced silencing complex (RISC). A fluctuation in AGO1 expression influences various plant-pathogen interactions, and the homeostasis of AGO1 and miR168 accumulation is maintained by a complicated feedback regulatory loop. In this study, the connection between miR168 and the resistance of Malus hupehensis to Botryosphaeria dothidea is revealed. The induction of both the mature miR168 and its precursor in plants subjected to B. dothidea infection indicate the transcriptional activation of MIR168a. MIR168a promoter analysis demonstrates that the promoter can be activated by B. dothidea and salicylic acid (SA). However, the direct target of miR168, M. hupehensis ARGONAUTE1 (MhAGO1), is shown to be induced under the infection. Expression and transcription activity analysis demonstrate the transcriptional activation and the post-transcriptional suppression of MhAGO1 in response to B. dothidea infection. By inhibiting reactive oxygen species (ROS) production and enhancing SA-mediated defense responses, miR168a delays the symptom development of leaves inoculated with B. dothidea and impedes the pathogen growth, while MhAGO1 is found to have the opposite effects. Collectively, these findings suggest that the expression of miR168 and MhAGO1 in M. hupehensis in response to B. dothidea infection is regulated by a complicated mechanism. Targeting to MhAGO1, a negative regulator, miR168 plays a positive role in the resistance by alterations in diverse defense responses.
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Affiliation(s)
- Xinyi Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China
| | - Yingjun Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Weiping Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Sanhong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Peihong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shenchun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
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238
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González-Villagra J, Kurepin LV, Reyes-Díaz MM. Evaluating the involvement and interaction of abscisic acid and miRNA156 in the induction of anthocyanin biosynthesis in drought-stressed plants. PLANTA 2017; 246:299-312. [PMID: 28534253 DOI: 10.1007/s00425-017-2711-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/13/2017] [Indexed: 05/11/2023]
Abstract
ABA is involved in anthocyanin synthesis through the regulation of microRNA156, augmenting the level of expression of anthocyanin synthesis-related genes and, therefore, increasing anthocyanin level. Drought stress is the main cause of agricultural crop loss in the world. However, plants have developed mechanisms that allow them to tolerate drought stress conditions. At cellular level, drought stress induces changes in metabolite accumulation, including increases in anthocyanin levels due to upregulation of the anthocyanin biosynthetic pathway. Recent studies suggest that the higher anthocyanin content observed under drought stress conditions could be a consequence of a rise in the abscisic acid (ABA) concentration. This plant hormone crosses the plasma membrane by specific transporters, and it is recognized at the cytosolic level by receptors known as pyrabactin resistance (PYR)/regulatory component of ABA receptors (PYR/RCARs) that regulate downstream components. In this review, we discuss the hypothesis regarding the involvement of ABA in the regulation of microRNA156 (miRNA156), which is upregulated as part of dehydration stress responsiveness in different species. The miRNA156 upregulation produces a greater level of anthocyanin gene expression, forming the multienzyme complex that will synthesize an increased level of anthocyanins at the cytosolic face of the rough endoplasmic reticulum (RER). After synthesis, anthocyanins are transported from the RER to the vacuole by two possible models of transport: (1) membrane vesicle-mediated transport, or (2) membrane transporter-mediated transport. Thus, the aim was to analyze the recent findings on synthesis, transport and the possible mechanism by which ABA could increase anthocyanin synthesis under drought stress conditions potentially throughout microRNA156 (miRNA156).
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Affiliation(s)
- Jorge González-Villagra
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Leonid V Kurepin
- Department of Biology and The Biotron Centre for Experimental Climate Change Research, Western University, London, ON, N6A 5B7, Canada
| | - Marjorie M Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
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239
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Cui X, Yan Q, Gan S, Xue D, Dou D, Guo N, Xing H. Overexpression of gma-miR1510a/b suppresses the expression of a NB-LRR domain gene and reduces resistance to Phytophthora sojae. Gene 2017; 621:32-39. [PMID: 28411083 DOI: 10.1016/j.gene.2017.04.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 04/02/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are universal regulators that repress target gene expression in eukaryotes and play essential roles in plant immune responses. miRNAs were recently found to be involved in soybean and Phytophthora sojae interactions. Here, we screened miR1510, which was repressed in soybean during infection with P. sojae, indicating that it might be involved in soybean response to pathogens. To further uncover the roles of miRNAs in soybean, gma-miR1510a/b was overexpressed in the hairy roots of soybean using an Arabidopsis miR319a precursor as the backbone. The gma-miR1510a/b-overexpressing hairy roots showed enhanced susceptibility to P. sojae, and the results showed that miR1510 guides the cleavage of the Glyma.16G135500 gene, which encodes a classic type of plant disease resistance-associated gene that harbors the Toll-interleukin-like receptor (TIR) domain and nucleotide-binding site-leucine-rich repeat (NB-LRR) domain. Noticeably, several biotic stresses and hormone-responsive cis-regulatory elements were found to be present in the promoters of gma-MIR1510a and the target gene. Collectively, the results obtained in the current study reveal that gma-miR1510 regulates the target NB-LRR immune receptor gene Glyma.16G135500 and thus plays a crucial role in regulating the resistance of soybean to P. sojae.
