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Nikalje GC, Srivastava AK, Shelake RM, Kadam US, Hong JC, Kim JY, Nikam TD, Suprasanna P. Profiling of conserved orthologs and miRNAs for understanding their role in salt tolerance mechanism of Sesuvium portulacastrum L. Mol Biol Rep 2023; 50:9731-9738. [PMID: 37819497 DOI: 10.1007/s11033-023-08892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline environment. Despite molecular studies conducted to unravel its salt adaptation mechanism, there is a paucity of information on the role of salt-responsive orthologs and microRNAs (miRNAs) in this halophyte. Here, we searched the orthology to identify salt-responsive orthologs and miRNA targets of Sesuvium using the Arabidopsis genome. METHODS The relative fold change of orthologs, conserved miRNAs, and miRNA targets of Sesuvium was analyzed under 100 mM (LS) and 250 mM NaCl (HS) treatment at 24 h using qRT-PCR. The comparison between the expression of Sesuvium orthologs and Arabidopsis orthologs (Arabidopsis eFP browser database) was used to identify differentially expressed genes. RESULTS Upon salt treatment, we found that SpCIPK3 (1.95-fold in LS and 2.90-fold in HS) in Sesuvium roots, and SpNHX7 (1.61-fold in LS and 6.39-fold in HS) and, SpSTPK2 (2.54-fold in LS and 7.65-fold in HS) in Sesuvium leaves were upregulated in a salt concentration-specific manner. In Arabidopsis, these genes were either downregulated or did not show significant variation, implicating its significance in the halophytic nature of Sesuvium. Furthermore, miRNAs like miR394a, miR396a, and miR397a exhibited a negative correlation with their targets-Frigida interacting protein 1, Cysteine proteinases superfamily protein, and Putative laccase, respectively under different salt treatments. CONCLUSION The study revealed that the high salt tolerance in Sesuvium is associated with distinct transcriptional reprogramming, hence, to gain holistic mechanistic insights, global-scale profiling is required.
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Affiliation(s)
- Ganesh Chandrakant Nikalje
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
- Department of Botany, Savitribai Phule Pune University, Pune, 411 007, India.
- Department of Botany, R. K. Talreja College of Arts, Science and Commerce, Ulhasnagar, Thane, 421 003, India.
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do, 52828, Republic of Korea
| | - Ulhas Sopanrao Kadam
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do, 52828, Republic of Korea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do, 52828, Republic of Korea
| | - T D Nikam
- Department of Botany, Savitribai Phule Pune University, Pune, 411 007, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
- Amity Institute of Biotechnology, Amity University of Maharashtra, Mumbai, India.
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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Mann A, Lata C, Kumar N, Kumar A, Kumar A, Sheoran P. Halophytes as new model plant species for salt tolerance strategies. FRONTIERS IN PLANT SCIENCE 2023; 14:1137211. [PMID: 37251767 PMCID: PMC10211249 DOI: 10.3389/fpls.2023.1137211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023]
Abstract
Soil salinity is becoming a growing issue nowadays, severely affecting the world's most productive agricultural landscapes. With intersecting and competitive challenges of shrinking agricultural lands and increasing demand for food, there is an emerging need to build resilience for adaptation to anticipated climate change and land degradation. This necessitates the deep decoding of a gene pool of crop plant wild relatives which can be accomplished through salt-tolerant species, such as halophytes, in order to reveal the underlying regulatory mechanisms. Halophytes are generally defined as plants able to survive and complete their life cycle in highly saline environments of at least 200-500 mM of salt solution. The primary criterion for identifying salt-tolerant grasses (STGs) includes the presence of salt glands on the leaf surface and the Na+ exclusion mechanism since the interaction and replacement of Na+ and K+ greatly determines the survivability of STGs in saline environments. During the last decades or so, various salt-tolerant grasses/halophytes have been explored for the mining of salt-tolerant genes and testing their efficacy to improve the limit of salt tolerance in crop plants. Still, the utility of halophytes is limited due to the non-availability of any model halophytic plant system as well as the lack of complete genomic information. To date, although Arabidopsis (Arabidopsis thaliana) and salt cress (Thellungiella halophila) are being used as model plants in most salt tolerance studies, these plants are short-lived and can tolerate salinity for a shorter duration only. Thus, identifying the unique genes for salt tolerance pathways in halophytes and their introgression in a related cereal genome for better tolerance to salinity is the need of the hour. Modern technologies including RNA sequencing and genome-wide mapping along with advanced bioinformatics programs have advanced the decoding of the whole genetic information of plants and the development of probable algorithms to correlate stress tolerance limit and yield potential. Hence, this article has been compiled to explore the naturally occurring halophytes as potential model plant species for abiotic stress tolerance and to further breed crop plants to enhance salt tolerance through genomic and molecular tools.
