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Zhang Y, Zhang X, Kai T, Zhang L, Li A. Lycium ruthenicum Murray derived exosome-like nanovesicles inhibit Aβ-induced apoptosis in PC12 cells via MAPK and PI3K/AKT signaling pathways. Int J Biol Macromol 2024; 277:134309. [PMID: 39089544 DOI: 10.1016/j.ijbiomac.2024.134309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/21/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
Plant-derived exosome-like nanovesicles (ELNs) are nano-sized vesicles extracted from edible plants. Lycium ruthenicum Murray (LRM) has been gaining increasing attention due to its nutritional and medicinal value, but the ELNs in LRM has not been reported. In this study, LRM-ELNs were obtained, and the proteins, lipids, microRNAs (miRNAs) and active components in LRM tissues and LRM-ELNs was analyzed by LC-MS/MS, LC-MS, high-throughput sequencing techniques, and physical and chemical analysis. LRM-ELNs can be uptaken by PC12 cells through macropinocytosis and caveolin-mediated endocytosis primarily. Transcriptomic and western blot experiments indicate that LRM-ELNs can inhibit Aβ-induced apoptosis in PC12 cells through the MAPK and PI3K/AKT signaling pathways, with miRNAs playing a crucial role. These results indicate that LRM-ELNs have the protection effect on PC12 cells and can be considered as dietary supplements for alleviating neurodegenerative diseases.
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Affiliation(s)
- Yadan Zhang
- College of Food Science and Engineering, Hunan Key Laboratory of Processed Food for Special Medical Purpose, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiaoyu Zhang
- College of Food Science and Engineering, Hunan Key Laboratory of Processed Food for Special Medical Purpose, Central South University of Forestry and Technology, Changsha 410004, China
| | - Tianhan Kai
- Xiang Ya School of Public Health, Central South University, Changsha 410078, China
| | - Lin Zhang
- College of Food Science and Engineering, Hunan Key Laboratory of Processed Food for Special Medical Purpose, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Anping Li
- College of Food Science and Engineering, Hunan Key Laboratory of Processed Food for Special Medical Purpose, Central South University of Forestry and Technology, Changsha 410004, China.
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2
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Chandra T, Jaiswal S, Tomar RS, Iquebal MA, Kumar D. Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources. PLANTA 2024; 260:103. [PMID: 39304579 DOI: 10.1007/s00425-024-04520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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3
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Jiang C, Zhang X, Rao J, Luo S, Luo L, Lu W, Li M, Zhao S, Ren D, Liu J, Song Y, Zheng Y, Sun YB. Enhancing Pseudomonas syringae pv. Actinidiae sensitivity in kiwifruit by repressing the NBS-LRR genes through miRNA-215-3p and miRNA-29-3p identification. FRONTIERS IN PLANT SCIENCE 2024; 15:1403869. [PMID: 39086918 PMCID: PMC11288850 DOI: 10.3389/fpls.2024.1403869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024]
Abstract
Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (PSA), poses a grave threat to the global kiwifruit industry. In this study, we examined the role of microRNAs (miRNAs) in kiwifruit's response to PSA. Kiwifruit seedlings subjected to PSA treatment showed significant changes in both miRNA and gene expression compared to the control group. We identified 364 differentially expressed miRNAs (DEMs) and 7170 differentially expressed genes (DEGs). Further analysis revealed 180 miRNAs negatively regulating 641 mRNAs. Notably, two miRNAs from the miRNA482 family, miRNA-215-3p and miRNA-29-3p, were found to increase kiwifruit's sensitivity to PSA when overexpressed. These miRNAs were linked to the regulation of NBS-LRR target genes, shedding light on their role in kiwifruit's defence against PSA. This study offers insights into the miRNA482-NBS-LRR network as a crucial component in enhancing kiwifruit bioresistance to PSA infestation and provides promising candidate genes for further research.
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Affiliation(s)
- Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoying Zhang
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Jiahui Rao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Shu Luo
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Liang Luo
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Shumei Zhao
- Key Laboratory of Agricultural Engineering in Structure and Environment, China Agricultural University, Beijing, China
| | - Dan Ren
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Jiaming Liu
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Yu Song
- Research Institute of Crop Germplasm Resources, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics, School of Basic & Medical Biosciences, King’s College London, London, United Kingdom
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4
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Yang L, Zhou Q, Sheng X, Chen X, Hua Y, Lin S, Luo Q, Yu B, Shao T, Wu Y, Chang J, Li Y, Tu M. Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications. Int J Mol Sci 2023; 24:14549. [PMID: 37833996 PMCID: PMC10573072 DOI: 10.3390/ijms241914549] [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: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.