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Affiliation(s)
- Xiaoxia Cui
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiang Yan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuping Gan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xue
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Guo
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Han Xing
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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240
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Wu J, Wang L, Wang S. MicroRNAs associated with drought response in the pulse crop common bean (Phaseolus vulgaris L.). Gene 2017; 628:78-86. [PMID: 28711666 DOI: 10.1016/j.gene.2017.07.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/20/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
Abstract
Drought stress significantly reduces common bean yields. Recently, some drought-related miRNAs were found in various plants. However, reports of miRNAs involved in drought stress in common bean are limited. Here, we obtained four sRNA samples from drought-tolerant and -sensitive cultivars of common bean that experienced with or without drought treatment. A total of 49 novel miRNAs and 120 known miRNAs were detected. Under drought treatment, 9 and 7 known miRNAs were down and up-regulated, respectively, and 5 and 3 of the novel miRNAs were increased and decreased, respectively. Among these miRNAs, four miRNAs shared the same pattern of expression between Long 22-0579 and Naihua. Target genes of these miRNAs included transcription factors, protein kinases, and nuclear transcription factors. Finally, we verified all of the differentially expressed miRNAs by RT-qPCR, and we identified 16 miRNAs that are potentially associated with the drought stress response. These miRNAs and target genes will be useful in future basic studies and in applied studies investigating how miRNA regulation can be used to enhance drought resistance in plant species.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing 100081, China
| | - Lanfen Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing 100081, China
| | - Shumin Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing 100081, China.
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241
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Bielach A, Hrtyan M, Tognetti VB. Plants under Stress: Involvement of Auxin and Cytokinin. Int J Mol Sci 2017; 18:E1427. [PMID: 28677656 PMCID: PMC5535918 DOI: 10.3390/ijms18071427] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
Plant growth and development are critically influenced by unpredictable abiotic factors. To survive fluctuating changes in their environments, plants have had to develop robust adaptive mechanisms. The dynamic and complementary actions of the auxin and cytokinin pathways regulate a plethora of developmental processes, and their ability to crosstalk makes them ideal candidates for mediating stress-adaptation responses. Other crucial signaling molecules responsible for the tremendous plasticity observed in plant morphology and in response to abiotic stress are reactive oxygen species (ROS). Proper temporal and spatial distribution of ROS and hormone gradients is crucial for plant survival in response to unfavorable environments. In this regard, the convergence of ROS with phytohormone pathways acts as an integrator of external and developmental signals into systemic responses organized to adapt plants to their environments. Auxin and cytokinin signaling pathways have been studied extensively. Nevertheless, we do not yet understand the impact on plant stress tolerance of the sophisticated crosstalk between the two hormones. Here, we review current knowledge on the function of auxin and cytokinin in redirecting growth induced by abiotic stress in order to deduce their potential points of crosstalk.
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Affiliation(s)
- Agnieszka Bielach
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Czech 62500, Brno, Czech Republic.
| | - Monika Hrtyan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Czech 62500, Brno, Czech Republic.
| | - Vanesa B Tognetti
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Czech 62500, Brno, Czech Republic.