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Affiliation(s)
- Anita Mann
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
| | - Charu Lata
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
- ICAR-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pardesh, India
| | - Naresh Kumar
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
- Department of Biochemistry, Eternal University, Baru Sahib, Himachal Pardesh, Ludhiana, India
| | - Ashwani Kumar
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
| | - Arvind Kumar
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
| | - Parvender Sheoran
- ICAR-Central Soil Salinity Research Institute, Karnl, Haryana, India
- ICAR-Agriculture Technology Application Research Center, Ludhiana, India
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Abideen Z, Hanif M, Munir N, Nielsen BL. Impact of Nanomaterials on the Regulation of Gene Expression and Metabolomics of Plants under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050691. [PMID: 35270161 PMCID: PMC8912827 DOI: 10.3390/plants11050691] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 05/14/2023]
Abstract
Plant salinity resistance results from a combination of responses at the physiological, molecular, cellular, and metabolic levels. This article focuses on plant stress tolerance mechanisms for controlling ion homeostasis, stress signaling, hormone metabolism, anti-oxidative enzymes, and osmotic balance after nanoparticle applications. Nanoparticles are used as an emerging tool to stimulate specific biochemical reactions related to plant ecophysiological output because of their small size, increased surface area and absorption rate, efficient catalysis of reactions, and adequate reactive sites. Regulated ecophysiological control in saline environments could play a crucial role in plant growth promotion and survival of plants under suboptimal conditions. Plant biologists are seeking to develop a broad profile of genes and proteins that contribute to plant salt resistance. These plant metabolic profiles can be developed due to advancements in genomic, proteomic, metabolomic, and transcriptomic techniques. In order to quantify plant stress responses, transmembrane ion transport, sensors and receptors in signaling transduction, and metabolites involved in the energy supply require thorough study. In addition, more research is needed on the plant salinity stress response based on molecular interactions in response to nanoparticle treatment. The application of nanoparticles as an aspect of genetic engineering for the generation of salt-tolerant plants is a promising area of research. This review article addresses the use of nanoparticles in plant breeding and genetic engineering techniques to develop salt-tolerant crops.
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Affiliation(s)
- Zainul Abideen
- Dr. Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan;
| | - Maria Hanif
- Department of Biotechnology, Lahore College for Women University, Lahore 54000, Pakistan;
| | - Neelma Munir
- Department of Biotechnology, Lahore College for Women University, Lahore 54000, Pakistan;
- Correspondence: (N.M.); (B.L.N.)
| | - Brent L. Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (N.M.); (B.L.N.)
