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Chaudhary V, Jangra S, Yadav NR. In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses. Front Genet 2022; 13:930113. [PMID: 35846150 PMCID: PMC9280363 DOI: 10.3389/fgene.2022.930113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cluster bean popularly known as “guar” is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8–177.3 (−kcal/mol) with an average value of 25.4 (−kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.
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Taheri-Dehkordi A, Naderi R, Martinelli F, Salami SA. Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining. PLANTA 2021; 254:117. [PMID: 34751821 DOI: 10.1007/s00425-021-03761-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
A robust workflow for the identification of miRNAs and their targets in saffron was developed. MicroRNA-mediated gene regulation in saffron is potentially involved in several biological processes, including the biosynthesis of highly valuable apocarotenoids. Saffron (Crocus sativus L.) is the most expensive spice in the world and a major source of apocarotenoids. Even though miRNAs (20-24 nt non-coding small RNAs) are important regulators of gene expression at transcriptional and post-transcriptional levels, their role in saffron has not been thoroughly investigated. As a result, a workflow for computational identification of miRNAs and their targets can be useful to uncover the regulatory networks underlying biological processes in this valuable plant. The efficiency of several assembly tools such as Trans-ABySS, Trinity, Bridger, rnaSPAdes, and EvidentialGene was evaluated based on both reference-based and reference-free metrics using transcriptome data. A reliable workflow for computational identification of miRNAs and their targets in saffron was described. The EvidentialGene was found to be the most efficient de novo transcriptome assembler for saffron as a complex triploid model, followed by the Trinity. In total, 66 miRNAs from 19 different families that target 2880 genes, including several transcription factors involved in the flowering transition, were identified. Three of the identified targets were involved in the terpenoids backbone biosynthesis. CsCCD and CsUGT genes involved in the apocarotenoids biosynthetic pathway were targeted by csa-miR156g and csa-miR156b-3p, revealing a unique post-transcriptional regulation dynamic in saffron. The identified miRNAs and their targets add to our understanding of the many biological roles of miRNAs in saffron and shed new light on the control of the apocarotenoid biosynthetic pathway in this valuable plant.
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Affiliation(s)
- Ayat Taheri-Dehkordi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | | | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
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Motamedpour L, Dalimi A, Pirestani M, Ghaffarifar F. In silico analysis and expression of a new chimeric antigen as a vaccine candidate against cutaneous leishmaniasis. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:1409-1418. [PMID: 33235698 PMCID: PMC7671421 DOI: 10.22038/ijbms.2020.45394.10561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Objective(s): Since leishmaniasis is one of the health problems in many countries, the development of preventive vaccines against it is a top priority. Peptide vaccines may be a new way to fight the Leishmania infection. In this study, a silicon method was used to predict and analyze B and T cells to produce a vaccine against cutaneous leishmaniasis. Materials and Methods: Immunodominant epitope of Leishmania were selected from four TSA, LPG3, GP63, and Lmsti1 antigens and linked together using a flexible linker (SAPGTP). The antigenic and allergenic features, 2D and 3D structures, and physicochemical features of a chimeric protein were predicted. Finally, through bioinformatics methods, the mRNA structure was predicted and was produced chemically and cloned into the pLEXY-neo2 vector. Results: Results indicated, polytope had no allergenic properties, but its antigenicity was estimated to be 0.92%. The amino acids numbers, molecular weight as well as negative and positive charge residuals were estimated 390, ~41KDa, 41, and 30, respectively. The results showed that the designed polytope has 50 post-translationally modified sites. Also, the secondary structure of the protein is composed of 25.38% alpha-helix, 12.31% extended strand, and 62.31% random coil. The results of SDS-PAGE and Western blotting revealed the recombinant protein with ~ 41 kDa. The results of Ramachandran plot showed that 96%, 2.7%, and 1.3% of amino acid residues were located in the preferred, permitted, and outlier areas, respectively. Conclusion: It is expected that the TLGL polytope will produce a cellular immune response. Therefore, the polytope could be a good candidate for an anti-leishmanial vaccine.