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Affiliation(s)
- Lin Yang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qin Zhou
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Xuan Sheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiangqian Chen
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Yuqing Hua
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Shuang Lin
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qiyun Luo
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Ti Shao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yixiao Wu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
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5
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Yin L, Yan L, Yu Q, Wang J, Liu C, Wang L, Zheng L. Characterization of the MicroRNA Profile of Ginger Exosome-like Nanoparticles and Their Anti-Inflammatory Effects in Intestinal Caco-2 Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4725-4734. [PMID: 35261246 DOI: 10.1021/acs.jafc.1c07306] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant-derived exosome-like nanoparticles (PELNs) have been shown to enter mammalian cells for disease treatment. Although abundant miRNAs are contained in ginger exosome-like nanoparticles (GELNs), little is known about their type and function. Herein, we extracted GELNs with desirable particle sizes (156 ± 36 nm) and a negative surface charge (-26.6 ± 5 mV). The miRNA profiles in ginger and GELNs were analyzed using high-throughput sequencing, and the results of the sequencing were validated by real-time quantitative polymerase chain reaction (RT-qPCR). There were 27 miRNAs with higher expression levels in the GELNs, and they were mainly involved in the regulation of inflammatory and cancer-related pathways. Furthermore, GELNs could be specifically internalized by intestine cells via caveolin-mediated endocytosis and micropinocytosis, as well as counteract lipopolysaccharide (LPS)-induced inflammation by downregulating NF-κβ, IL-6, IL-8, and TNF-α expression. Importantly, the positive effects were further proved to be possibly related to the miRNAs enriched in the GELNs. Overall, these results indicated that PELNs could target human digestive organs and play a cross-kingdom physiological regulation role through miRNAs.
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Affiliation(s)
- Lifen Yin
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Ling Yan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qian Yu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Ju Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Changhong Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lei Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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6
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Jia W, Lin K, Lou T, Feng J, Lv S, Jiang P, Yi Z, Zhang X, Wang D, Guo Z, Tang Y, Qiu R, Li Y. Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance. PLANTA 2021; 254:16. [PMID: 34185181 DOI: 10.1007/s00425-021-03669-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance. As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA-mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.
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Affiliation(s)
- Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, People's Republic of China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Tengxue Lou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ze Yi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zijing Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yetao Tang
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Rongliang Qiu
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China.
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7
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Zhang Y, Xiang D, Hu X, Ruan Q, Wang L, Bao Z. Identification and study of differentially expressed miRNAs in aged NAFLD rats based on high-throughput sequencing. Ann Hepatol 2021; 19:302-312. [PMID: 31899128 DOI: 10.1016/j.aohep.2019.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVES Hepatic microRNA (miR) expression profiles were explored in aged rats with NAFLD, in order to clarify the molecular mechanisms underlying the pathophysiological processes of aging-related NAFLD. PATIENTS OR MATERIALS AND METHODS 24 aged rats (18-month-old) and 24 young rats (2-month-old) were randomly divided into two subgroups according to diet, control group and NAFLD group. After 8 weeks of administering 45% high-fat diet or normal diet, total hepatic RNA was extracted from liver tissues of the aged rats. Differentially expressed microRNAs (DE-miRs) in aged NAFLD group were detected and screened out using high-throughput sequencing technology. The data were subjected to Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses using a bioinformatics approach. The sequencing results were further verified by RT-qPCR. RESULTS Compared with the aged control liver tissues, 6 significantly upregulated miRs (miR-881-3p, miR-871-3p, miR-335, miR-223-3p, miR-155-5p, miR-146b-5p) and 4 significantly downregulated miRs (miR-182, miR-193-3p, miR-31a-5p and miR-96-5p) were identified in the aged NAFLD liver tissues. These DE-miRs were found to be involved in the regulation of cell signaling transduction and metabolism processes, probably affecting signaling pathways relevant to insulin secretion and some senile diseases. RT-qPCR results corroborated the sequencing results and demonstrated that 6 significantly upregulated miRs were not identified in the young group. CONCLUSIONS A total of 10 DE-miRs identified in the aged NAFLD rats were involved in some certain insulin secretion and age-related functional pathways, which may serve as novel candidate targets for the diagnosis and treatment of aging-associated NAFLD.
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Affiliation(s)
- Ying Zhang
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Danni Xiang
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China
| | - Xiaona Hu
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Qingwei Ruan
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Lina Wang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Zhijun Bao
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China.