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Elnaggar A, Mosa KA, Ramamoorthy K, El-Keblawy A, Navarro T, Soliman SSM. De novo transcriptome sequencing, assembly, and gene expression profiling of a salt-stressed halophyte (Salsola drummondii) from a saline habitat. PHYSIOLOGIA PLANTARUM 2021; 173:1695-1714. [PMID: 34741316 DOI: 10.1111/ppl.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/30/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Salsola drummondii is a perennial habitat-indifferent halophyte growing in saline and nonsaline habitats of the Arabian hyperarid deserts. It offers an invaluable opportunity to examine the molecular mechanisms of salt tolerance. The present study was conducted to elucidate these mechanisms through transcriptome profiling of seedlings grown from seeds collected in a saline habitat. The Illumina Hiseq 2500 platform was employed to sequence cDNA libraries prepared from shoots and roots of nonsaline-treated plants (controls) and plants treated with 1200 mM NaCl. Transcriptomic comparison between salt-treated and control samples resulted in 17,363 differentially expressed genes (DEGs), including 12,000 upregulated genes (7870 in roots, 4130 in shoots) and 5363 downregulated genes (4258 in roots and 1105 in shoots). The majority of identified DEGs are known to be involved in transcription regulation (79), signal transduction (82), defense metabolism (101), transportation (410), cell wall metabolism (27), regulatory processes (392), respiration (85), chaperoning (9), and ubiquitination (98) during salt tolerance. This study identified potential genes associated with the salt tolerance of S. drummondii and demonstrated that this tolerance may depend on the induction of certain genes in shoot and root tissues. These gene expressions were validated using reverse-transcription quantitative PCR, the results of which were consistent with transcriptomics results. To the best of our knowledge, this is the first study providing genetic information on salt tolerance mechanisms in S. drummondii.
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Affiliation(s)
- Attiat Elnaggar
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
- Departmento de Botanica y Fisiologia Vegetal, Universidad de Málaga, Málaga, Spain
| | - Kareem A Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Kalidoss Ramamoorthy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
| | - Ali El-Keblawy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Biology, Faculty of Science, Al-Arish University, Egypt
| | - Teresa Navarro
- Departmento de Botanica y Fisiologia Vegetal, Universidad de Málaga, Málaga, Spain
| | - Sameh S M Soliman
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
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Xu T, Zhang L, Yang Z, Wei Y, Dong T. Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:665439. [PMID: 34220888 PMCID: PMC8247772 DOI: 10.3389/fpls.2021.665439] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 05/07/2023]
Abstract
Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.
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Affiliation(s)
- Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Tao Xu,
| | - Long Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tingting Dong,
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Boulc'h PN, Caullireau E, Faucher E, Gouerou M, Guérin A, Miray R, Couée I. Abiotic stress signalling in extremophile land plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5771-5785. [PMID: 32687568 DOI: 10.1093/jxb/eraa336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.
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Affiliation(s)
- Pierre-Nicolas Boulc'h
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Emma Caullireau
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Elvina Faucher
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Maverick Gouerou
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
- University of Rennes 1, CNRS, ECOBIO (Ecosystems-Biodiversity-Evolution) - UMR, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Amandine Guérin
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Romane Miray
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
| | - Ivan Couée
- University of Rennes 1, Department of Life Sciences and Environment, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
- University of Rennes 1, CNRS, ECOBIO (Ecosystems-Biodiversity-Evolution) - UMR, Campus de Beaulieu, avenue du Général Leclerc, Rennes, France
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Parmar S, Gharat SA, Tagirasa R, Chandra T, Behera L, Dash SK, Shaw BP. Identification and expression analysis of miRNAs and elucidation of their role in salt tolerance in rice varieties susceptible and tolerant to salinity. PLoS One 2020; 15:e0230958. [PMID: 32294092 PMCID: PMC7159242 DOI: 10.1371/journal.pone.0230958] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/12/2020] [Indexed: 12/31/2022] Open
Abstract