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Affiliation(s)
- Leila Motamedpour
- Parasitology Department, Medical Sciences Faculty, Tarbiat Modares University, Tehran, Iran
| | - Abdolhossein Dalimi
- Parasitology Department, Medical Sciences Faculty, Tarbiat Modares University, Tehran, Iran
| | - Majid Pirestani
- Parasitology Department, Medical Sciences Faculty, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Ghaffarifar
- Parasitology Department, Medical Sciences Faculty, Tarbiat Modares University, Tehran, Iran
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Tang C, Han R, Zhou Z, Yang Y, Zhu M, Xu T, Wang A, Li Z, Dong T. Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing. JOURNAL OF PLANT PHYSIOLOGY 2020; 251:153224. [PMID: 32634748 DOI: 10.1016/j.jplph.2020.153224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 05/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.
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Affiliation(s)
- Cheng Tang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Rongpeng Han
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zhengkun Zhou
- College of Health Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Yiyu Yang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Aimin Wang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
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Ayachit G, Pandya H, Das J. miRDetect: A combinatorial approach for automated detection of novel miRNA precursors from plant EST data using homology and Random Forest classification. Genomics 2020; 112:3201-3206. [PMID: 32380232 DOI: 10.1016/j.ygeno.2020.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/25/2020] [Accepted: 05/02/2020] [Indexed: 01/23/2023]
Abstract
Identification of microRNAs from plants is a crucial step for understanding the mechanisms of pathways and regulation of genes. A number of tools have been developed for the detection of microRNAs from small RNA-seq data. However, there is a lack of pipeline for detection of miRNA from EST dataset even when a huge resource is publicly available and the method is known. Here we present miRDetect, a python implementation to detect novel miRNA precursors from plant EST data using homology and machine learning approach. 10-fold cross validation was applied to choose best classifier based on ROC, accuracy, MCC and F1-scores using 112 features. miRDetect achieved a classification accuracy of 93.35% on a Random Forest classifier and outperformed other precursor detection tools in terms of performance. The miRDetect pipeline aids in identifying novel plant precursors using a mixed approach and will be helpful to researchers with less informatics background.
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Affiliation(s)
- Garima Ayachit
- Department of Botany, Bioinformatics and Climate Change, Gujarat University, Ahmedabad, India
| | - Himanshu Pandya
- Department of Botany, Bioinformatics and Climate Change, Gujarat University, Ahmedabad, India.
| | - Jayashankar Das
- Centre for Genomics & Biomedical Informatics, IMS and SUM Hospital, Siksha "O" Anusandhan University (Deemed to be), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003, India.
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Mishra R, Mohapatra R, Mahanty B, Joshi RK. Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs). Bioinformation 2019; 15:907-917. [PMID: 32256010 PMCID: PMC7088424 DOI: 10.6026/97320630015907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 01/31/2023] Open
Abstract
MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. We report 14 potential miRNAs belonging to 13 different families (miR162, miR168, miR172c, miR172e, miR398, miR400, miR414, miR1134, miR1223, miR6219, miR7725, miR8570, miR8703 and miR8752). BLAST analysis using psRNATarget server predicted 39 potential targets for the identified miRNAs majority of which were transcription factors implicated in plant growth, development, hormone signaling and stress responses. These data forms the basis for further analysis and verification towards understanding the miRNA mediated regulatory mechanism in Allium cepa.