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8
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Paul S, Reyes-Pérez P, Angulo-Bejarano PI, Srivastava A, Ramalingam S, Sharma A. Characterization of microRNAs from neem ( Azadirachta indica) and their tissue-specific expression study in leaves and stem. 3 Biotech 2021; 11:277. [PMID: 34040926 DOI: 10.1007/s13205-021-02839-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/08/2021] [Indexed: 01/29/2023] Open
Abstract
Neem (Azadirachta indica) is a very popular traditional medicinal plant used since ancient times to treat numerous ailments. MicroRNAs (miRNAs) are highly conserved, non-coding, short RNA molecules that play important regulatory roles in plant development and metabolism. In this study, deploying a high stringent genome-wide computational-based approach and following a set of strict filtering norms a total of 44 potential conserved neem miRNAs belonging to 21 families and their corresponding 48 potential target transcripts were identified. Important targets include Squamosa promoter binding protein-like proteins, NAC, Scarecrow proteins, Auxin response factor, and F-box proteins. A biological network has also been developed to understand the miRNA-mediated gene regulation using the minimum free energy (MFE) values of the miRNA-target interaction. Moreover, six selected miRNAs were reported to be involved in secondary metabolism in other plant species (miR156a, miR156l, miR160, miR164, miR171, miR395) were validated by qPCR and their tissue-specific differential expression pattern was observed in leaves and stem. Except for ain-miR395, all the other miRNAs were found overexpressed in the stem as compared to leaves. To the best of our knowledge, this is the first report of neem miRNAs and we believe the finding of the present study will be useful for the functional genomic study of medicinal plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02839-z.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Paula Reyes-Pérez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Paola Isabel Angulo-Bejarano
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
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9
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Su W, Zhang C, Feng J, Feng A, You C, Ren Y, Wang D, Sun T, Su Y, Xu L, Chen N, Que Y. Genome-wide identification, characterization and expression analysis of the carotenoid cleavage oxygenase (CCO) gene family in Saccharum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:196-210. [PMID: 33691250 DOI: 10.1016/j.plaphy.2021.02.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Carotenoid cleavage oxygenases (CCOs) play crucial roles in plant growth and development, as well as in the response to phytohormonal, biotic and abiotic stresses. However, comprehensive and systematic research on the CCO gene family has not yet been conducted in Saccharum. In this study, 47 SsCCO and 14 ShCCO genes were identified and characterized in Saccharum spontaneum and Saccharum spp. R570 cultivar, respectively. The SsCCOs consisted of 38 SsCCDs and 9 SsNCEDs, while ShCCOs contained 11 ShCCDs and 3 ShNCEDs. The SsCCO family could be divided into 7 groups, while ShCCO family into 5 groups. The genes/proteins contained similar compositions within the same group, and the evolutionary mechanisms differed between S. spontaneum and R570. Gene Ontology annotation implied that CCOs were involved in many physiological and biochemical processes. Additionally, 41 SsCCOs were regulated by 19 miRNA families, and 8 ShCCOs by 9 miRNA families. Cis-regulatory elements analysis suggested that CCO genes functioned in the process of growth and development or under the phytohormonal, biotic and abiotic stresses. qRT-PCR analysis indicated that nine CCO genes from different groups exhibited similar expression patterns under abscisic acid treatment, while more divergent profiles were observed in response to Sporisorium scitamineum and cold stresses. Herein, comparative genomics analysis of the CCO gene family between S. spontaneum and R570 was conducted to investigate its evolution and functions. This is the first report on the CCO gene family in S. spontaneum and R570, thus providing valuable information and facilitating further investigation into its function in the future.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingfang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Niandong Chen
- New Huadu Business School, Minjiang University, Fuzhou, 350108, Fujian, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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10
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Wang G, Guo X, Cheng L, Chu P, Chen M, Chen Y, Chang C. An integrated analysis of the circRNA-miRNA-mRNA network reveals novel insights into potential mechanisms of cell proliferation during liver regeneration. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 47:3873-3884. [PMID: 31566012 DOI: 10.1080/21691401.2019.1669623] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cell proliferation constitutes the fundamental process and driving force behind regrowth during liver regeneration (LR). However, it remains unclear how competing endogenous RNA (ceRNA) networks affect hepatocyte proliferation and liver regeneration. Therefore, this study was designed to explore an LR-specific ceRNA network, which regulates cell proliferation. Based on the microarray data of mRNAs, and high-throughput sequencing data of miRNAs and circRNAs from regenerating livers, this study initially applied known 1484 LR associated mRNAs to perform GO analysis, and then selected 169 LR associated mRNAs involved in cell proliferation and the cell cycle. Subsequently, 188 interactive miRNA-mRNA pairs and 5206 circRNA-miRNA pairs, respectively, were predicted using bioinformatics methods. Next, in view of the differential expressions of these ceRNAs during LR, 26 miRNA-mRNA pairs and 71 circRNA-miRNA pairs were applied to generate a circRNA-miRNA-mRNA regulatory network, and only 14 triple interactive groups were obtained based on the predicted inverse interactions among ceRNAs. Finally, circ_19698/miR-423-5p axis was demonstrated to promote cell proliferation by modulating the expression of MYC, CCNA2, and CCND1 in rat BRL-3A cells. This study suggests a potential regulatory mechanism of cell proliferation in regenerating livers, as well as a novel pathway for modulating ceRNA networks to promote liver regeneration.