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242
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Liu B, Sun G. microRNAs contribute to enhanced salt adaptation of the autopolyploid Hordeum bulbosum compared with its diploid ancestor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:57-69. [PMID: 28370696 DOI: 10.1111/tpj.13546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/14/2017] [Accepted: 03/20/2017] [Indexed: 05/21/2023]
Abstract
Several studies have shown that autopolyploid can tolerate abiotic stresses better than its diploid ancestor. However, the underlying molecular mechanism is poorly known. microRNAs (miRNAs) are small RNAs that regulate the target gene expression post-transcriptionally and play a critical role in the response to abiotic stresses. Duplication of the whole genome can result in the expansion of miRNA families, and the innovative miRNA-target interaction is important for adaptive responses to various environments. We identified new microRNAs induced by genome duplication, that are also associated with stress response and the distinctive microRNA networks in tetraploid and diploid Hordeum bulbosum using high-throughput sequencing. Physiological results showed that autotetraploid Hordeum bulbosum tolerated salt stress better than its diploid. Comparison of miRNAs expression between diploid and tetraploid check (CK) and salt stress revealed that five miRNAs affected by genome doubling were also involved in salt stress response. Of these, miR528b-3p was only detected in the tetraploid, and downregulated under salt stress relative to that in tetraploid CK. Moreover, through target prediction, it was found that miR528b-3p was not only involved in DNA replication and repair but also participated in salt stress response. Finally, by analyzing all the differentially expressed microRNAs and their targets, we also discovered distinguished microRNAs-target regulatory networks in diploid and tetraploid, respectively. Overall, the results demonstrated the critical role of microRNAs in autopolyploid to have better tolerance salt stress.
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Affiliation(s)
- Beibei Liu
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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243
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Yue E, Liu Z, Li C, Li Y, Liu Q, Xu JH. Overexpression of miR529a confers enhanced resistance to oxidative stress in rice (Oryza sativa L.). PLANT CELL REPORTS 2017; 36:1171-1182. [PMID: 28451819 DOI: 10.1007/s00299-017-2146-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/18/2017] [Indexed: 05/23/2023]
Abstract
Overexpressing miR529a can enhance oxidative stress resistance by targeting OsSPL2 and OsSPL14 genes that can regulate the expression of their downstream SOD and POD related genes. MicroRNAs are involved in the regulation of plant developmental and physiological processes, and their expression can be altered when plants suffered environment stresses, including salt, oxidative, drought and Cadmium. The expression of microRNA529 (miR529) can be induced under oxidative stress. However, its biological function under abiotic stress responses is still unclear. In this study, miR529a was overexpressed to investigate the function of miR529a under oxidative stress in rice. Our results demonstrated that the expression of miR529a can be induced by exogenous H2O2, and overexpressing miR529a can increase plant tolerance to high level of H2O2, resulting in increased seed germination rate, root tip cell viability, reduced leaf rolling rate and chlorophyll retention. The expression of oxidative stress responsive genes and the activities of superoxide dismutase (SOD) and peroxidase (POD) were increased in miR529a overexpression plant, which could help to reduce redundant reactive oxygen species (ROS). Furthermore, only OsSPL2 and OsSPL14 were targeted by miR529a in rice seedlings, repressing their expression in miR529aOE plants could lead to strengthen plant tolerance to oxidation stress. Our study provided the evidence that overexpression of miR529a could strengthen oxidation resistance, and its target genes OsSPL2 and OsSPL14 were responsible for oxidative tolerance, implied the manipulation of miR529a and its target genes regulation on H2O2 related response genes could improve oxidative stress tolerance in rice.