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Affiliation(s)
- Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Rupesh Mohapatra
- Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751030, Odisha, India
| | - Bijayalaxmi Mahanty
- Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India
| | - Raj Kumar Joshi
- Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India
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Garbus I, Selva JP, Pasten MC, Bellido AM, Carballo J, Albertini E, Echenique V. Characterization and discovery of miRNA and miRNA targets from apomictic and sexual genotypes of Eragrostis curvula. BMC Genomics 2019; 20:839. [PMID: 31718556 PMCID: PMC6852985 DOI: 10.1186/s12864-019-6169-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/02/2019] [Indexed: 01/01/2023] Open
Abstract
Background Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass found in semi-arid regions that is well adapted for growth in sandy soils and drought conditions. E. curvula constitutes a polymorphic complex that includes cytotypes with different ploidy levels (from 2x to 8x), where most polyploids are facultative apomicts, although both sexual reproduction and full apomixis have been reported in this species. Apomixis is thought to be associated with silencing of the sexual pathway, which would involve epigenetic mechanisms. However, a correlation between small RNAs and apomixis has not yet been conclusively established. Results Aiming to contribute to the elucidation of their role in the expression of apomixis, we constructed small RNA libraries from sexual and apomictic E. curvula genotypes via Illumina technology, characterized the small RNA populations, and conducted differential expression analysis by comparing these small RNAs with the E. curvula reference transcriptome. We found that the expression of two genes is repressed in the sexual genotype, which is associated with specific microRNA expression. Conclusion Our results support the hypothesis that in E. curvula the expression of apomixis leads to sexual repression.
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Affiliation(s)
- Ingrid Garbus
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina.
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - María Cielo Pasten
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - Andrés Martín Bellido
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - José Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
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Natarajan B, Kondhare KR, Hannapel DJ, Banerjee AK. Mobile RNAs and proteins: Prospects in storage organ development of tuber and root crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:73-81. [PMID: 31084881 DOI: 10.1016/j.plantsci.2019.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 05/04/2023]
Abstract
Storage tuber and root crops make up a significant portion of the world's subsistence food supply. Because of their importance in food security, yield enhancement has become a priority. A major focus has been to understand the biology of belowground storage organ development. Considerable insights have been gained studying tuber development in potato. We now know that two mobile signals, a full-length mRNA, StBEL5, and a protein, StSP6A, play pivotal roles in regulating tuber development. Under favorable conditions, these signals move from leaves to a belowground modified stem (stolon) and regulate genes that activate tuberization. Overexpression of StBEL5 or StSP6A increases tuber yield even under non-inductive conditions. The mRNAs of two close homologs of StBEL5, StBEL11 and StBEL29, are also known to be mobile but act as repressors of tuberization. Polypyrimidine tract-binding proteins (PTBs) are RNA-binding proteins that facilitate the movement of these mRNAs. Considering their role in tuberization, it is possible that these mobile signals play a major role in storage root development as well. In this review, we explore the presence of these signals and their relevance in the development and yield potential of several important storage root crops.
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Affiliation(s)
- Bhavani Natarajan
- Indian Institute of Science Education and Research (IISER), Biology Division, Pune, 411008, India
| | - Kirtikumar R Kondhare
- Indian Institute of Science Education and Research (IISER), Biology Division, Pune, 411008, India
| | - David J Hannapel
- Plant Biology Major, 253 Horticulture Hall, Iowa State University (ISU), Ames, IA, United States
| | - Anjan K Banerjee
- Indian Institute of Science Education and Research (IISER), Biology Division, Pune, 411008, India.
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He L, Tang R, Shi X, Wang W, Cao Q, Liu X, Wang T, Sun Y, Zhang H, Li R, Jia X. Uncovering anthocyanin biosynthesis related microRNAs and their target genes by small RNA and degradome sequencing in tuberous roots of sweetpotato. BMC PLANT BIOLOGY 2019; 19:232. [PMID: 31159725 PMCID: PMC6547535 DOI: 10.1186/s12870-019-1790-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/18/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known. RESULTS In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target ibSPL in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in Arabidopsis. Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of SPL and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic Arabidopsis plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed. CONCLUSIONS The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.
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Affiliation(s)
- Liheng He
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Ruimin Tang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Xiaowen Shi
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Wenbing Wang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Xiayu Liu
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Ting Wang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Yan Sun
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Hongmei Zhang
- Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou, China
| | - Runzhi Li
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China.
| | - Xiaoyun Jia
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China.