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Affiliation(s)
- Gaiping Wang
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
| | - Xueqiang Guo
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
| | - Liya Cheng
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
| | - Peipei Chu
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
| | - Meng Chen
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
| | - Yanhui Chen
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
| | - Cuifang Chang
- College of Life Science, Henan Normal University , Xinxiang , Henan , China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation , Xinxiang , Henan , China
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11
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Wang M, Zang L, Jiao F, Perez-Garcia MD, Ogé L, Hamama L, Le Gourrierec J, Sakr S, Chen J. Sugar Signaling and Post-transcriptional Regulation in Plants: An Overlooked or an Emerging Topic? FRONTIERS IN PLANT SCIENCE 2020; 11:578096. [PMID: 33224165 PMCID: PMC7674178 DOI: 10.3389/fpls.2020.578096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/02/2020] [Indexed: 05/21/2023]
Abstract
Plants are autotrophic organisms that self-produce sugars through photosynthesis. These sugars serve as an energy source, carbon skeletons, and signaling entities throughout plants' life. Post-transcriptional regulation of gene expression plays an important role in various sugar-related processes. In cells, it is regulated by many factors, such as RNA-binding proteins (RBPs), microRNAs, the spliceosome, etc. To date, most of the investigations into sugar-related gene expression have been focused on the transcriptional level in plants, while only a few studies have been conducted on post-transcriptional mechanisms. The present review provides an overview of the relationships between sugar and post-transcriptional regulation in plants. It addresses the relationships between sugar signaling and RBPs, microRNAs, and mRNA stability. These new items insights will help to reach a comprehensive understanding of the diversity of sugar signaling regulatory networks, and open onto new investigations into the relevance of these regulations for plant growth and development.
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Affiliation(s)
- Ming Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Lili Zang
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | | | - Laurent Ogé
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Latifa Hamama
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - José Le Gourrierec
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Soulaiman Sakr
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
- Soulaiman Sakr,
| | - Jingtang Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Jingtang Chen,
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12
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Li Y, Tu M, Feng Y, Wang W, Messing J. Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:274. [PMID: 31832097 PMCID: PMC6868837 DOI: 10.1186/s13068-019-1612-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/09/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Sorghum bicolor (L.) is an important bioenergy source. The stems of sweet sorghum function as carbon sinks and accumulate large amounts of sugars and lignocellulosic biomass and considerable amounts of starch, therefore providing a model of carbon allocation and accumulation for other bioenergy crops. While omics data sets for sugar accumulation have been reported in different genotypes, the common features of primary metabolism in sweet genotypes remain unclear. To obtain a cohesive and comparative picture of carbohydrate metabolism between sorghum genotypes, we compared the phenotypes and transcriptome dynamics of sugar-accumulating internodes among three different sweet genotypes (Della, Rio, and SIL-05) and two non-sweet genotypes (BTx406 and R9188). RESULTS Field experiments showed that Della and Rio had similar dynamics and internode patterns of sugar concentration, albeit distinct other phenotypes. Interestingly, cellulose synthases for primary cell wall and key genes in starch synthesis and degradation were coordinately upregulated in sweet genotypes. Sweet sorghums maintained active monolignol biosynthesis compared to the non-sweet genotypes. Comparative RNA-seq results support the role of candidate Tonoplast Sugar Transporter gene (TST), but not the Sugars Will Eventually be Exported Transporter genes (SWEETs) in the different sugar accumulations between sweet and non-sweet genotypes. CONCLUSIONS Comparisons of the expression dynamics of carbon metabolic genes across the RNA-seq data sets identify several candidate genes with contrasting expression patterns between sweet and non-sweet sorghum lines, including genes required for cellulose and monolignol synthesis (CesA, PTAL, and CCR), starch metabolism (AGPase, SS, SBE, and G6P-translocator SbGPT2), and sucrose metabolism and transport (TPP and TST2). The common transcriptome features of primary metabolism identified here suggest the metabolic networks contributing to carbon sink strength in sorghum internodes, prioritize the candidate genes for manipulating carbon allocation with bioenergy purposes, and provide a comparative and cohesive picture of the complexity of carbon sink strength in sorghum stem.