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Affiliation(s)
- Erkui Yue
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Zhen Liu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Chao Li
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Yu Li
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Qiuxiang Liu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Jian-Hong Xu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
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244
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Liu M, Yu H, Zhao G, Huang Q, Lu Y, Ouyang B. Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. BMC Genomics 2017; 18:481. [PMID: 28651543 PMCID: PMC5485680 DOI: 10.1186/s12864-017-3869-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/19/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Abiotic stresses cause severe loss of crop production. Among them, drought is one of the most frequent environmental stresses, which limits crop growth, development and productivity. Plant drought tolerance is fine-tuned by a complex gene regulatory network. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success to improve plant yield and quality. Recent studies have demonstrated that microRNAs play critical roles in plant drought tolerance. However, little is known about the microRNA in drought response of the model plant tomato. Here, we described the profiling of drought-responsive microRNA and mRNA in tomato using high-throughput next-generation sequencing. RESULTS Drought stress was applied on the seedlings of M82, a drought-sensitive cultivated tomato genotype, and IL9-1, a drought-tolerant introgression line derived from the stress-resistant wild species Solanum pennellii LA0716 and M82. Under drought, IL9-1 performed superior than M82 regarding survival rate, H2O2 elimination and leaf turgor maintenance. A total of four small RNA and eight mRNA libraries were constructed and sequenced using Illumina sequencing technology. 105 conserved and 179 novel microRNAs were identified, among them, 54 and 98 were differentially expressed upon drought stress, respectively. The majority of the differentially-expressed conserved microRNAs was up-regulated in IL9-1 whereas down-regulated in M82. Under drought stress, 2714 and 1161 genes were found to be differentially expressed in M82 and IL9-1, respectively, and many of their homologues are involved in plant stress, such as genes encoding transcription factor and protein kinase. Various pathways involved in abiotic stress were revealed by Gene Ontology and pathway analysis. The mRNA sequencing results indicated that most of the target genes were regulated by their corresponding microRNAs, which suggested that microRNAs may play essential roles in the drought tolerance of tomato. CONCLUSION In this study, numerous microRNAs and mRNAs involved in the drought response of tomato were identified using high-throughput sequencing, which will provide new insights into the complex regulatory network of plant adaption to drought stress. This work will also help to exploit new players functioning in plant drought-stress tolerance.
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Affiliation(s)
- Minmin Liu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Gangjun Zhao
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiufeng Huang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
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245
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Shin SJ, Lee JH, Kwon HB. Genome-wide identification and characterization of drought responsive MicroRNAs in Solanum tuberosum L. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0586-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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246
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Kubota A, Ito S, Shim JS, Johnson RS, Song YH, Breton G, Goralogia GS, Kwon MS, Laboy Cintrón D, Koyama T, Ohme-Takagi M, Pruneda-Paz JL, Kay SA, MacCoss MJ, Imaizumi T. TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet 2017. [PMID: 28628608 PMCID: PMC5495492 DOI: 10.1371/journal.pgen.1006856] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Photoperiod is one of the most reliable environmental cues for plants to regulate flowering timing. In Arabidopsis thaliana, CONSTANS (CO) transcription factor plays a central role in regulating photoperiodic flowering. In contrast to posttranslational regulation of CO protein, still little was known about CO transcriptional regulation. Here we show that the CINCINNATA (CIN) clade of class II TEOSINTE BRANCHED 1/ CYCLOIDEA/ PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR (TCP) proteins act as CO activators. Our yeast one-hybrid analysis revealed that class II CIN-TCPs, including TCP4, bind to the CO promoter. TCP4 induces CO expression around dusk by directly associating with the CO promoter in vivo. In addition, TCP4 binds to another flowering regulator, GIGANTEA (GI), in the nucleus, and induces CO expression in a GI-dependent manner. The physical association of TCP4 with the CO promoter was reduced in the gi mutant, suggesting that GI may enhance the DNA-binding ability of TCP4. Our tandem affinity purification coupled with mass spectrometry (TAP-MS) analysis identified all class II CIN-TCPs as the components of the in vivo TCP4 complex, and the gi mutant did not alter the composition of the TCP4 complex. Taken together, our results demonstrate a novel function of CIN-TCPs as photoperiodic flowering regulators, which may contribute to coordinating plant development with flowering regulation. For plant adaptation to seasonal environments, a crucial developmental event is flowering, as proper timing of flowering affects reproductive success. Although plants monitor various environmental parameters to optimize this timing, photoperiod information is important for plants to regulate seasonal flowering time, because changes in photoperiod occur in a predictable manner throughout the year. The model plant Arabidopsis thaliana responds to photoperiodic changes and flowers under long-day conditions. Based on genetic analyses using mutants defective in the photoperiodic flowering response, we learned that the transcription factor referred to as CONSTANS (CO) plays a central role in regulating the timing of flowering by directly controlling the expression of florigen (flowering-inducing substrate) gene. Long-day afternoon expression of CO is critical for this regulation; however, we had limited knowledge of CO transcriptional regulation. Here we identified that a group of plant-specific transcription factors belonging to the TCP gene family function as novel CO transcriptional activators. We demonstrated that TCP transcription factors regulate CO transcription together with known regulators of CO. Our results imply that plants utilize multiple transcription factors to precisely coordinate the expression of the key regulator gene, CO, which will directly affect flowering time.