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In silico analysis and expression of a novel chimeric antigen as a vaccine candidate against Toxoplasma gondii. Microb Pathog 2019; 132:275-281. [PMID: 31078709 DOI: 10.1016/j.micpath.2019.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
Abstract
Toxoplasma gondii is an obligate intracellular parasite that causes one of the most common parasitic infections in humans and other warm-blooded animals. Currently, there are no effective treatments for inhibiting the formation of chronic tissue cysts in infected hosts. Thus, the development of a vaccine to protect against toxoplasmosis is an attractive option for avoiding infection. The aim of this study was to design an epitope-based vaccine for T. gondii. In the present study, an in silico approach was used to predict and analyze B-cell and T-cell epitopes and the transmembrane domain of proteins SAG1, MIC3, and ROP8. We also predicted the antigenicity, allergenicity, secondary and tertiary structures, and physicochemical characteristics of a chimeric protein. Next, codon optimization and mRNA structure prediction were conducted using bioinformatics tools, and the designed construct was chemically synthesized and cloned into the pET28a vector. SAG1 (amino acid positions 85-235), MIC3 (30-180), and ROP8 (85-185) were found to have several strong immunodominant epitopes that were joined with a rigid linker A(EAAAK)2A. Although the resultant protein called MRS (MIC3, ROP8, and SAG1) did not turn out to be an allergen, its antigenicity was estimated to be 0.7983. Additionally, MRS was selected as the best vaccine candidate on the basis of its secondary and tertiary structures. The number of amino acids, molecular weight, and numbers of negatively and positively charged residues of MRS were 427 and 45,661.31 Da, 45, and 50, respectively. ΔG of the best-predicted structure was -413.0 kcal/mol, and the first nucleotides at the 5' end did not form a stable hairpin or pseudoknot. Finally, successful expression and verification of the expressed MRS protein showed that in silico analysis was almost accurate. This vaccine candidate selected by in silico tools should be validated in experimental studies.
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Curcio JSD, Batista MP, Paccez JD, Novaes E, Soares CMDA. In silico characterization of microRNAs-like sequences in the genome of Paracoccidioides brasiliensis. Genet Mol Biol 2019; 42:95-107. [PMID: 30776047 PMCID: PMC6428129 DOI: 10.1590/1678-4685-gmb-2018-0014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/22/2018] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells have different mechanisms of post-transcriptional regulation.
Among these mechanisms, microRNAs promote regulation of targets by cleavage or
degradation of the mRNA. Fungi of the Paracoccidioides complex
are the etiological agents of the main systemic mycosis of Latin America. These
fungi present a plasticity to adapt and survive in different conditions, and the
presence of microRNAs-like molecules could be part of the mechanisms that
provide such plasticity. MicroRNAs produced by the host influence the
progression of this mycosis in the lungs besides regulating targets involved in
apoptosis in macrophage, activation of T and B cells and the production of
cytokines. Therefore, this work analyzed the presence of regions in the genome
of this fungus with a potential to encode microRNAs-like molecules. Here we show
by analysis of sequence similarity the presence of 18 regions, putatively coding
for microRNAs-like molecules in the Paracoccidioides
brasiliensis genome. We also described the conservation of dicer
and argonaut proteins and the cognate transcripts induced in the yeast parasitic
phase. This work represents a starting point for the analysis of the presence of
those molecules in the morphological stages of the fungus and their role in
fungal development.
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Affiliation(s)
- Juliana S de Curcio
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brazil
| | - Mariana P Batista
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil
| | - Juliano D Paccez
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Minas Gerais, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil
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Jike W, Sablok G, Bertorelle G, Li M, Varotto C. In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L. Sci Rep 2018; 8:16667. [PMID: 30420632 PMCID: PMC6232160 DOI: 10.1038/s41598-018-34982-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5′-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.