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Affiliation(s)
- Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Min Tu
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Wenqing Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dong Chuan Road, Shanghai, 200240 China
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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13
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Dhaka N, Sharma S, Vashisht I, Kandpal M, Sharma MK, Sharma R. Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum. Genomics 2019; 112:1598-1610. [PMID: 31521711 DOI: 10.1016/j.ygeno.2019.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 02/06/2023]
Abstract
Understanding male gametophyte development is essential to augment hybrid production in sorghum. Although small RNAs are known to critically influence anther/pollen development, their roles in sorghum reproduction have not been deciphered yet. Here, we report small RNA profiling and high-confidence annotation of microRNAs (miRNAs) from meiotic and post-meiotic anthers in sorghum. We identified 262 miRNAs (82 known and 180 novel), out of which 58 (35 known and 23 novel) exhibited differential expression between two stages. Out of 35 differentially expressed known miRNAs, 13 are known to regulate anther/pollen development in other plant species. We also demonstrated conserved spatiotemporal patterns of 21- and 24-nt phasiRNAs and their respective triggers, miR2118 and miR2275, in sorghum anthers as evidenced in other monocots. miRNA target identification yielded 5622 modules, of which 46 modules comprising 16 known and 8 novel miRNA families with 38 target genes are prospective candidates for engineering male fertility in grasses.
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Affiliation(s)
- Namrata Dhaka
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Shalini Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Ira Vashisht
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manu Kandpal
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manoj Kumar Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India.
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Multi-Omics Analysis Reveals Up-Regulation of APR Signaling, LXR/RXR and FXR/RXR Activation Pathways in Holstein Dairy Cows Exposed to High-Altitude Hypoxia. Animals (Basel) 2019; 9:ani9070406. [PMID: 31266191 PMCID: PMC6680605 DOI: 10.3390/ani9070406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Blood has been widely collected and analyzed for diagnosing and monitoring diseases in human beings and animals. A range of plasma proteins and peptides were set as biomarkers for pathological and physiological status. Previous researchers have explored how humans, pigs, dogs, and horses adapt to hypoxia at high altitudes. Additionally, the mechanism of hypoxia adaptation in human, mice, and shrimp was studied by proteomics. However, information on the adaptation mechanism of Holstein cows introduced to high altitudes is limited. The present study was conducted to the adaptation mechanism of Holstein dairy cows to high-altitude hypoxia by miRNA microarray analysis and the isobaric tags for relative and absolute quantitation (iTRAQ) iTRAQ technology. Based on the obtained results, Holstein dairy cows transported to Nyingchi may adapt to the high-altitude hypoxia through regulation of inflammatory homeostasis by up-regulating the acute phase response (APR) APR and activation of the liver X receptor/retinoid X receptor (LXR/RXR)LXR/RXR and farnesoid X receptor/ retinoid X receptor (FXR/RXR) FXR/RXR pathways. Abstract Changes in the environment such as high-altitude hypoxia (HAH) high-altitude hypoxia can lead to adaptive changes in the blood system of mammals. However, there is limited information about the adaptation of Holstein dairy cows introduced to high-altitude areas. This study used 12 multiparous Holstein dairy cows (600 ± 55 kg, average three years old) exposed to HAH conditions in Nyingchi of Tibet (altitude 3000 m) and HAH-free conditions in Shenyang (altitude 50 m). The miRNA microarray analysis and iTRAQ proteomics approach (accepted as more suitable for accurate and comprehensive prediction of miRNA targets) were applied to explore the differences in the plasma proteomic and miRNA profiles in Holstein dairy cows. A total of 70 differential miRNAs (54 up-regulated, Fold change (FC) FC > 2, and 16 down-regulated, FC < 0.5) and 226 differential proteins (132 up-regulated, FC > 1.2, and 94 down-regulated, FC < 0.8) were found in the HAH-stressed group compared with the HAH-free group. Integrative analysis of proteomic and miRNA profiles demonstrated the biological processes associated with differential proteins were the immune response, complement activation, protein activation, and lipid transport. The integrative analysis of canonical pathways were most prominently associated with the APR signaling (z = 1.604), and LXR/RXR activation (z = 0.365), and FXR/RXR activation (z = 0.446) pathways. The current results indicated that Holstein dairy cows exposed to HAH could adapt to high-altitude hypoxia by up-regulating the APR, activating the LXR/RXR and FXE/RXR pathways.