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Affiliation(s)
- Akane Kubota
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Shogo Ito
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Jae Sung Shim
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Yong Hun Song
- Department of Life Sciences, Ajou University, Suwon, Korea
| | - Ghislain Breton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Michael S. Kwon
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Dianne Laboy Cintrón
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Tomotsugu Koyama
- Bioorganic Research Center, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Jose L. Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Steve A. Kay
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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247
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Zhang H, Sonnewald U. Differences and commonalities of plant responses to single and combined stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:839-855. [PMID: 28370754 DOI: 10.1111/tpj.13557] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 03/20/2017] [Accepted: 03/27/2017] [Indexed: 05/21/2023]
Abstract
In natural or agricultural environments, plants are constantly exposed to a wide range of biotic and abiotic stresses. Given the forecasted global climate changes, plants will cope with heat waves, drought periods and pathogens at the same time or consecutively. Heat and drought cause opposing physiological responses, while pathogens may or may not profit from climate changes depending on their lifestyle. Several studies have been conducted to find stress-specific signatures or stress-independent commonalities. Previously this has been done by comparing different single stress treatments. This approach has been proven difficult since most studies, comparing single and combined stress conditions, have come to the conclusion that each stress treatment results in specific transcriptional changes. Although transcriptional changes at the level of individual genes are highly variable and stress-specific, central metabolic and signaling responses seem to be common, often leading to an overall reduced plant growth. Understanding how specific transcriptional changes are linked to stress adaptations and identifying central hubs controlling this interaction will be the challenge for the coming years. In this review, we will summarize current knowledge on plant responses to different individual and combined stresses and try to find a common thread potentially underlying these responses. We will begin with a brief summary of known physiological, metabolic, transcriptional and hormonal responses to individual stresses, elucidate potential commonalities and conflicts and finally we will describe results obtained during combined stress experiments. Here we will concentrate on simultaneous application of stress conditions but we will also touch consequences of sequential stress treatments.
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Affiliation(s)
- Haina Zhang
- Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
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248
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Zuo J, Wang Q, Han C, Ju Z, Cao D, Zhu B, Luo Y, Gao L. SRNAome and degradome sequencing analysis reveals specific regulation of sRNA in response to chilling injury in tomato fruit. PHYSIOLOGIA PLANTARUM 2017; 160:142-154. [PMID: 27595790 DOI: 10.1111/ppl.12509] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/12/2016] [Accepted: 07/18/2016] [Indexed: 05/15/2023]
Abstract
Plant genomes encode diverse small RNA classes that function in distinct gene-silencing pathways. To elucidate the intricate regulation of microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling-injured groups. Except for the known miRNAs and ta-siRNAs, 85 novel miRNAs and 5 ta-siRNAs members belonging to 3 TAS families (TAS5, TAS9 and TAS10) were identified, 34 putative phased small RNAs and 740 cis/trans-natural antisense small-interfering RNAs (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository. A large number of genes targeted by those miRNAs and siRNAs were predicted to be involved in the chilling injury responsive process and five of them were verified via degradome sequencing. Based on the above results, a regulatory model that comprehensively reveals the relationships between the small RNAs and their targets was set up. This work provides a foundation for further study of the regulation of miRNAs and siRNAs in the plant in response to chilling injury.
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Affiliation(s)
- Jinhua Zuo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
| | - Qing Wang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
| | - Cong Han
- Laboratory of Postharvest Physiology and Technology of Fruits and Vegetables, Department of Food Science, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zheng Ju
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Dongyan Cao
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Lipu Gao
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
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249
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Khatun K, Robin AHK, Park JI, Nath UK, Kim CK, Lim KB, Nou IS, Chung MY. Molecular Characterization and Expression Profiling of Tomato GRF Transcription Factor Family Genes in Response to Abiotic Stresses and Phytohormones. Int J Mol Sci 2017; 18:ijms18051056. [PMID: 28505092 PMCID: PMC5454968 DOI: 10.3390/ijms18051056] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 12/22/2022] Open
Abstract
Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (Solanum lycopersicum) have not been extensively explored. In this study, we characterized the 13 SlGRF genes. In silico analysis of protein motif organization, intron–exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the SlGRF genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that SlGRFs are important during growth and development of these tissues. Some of the SlGRF genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different SlGRFs under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of SlGRF genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.
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Affiliation(s)
- Khadiza Khatun
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Chang Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701, Korea.
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701, Korea.
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Mi-Young Chung
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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