Soil salinization is a serious problem for cultivation of rice, as among cereals rice is the most salt sensitive crop, and more than 40% of the total agricultural land amounting to approximately 80 million ha the world over is salt affected. Salinity affects a plant in a varieties of ways, including ion toxicity, osmotic stress and oxidative damage. Since miRNAs occupy the top place in biochemical events determining a trait, understanding their role in salt tolerance is highly desirable, which may allow introduction of the trait in the rice cultivars of choice through biotechnological interventions. High throughput sequencing of sRNAs in the root and shoot tissues of the seedlings of the control and NaCl treated Pokkali, a salt-tolerant rice variety, identified 75 conserved miRNAs and mapped 200 sRNAs to the rice genome as novel miRNAs. Expression of nine novel miRNAs and two conserved miRNAs were confirmed by Northern blotting. Several of both conserved and novel miRNAs that expressed differentially in root and/or shoot tissues targeted transcription factors like AP2/EREBP domain protein, ARF, NAC, MYB, NF-YA, HD-Zip III, TCP and SBP reported to be involved in salt tolerance or in abiotic stress tolerance in general. Most of the novel miRNAs expressed in the salt tolerant wild rice Oryza coarctata, suggesting conservation of miRNAs in taxonomically related species. One of the novel miRNAs, osa-miR12477, also targeted L-ascorbate oxidase (LAO), indicating build-up of oxidative stress in the plant upon salt treatment, which was confirmed by DAB staining. Thus, salt tolerance might involve miRNA-mediated regulation of 1) cellular abundance of the hormone signaling components like EREBP and ARF, 2) synthesis of abiotic stress related transcription factors, and 3) antioxidative component like LAO for mitigation of oxidative damage. The study clearly indicated importance of osa-miR12477 regulated expression of LAO in salt tolerance in the plant.
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Affiliation(s)
- Shaifaly Parmar
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Sachin Ashruba Gharat
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Ravichandra Tagirasa
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Tilak Chandra
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Lambodar Behera
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Sushant Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Birendra Prasad Shaw
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
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Awasthi JP, Chandra T, Mishra S, Parmar S, Shaw BP, Nilawe PD, Chauhan NK, Sahoo S, Panda SK. Identification and characterization of drought responsive miRNAs in a drought tolerant upland rice cultivar KMJ 1-12-3. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 137:62-74. [PMID: 30738218 DOI: 10.1016/j.plaphy.2019.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Shortfall of rain that creates drought like situation in non-irrigated agriculture system often limits rice production, necessitating introduction of drought tolerance trait into the cultivar of interest. The mechanism governing drought tolerance is, however, largely unknown, particularly the involvement of miRNAs, the master regulators of biochemical events. In this regard, response study on a drought tolerant rice variety KMJ 1-12-3 to 20% PEG (osmolality- 315 mOsm/kg) as drought stress revealed significant changes in abundance of several conserved miRNAs targeting transcription factors like homeodomain-leucine zipper, MADS box family protein, C2H2 zinc finger protein and Myb, well known for their importance in drought tolerance in plants. The response study also revealed significant PEG-induced decrease in abundance of the miRNAs targeting cyclin A, cyclin-dependent kinase, guanine nucleotide exchange factor, GTPase-activating protein, 1-aminocyclopropane-1-carboxylic acid oxidase and indole-3-acetic beta-glucosyl transferase indicating miRNA-regulated role of the cell cycle regulators, G-protein signalling and the plant hormones ethylene and IAA in drought tolerance in plants. The study confirmed the existence of four novel miRNAs, including osa-miR12470, osa-miR12471, osa-miR12472 and osa-miR12473, and the targets of three of them could be successfully validated. The PEG-induced decrease in abundance of the novel miRNAs osa-miR12470 and osa-miR12473 targeting RNA dependent RNA polymerase and equilibrative nucleoside transporter, respectively suggested an overall increase in both degradation and synthesis of nucleic acids in plants challenged with drought stress. The drought-responsive miRNAs identified in the study may be proved useful in introducing the trait in the rice cultivars of choice by manipulation of their cellular abundance.
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Affiliation(s)
- Jay Prakash Awasthi
- Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India.
| | - Tilak Chandra
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Sagarika Mishra
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Shaifaly Parmar
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Pravin Daulat Nilawe
- Thermo Fisher Scientific India Pvt. Ltd, 403/404 B-Wing, Delphi, Hiranandani Business Park, Powai, Mumbai, 400076, India.
| | - Neeraj Kumar Chauhan
- Thermo Fisher Scientific India Pvt. Ltd, 403/404 B-Wing, Delphi, Hiranandani Business Park, Powai, Mumbai, 400076, India.
| | - Smita Sahoo
- Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India.
| | - Sanjib Kumar Panda
- Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India.