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15
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Kong Z, Zhou C, Li B, Jiao J, Chen L, Ren A, Jie H, Tan Z. Integrative plasma proteomic and microRNA analysis of Jersey cattle in response to high-altitude hypoxia. J Dairy Sci 2019; 102:4606-4618. [PMID: 30879823 DOI: 10.3168/jds.2018-15515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022]
Abstract
Blood has been widely collected and analyzed for diagnosing and monitoring diseases in humans and animals; a range of plasma proteins and peptide can be used as biomarkers to describe pathological or physiological status. Changes in the environment such as high-altitude hypoxia (HAH) can lead to adaptive changes in the blood system of mammals. However, the adaptation mechanism induced by HAH remains unclear. In this study, we used 12 multiparous Jersey cattle (400 ± 35 kg, average 3 yr old, dry period). We applied an iTRAQ (isobaric tags for relative and absolute quantitation) proteomics approach and microRNA (miRNA) microarray to explore differences in the plasma proteomic and miRNA profiles of Jersey cattle exposed to HAH conditions in Nyingchi, Tibet (altitude 3,000 m) and HAH-free conditions in Shenyang, China (altitude 50 m). Such quantitative proteomic strategies are suitable for accurate and comprehensive prediction of miRNA targets. In total, 264 differentially expressed proteins (127 upregulated, fold-change >1.2; 137 downregulated, fold-change <0.8) and 47 differential miRNAs (25 upregulated, fold-change >2; 22 downregulated, fold-change <0.5) were observed in the HAH-stressed group compared with the HAH-free group. Integrative analysis of proteomic and miRNA profiles demonstrated that the biological processes associated with differentially expressed proteins were immune response, complement system, and conjugation system. Integrative analysis of canonical pathways showed that most were associated with acute phase response signaling (z-score = -0.125), liver X receptor/retinoid X receptor (LXR/RXR) activation pathway (z-score = 1.134), coagulation system (z-score = -0.943), and complement system (z-score = -0.632). The current results indicated that Jersey cattle exposed to HAH could adapt to that condition through regulation of inflammatory homeostasis by inhibiting the acute phase response, coagulation system, and complement system and promoting LXR/RXR activation.
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Affiliation(s)
- Zhiwei Kong
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanshe Zhou
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; Hunan Co-Innovation Center of Safety Animal Production (CICSAP), Changsha, Hunan 410128, China.
| | - Bin Li
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Regional Academy of Agricultural Sciences, State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850000, China.
| | - Jinzhen Jiao
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; Hunan Co-Innovation Center of Safety Animal Production (CICSAP), Changsha, Hunan 410128, China
| | - Liang Chen
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Ao Ren
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Hongdong Jie
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; Hunan Co-Innovation Center of Safety Animal Production (CICSAP), Changsha, Hunan 410128, China
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Li Y, Wang W, Feng Y, Tu M, Wittich PE, Bate NJ, Messing J. Transcriptome and metabolome reveal distinct carbon allocation patterns during internode sugar accumulation in different sorghum genotypes. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:472-487. [PMID: 30051585 PMCID: PMC6335075 DOI: 10.1111/pbi.12991] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 05/03/2023]
Abstract
Sweet sorghum accumulates large amounts of soluble sugar in its stem. However, a system-based understanding of this carbohydrate allocation process is lacking. Here, we compared the dynamic transcriptome and metabolome between the conversion line R9188 and its two parents, sweet sorghum RIO and grain sorghum BTx406 that have contrasting sugar-accumulating phenotypes. We identified two features of sucrose metabolism, stable concentrations of sugar phosphates in RIO and opposite trend of trehalose-6-phosphate (T6P) between RIO vs R9188/BTx406. Integration of transcriptome and metabolome revealed R9188 is partially active in starch metabolism together with medium sucrose level, whereas sweet sorghum had the highest sucrose concentration and remained highly active in sucrose, starch, and cell wall metabolism post-anthesis. Similar expression pattern of genes involved in sucrose degradation decreased the pool of sugar phosphates for precursors of starch and cell wall synthesis in R9188 and BTx406. Differential T6P signal between RIO vs R9188/BTx406 is associated with introgression of T6P regulators from BTx406 into R9188, including C-group bZIP and trehalose 6-phosphate phosphatase (TPP). The inverted T6P signalling in R9188 appears to down-regulate sucrose and starch metabolism partly through transcriptome reprogramming, whereas introgressed metabolic genes could be related to reduced cell wall metabolism. Our results show that coordinated primary metabolic pathways lead to high sucrose demand and accumulation in sweet sorghum, providing us with targets for genetic improvements of carbohydrate allocation in bioenergy crops.