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Affiliation(s)
- Wuhe Jike
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.,Università degli Studi di Ferrara, Dipartimento di Scienze della Vita e Biotecnologie, Ferrara, Italy
| | - Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.,Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Giorgio Bertorelle
- Università degli Studi di Ferrara, Dipartimento di Scienze della Vita e Biotecnologie, Ferrara, Italy
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
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13
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Elevated carbon dioxide and drought modulate physiology and storage-root development in sweet potato by regulating microRNAs. Funct Integr Genomics 2018; 19:171-190. [PMID: 30244303 DOI: 10.1007/s10142-018-0635-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
Abstract
Elevated CO2 along with drought is a serious global threat to crop productivity. Therefore, understanding the molecular mechanisms plants use to protect these stresses is the key for plant growth and development. In this study, we mimicked natural stress conditions under a controlled Soil-Plant-Atmosphere-Research (SPAR) system and provided the evidence for how miRNAs regulate target genes under elevated CO2 and drought conditions. Significant physiological and biomass data supported the effective utilization of source-sink (leaf to root) under elevated CO2. Additionally, elevated CO2 partially rescued the effect of drought on total biomass. We identified both known and novel miRNAs differentially expressed during drought, CO2, and combined stress, along with putative targets. A total of 32 conserved miRNAs belonged to 23 miRNA families, and 25 novel miRNAs were identified by deep sequencing. Using the existing sweet potato genome database and stringent analyses, a total of 42 and 22 potential target genes were predicted for the conserved and novel miRNAs, respectively. These target genes are involved in drought response, hormone signaling, photosynthesis, carbon fixation, sucrose and starch metabolism, etc. Gene ontology and KEGG ontology functional enrichment revealed that these miRNAs might target transcription factors (MYB, TCP, NAC), hormone signaling regulators (ARF, AP2/ERF), cold and drought factors (corA), carbon metabolism (ATP synthase, fructose-1,6-bisphosphate), and photosynthesis (photosystem I and II complex units). Our study is the first report identifying targets of miRNAs under elevated CO2 levels and could support the molecular mechanisms under elevated CO2 in sweet potato and other crops in the future.
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14
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Yang X, Wang HL, Liang HW, Liang L, Wen DY, Zhang R, Chen G, Wei DM. Clinical significance of microRNA-449a in hepatocellular carcinoma with microarray data mining together with initial bioinformatics analysis. Exp Ther Med 2018; 15:3247-3258. [PMID: 29545842 PMCID: PMC5841030 DOI: 10.3892/etm.2018.5836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/03/2018] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence has demonstrated that microRNA (miR)-449a expression is reduced in various types of tumors and that it serves as a tumor suppressor. However, the molecular mechanism of miR-449a in hepatocellular carcinoma (HCC) has not been thoroughly elucidated and is disputed. Therefore, the aim of the present work was to systematically review the current literature and to utilize the public Gene Expression Omnibus database to determine the role of miR-449a and its significance in HCC. A total of eight original papers and seven microarrays were included in the present study. Based on the evidence, miR-449a was reduced in HCC. miR-449a is likely involved in various signaling pathways and is targeted to multiple mRNA as part of its function in HCC. In addition, a preliminary bioinformatic analysis was conducted for miR-449a to investigate the novel potential pathways that miR-449a may participate in regarding HCC.