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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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Nikalje G, Nikam T, Suprasanna P. Looking at Halophytic Adaptation to High Salinity Through Genomics Landscape. Curr Genomics 2017; 18:542-552. [PMID: 29204082 PMCID: PMC5684652 DOI: 10.2174/1389202918666170228143007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/15/2016] [Accepted: 10/30/2016] [Indexed: 12/22/2022] Open
Abstract
Soil salinity is an important stress factor that limits plant growth and productivity. For a given plant species, it is critical to sense and respond to salt stimuli followed by activation of multitude of mechanisms for plants to survive. Halophytes, the wonders of saline soils, have demonstrated ability to withstand and reproduce in at least 200 mM NaCl concentration, which makes them an ideal system to study mechanism of salt adaptation for imparting salt tolerance in glycophytes. Halophytes and salt sensitive glycophytes adapt different defense strategies towards salinity stress. These responses in halophytes are modulated by a well orchestrated network of signaling pathways, including calcium signaling, reactive oxygen species and phytohormones. Moreover, constitutive expression of salt stress response related genes, which is only salt inducible in glycophytes, maintains salt tolerance traits in halophytes. The focus of this review is on the adaptive considerations of halophytes through the genomics approaches from the point of view of sensing and signaling components involved in mediating plant responses to salinity.
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Affiliation(s)
- G.C. Nikalje
- Department of Botany, Savitribai Phule Pune University, Pune 411 007, India
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - T.D. Nikam
- Department of Botany, Savitribai Phule Pune University, Pune 411 007, India
| | - P. Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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12
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Kumar D, Dutta S, Singh D, Prabhu KV, Kumar M, Mukhopadhyay K. Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis. PLANTA 2017; 245:161-182. [PMID: 27699487 DOI: 10.1007/s00425-016-2600-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/27/2016] [Indexed: 05/09/2023]
Abstract
Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression. High-throughput sequencing was used for transcriptome-wide identification of miRNAs and their expression profiling in retort to leaf rust using mock and pathogen-inoculated resistant and susceptible near-isogenic wheat plants. A total of 1056 mature miRNAs were identified, of which 497 miRNAs were conserved and 559 miRNAs were novel. The pathogen-inoculated resistant plants manifested more miRNAs compared with the pathogen infected susceptible plants. The miRNA counts increased in susceptible isoline due to leaf rust, conversely, the counts decreased in the resistant isoline in response to pathogenesis illustrating precise spatial tuning of miRNAs during compatible and incompatible interaction. Stem-loop quantitative real-time PCR was used to profile 10 highly differentially expressed miRNAs obtained from high-throughput sequencing data. The spatio-temporal profiling validated the differential expression of miRNAs between the isolines as well as in retort to pathogen infection. Degradome analysis provided 701 predicted target genes associated with defense response, signal transduction, development, metabolism, and transcriptional regulation. The obtained results indicate that wheat isolines employ diverse arrays of miRNAs that modulate their target genes during compatible and incompatible interaction. Our findings contribute to increase knowledge on roles of microRNA in wheat-leaf rust interactions and could help in rust resistance breeding programs.
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Affiliation(s)
- Dhananjay Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Summi Dutta
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Dharmendra Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- QAAFI, Centre of Plant Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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13
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Gharat SA, Parmar S, Tambat S, Vasudevan M, Shaw BP. Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes. PLoS One 2016; 11:e0163485. [PMID: 27682829 PMCID: PMC5040429 DOI: 10.1371/journal.pone.0163485] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/10/2016] [Indexed: 01/02/2023] Open
Abstract
Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.
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Affiliation(s)
- Sachin Ashruba Gharat
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Shaifaly Parmar
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Subodh Tambat
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Madavan Vasudevan
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
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