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Affiliation(s)
- Yin Li
- Waksman Institute of MicrobiologyRutgers, The State University of New JerseyPiscatawayNJUSA
| | - Wenqin Wang
- Waksman Institute of MicrobiologyRutgers, The State University of New JerseyPiscatawayNJUSA
- Present address:
School of Agriculture and BiologyShanghai Jiaotong UniversityShanghaiChina
| | - Yaping Feng
- Waksman Institute of MicrobiologyRutgers, The State University of New JerseyPiscatawayNJUSA
| | - Min Tu
- Waksman Institute of MicrobiologyRutgers, The State University of New JerseyPiscatawayNJUSA
| | | | | | - Joachim Messing
- Waksman Institute of MicrobiologyRutgers, The State University of New JerseyPiscatawayNJUSA
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Xiao J, Feng S, Wang X, Long K, Luo Y, Wang Y, Ma J, Tang Q, Jin L, Li X, Li M. Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables. PeerJ 2018; 6:e5186. [PMID: 30083436 PMCID: PMC6074755 DOI: 10.7717/peerj.5186] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
Edible plant-derived exosome-like nanoparticles (EPDELNs) are novel naturally occurring plant ultrastructures that are structurally similar to exosomes. Many EPDELNs have anti-inflammatory properties. MicroRNAs (miRNAs) play a critical role in mediating physiological and pathological processes in animals and plants. Although miRNAs can be selectively encapsulated in extracellular vesicles, little is known about their expression and function in EPDELNs. In this study, we isolated nanovesicles from 11 edible fruits and vegetables and subjected the corresponding EPDELN small RNA libraries to Illumina sequencing. We identified a total of 418 miRNAs-32 to 127 per species-from the 11 EPDELN samples. Target prediction and functional analyses revealed that highly expressed miRNAs were closely associated with the inflammatory response and cancer-related pathways. The 418 miRNAs could be divided into three classes according to their EPDELN distributions: 26 "frequent" miRNAs (FMs), 39 "moderately present" miRNAs (MPMs), and 353 "rare" miRNAs (RMs). FMs were represented by fewer miRNA species than RMs but had a significantly higher cumulative expression level. Taken together, our in vitro results indicate that miRNAs in EPDELNs have the potential to regulate human mRNA.
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Affiliation(s)
- Juan Xiao
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Siyuan Feng
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Xun Wang
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Keren Long
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Yi Luo
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Yuhao Wang
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Jideng Ma
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Qianzi Tang
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Long Jin
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Xuewei Li
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Mingzhou Li
- Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People’s Republic of China
- Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
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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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20
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Huang Y, Yang YB, Gao XC, Ren HT, Xiong JL, Sun XH. Genome-wide identification and characterization of microRNAs and target prediction by computational approaches in common carp. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Swapna M, Kumar S. MicroRNAs and Their Regulatory Role in Sugarcane. FRONTIERS IN PLANT SCIENCE 2017; 8:997. [PMID: 28659947 PMCID: PMC5468422 DOI: 10.3389/fpls.2017.00997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/26/2017] [Indexed: 05/31/2023]
Abstract
Sugarcane, one of the most photosynthetically efficient crops, is an important source of sugar and feedstock for green energy and co-generation. The high level of polyploidy and genomic peculiarities in this crop point towards a complex mechanism of regulation for the economically important traits like sugar content, cane yield related traits, resistance to biotic and abiotic stresses etc. The regulatory pathways for these traits comprise of a number of genes, transcription factors and different categories of RNAs like small interference RNAs (siRNAs), and Micro RNAs (miRNAs). MicroRNAs (miRNAs) are found to play an important regulatory role in many crops. As in other crops, several miRNAs have been identified in sugarcane too and these are speculated to have a role in regulating the various metabolic processes. Role of miRNAs in relation to drought tolerance has been studied to a great extent in this crop. miRNAs have been predicted to be linked to expression of other traits like disease resistance, salinity tolerance, waterlogging and axillary bud growth in sugarcane. miRNAs can have a significant role in biomass production in sugarcane, as reported in several biofuel crops. Till now, miRNAs linked to sugar accumulation have not been identified in sugarcane, but studies suggest an important role for miRNAs in sugar metabolic pathway in crops like Sorghum and switch grass. It is presumed that in sugarcane too, sugar accumulation as well as the other important metabolic pathways might be regulated to some extent by the miRNAs. The review examines the progress made in understanding the miRNA regulation in sugarcane and the extent to which miRNA mediated regulation can be utilized in sugarcane improvement.
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Mathur S, Umakanth AV, Tonapi VA, Sharma R, Sharma MK. Sweet sorghum as biofuel feedstock: recent advances and available resources. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:146. [PMID: 28603553 PMCID: PMC5465577 DOI: 10.1186/s13068-017-0834-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/08/2023]
Abstract
Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.
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Affiliation(s)
- Supriya Mathur
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - A. V. Umakanth
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - V. A. Tonapi
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Rai KM, Thu SW, Balasubramanian VK, Cobos CJ, Disasa T, Mendu V. Identification, Characterization, and Expression Analysis of Cell Wall Related Genes in Sorghum bicolor (L.) Moench, a Food, Fodder, and Biofuel Crop. FRONTIERS IN PLANT SCIENCE 2016; 7:1287. [PMID: 27630645 PMCID: PMC5006623 DOI: 10.3389/fpls.2016.01287] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 08/11/2016] [Indexed: 05/20/2023]
Abstract
Biomass based alternative fuels offer a solution to the world's ever-increasing energy demand. With the ability to produce high biomass in marginal lands with low inputs, sorghum has a great potential to meet second-generation biofuel needs. Despite the sorghum crop importance in biofuel and fodder industry, there is no comprehensive information available on the cell wall related genes and gene families (biosynthetic and modification). It is important to identify the cell wall related genes to understand the cell wall biosynthetic process as well as to facilitate biomass manipulation. Genome-wide analysis using gene family specific Hidden Markov Model of conserved domains identified 520 genes distributed among 20 gene families related to biosynthesis/modification of various cell wall polymers such as cellulose, hemicellulose, pectin, and lignin. Chromosomal localization analysis of these genes revealed that about 65% of cell wall related genes were confined to four chromosomes (Chr. 1-4). Further, 56 tandem duplication events involving 169 genes were identified in these gene families which could be associated with expansion of genes within families in sorghum. Additionally, we also identified 137 Simple Sequence Repeats related to 112 genes and target sites for 10 miRNAs in some important families such as cellulose synthase, cellulose synthase-like, and laccases, etc. To gain further insight into potential functional roles, expression analysis of these gene families was performed using publically available data sets in various tissues and under abiotic stress conditions. Expression analysis showed tissue specificity as well as differential expression under abiotic stress conditions. Overall, our study provides a comprehensive information on cell wall related genes families in sorghum which offers a valuable resource to develop strategies for altering biomass composition by plant breeding and genetic engineering approaches.
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Affiliation(s)
- Krishan M. Rai
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
| | - Sandi W. Thu
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
| | - Vimal K. Balasubramanian
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
| | - Christopher J. Cobos
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
| | - Tesfaye Disasa
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural ResearchAddis Ababa, Ethiopia
| | - Venugopal Mendu
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
- *Correspondence: Venugopal Mendu
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Geng X, Chang C, Zang X, Sun J, Li P, Guo J, Xu C. Integrative proteomic and microRNA analysis of the priming phase during rat liver regeneration. Gene 2015; 575:224-32. [PMID: 26341052 DOI: 10.1016/j.gene.2015.08.066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/22/2015] [Accepted: 08/30/2015] [Indexed: 11/20/2022]
Abstract
The partial hepatectomy (PH) model provides an effective medium for study of liver regeneration (LR). Considering that LR is regulated by microRNAs (miRNAs), investigation of the regulatory role of miRNAs is critical for revealing how regenerative processes are initiated and controlled. Using high-throughput sequencing technology, we examined miRNA expression profiles of the regenerating rat liver after PH, and found that 23 miRNAs were related to rat LR. Among them, several miRNAs were significantly altered at 2h and 6h after PH, corresponding to the priming phase of LR. Furthermore, we examined the protein profiles in the regenerating rat liver at 2h and 6h after PH by iTRAQ coupled with LC-MS/MS, and found that 278 proteins were significantly changed. Subsequently, an integrative proteomic and microRNA analysis by Ingenuity Pathway Analysis 9.0 (IPA) software showed that miR-125a, miR-143, miR-150, miR-181c, miR-182, miR-183, miR-199a, miR-429 regulated the priming phase of rat LR by modulating the expression of proteins involved in networks critical for cell apoptosis, cell survival, cell cycle, inflammatory response, metabolism, etc. Thus, our studies provide novel evidence for a functional molecular network populated by the down-regulated targets of the up-regulated miRNAs in the priming phase of rat LR.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China
| | - Cuifang Chang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Jingyan Sun
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Pengfei Li
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Jianli Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.
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