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Affiliation(s)
- Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Han-Lin Wang
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hai-Wei Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Liang Liang
- Department of General Surgery, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530007, P.R. China
| | - Dong-Yue Wen
- Department of Ultrasonography, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Rui Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dan-Ming Wei
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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15
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Mondal TK, Panda AK, Rawal HC, Sharma TR. Discovery of microRNA-target modules of African rice (Oryza glaberrima) under salinity stress. Sci Rep 2018; 8:570. [PMID: 29330361 PMCID: PMC5766505 DOI: 10.1038/s41598-017-18206-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/22/2017] [Indexed: 11/09/2022] Open
Abstract
Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs. We also used smallRNAseq data of NCBI of O. glaberrima to discover additional 246 known miRNAs. Totally, 29 known and 32 novel miRNAs were differentially regulated under salinity stress. Gene ontology and KEGG analysis indicated several targets were involved in vital biological pathways of salinity stress tolerance. Expression of selected miRNAs as indicated by Illumina data were found to be coherent with real time-PCR analysis. However, target gene expression was inversely correlated with their corresponding miRNAs. Finally based upon present results as well as existing knowledge of literature, we proposed the miRNA-target modules that were induced by salinity stress. Therefore, the present findings provide valuable information about miRNA-target networks in salinity adaption of O. glaberrima.
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Affiliation(s)
- Tapan Kumar Mondal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India.
| | - Alok Kumar Panda
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India
| | - Hukam C Rawal
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, L.B.S. Building, IARI Campus, New Delhi, 110012, India
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16
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Srivastava S, Sharma A. Study of microRNA mediated gene regulation in Striga hermonthica through in-silico approach. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature. Sci Rep 2017; 7:16578. [PMID: 29185497 PMCID: PMC5707365 DOI: 10.1038/s41598-017-16871-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/06/2017] [Indexed: 01/31/2023] Open
Abstract
Sweetpotato (Impomoea batatas L.) is a globally important economic food crop with a potential of becoming a bioenergy and pharmaceutical crop. Thus, studying the molecular mechanism of tuberous root development and storage is very important. However, not too much progress has been made in this field. In this study, we employed the next generation high-throughput deep sequencing technology to sequence all small RNAs and degradome of sweetpotato for systematically investigating sweetpotato response to chilling stress during storage. A total of 190 known microRNAs (miRNAs) and 191 novel miRNAs were identified, and 428 transcripts were targeted by 184 identified miRNAs. More importantly, we identified 26 miRNAs differentially expressed between chilling stress and control conditions. The expression of these miRNAs and their targets was also confirmed by qRT-PCR. Integrated analysis of small RNAs and degradome sequencing reveals that miRNA-mediated SA signaling, ABA-dependent, and ROS response pathways are involved in sweetpotato root response to chilling stress during storage.
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18
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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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19
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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20
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Srivastava S, Singh N, Srivastava G, Sharma A. miRNA mediated gene regulatory network analysis of Cichorium intybus (chicory). ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2016.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Ferdous J, Sanchez-Ferrero JC, Langridge P, Milne L, Chowdhury J, Brien C, Tricker PJ. Differential expression of microRNAs and potential targets under drought stress in barley. PLANT, CELL & ENVIRONMENT 2017; 40:11-24. [PMID: 27155357 DOI: 10.1111/pce.12764] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 04/22/2016] [Accepted: 04/24/2016] [Indexed: 05/04/2023]
Abstract
Drought is a crucial environmental constraint limiting crop production in many parts of the world. microRNA (miRNA) based gene regulation has been shown to act in several pathways, including crop response to drought stress. Sequence based profiling and computational analysis have revealed hundreds of miRNAs and their potential targets in different plant species under various stress conditions, but few have been biologically verified. In this study, 11 candidate miRNAs were tested for their expression profiles in barley. Differences in accumulation of only four miRNAs (Ath-miR169b, Osa-miR1432, Hv-miRx5 and Hv-miR166b/c) were observed between drought-treated and well-watered barley in four genotypes. miRNA targets were predicted using degradome analysis of two, different genotypes, and genotype-specific target cleavage was observed. Inverse correlation of mature miRNA accumulation with miRNA target transcripts was also genotype dependent under drought treatment. Drought-responsive miRNAs accumulated predominantly in mesophyll tissues. Our results demonstrate genotype-specific miRNA regulation under drought stress and evidence for their role in mediating expression of target genes for abiotic stress response in barley.
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Affiliation(s)
- Jannatul Ferdous
- Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Juan Carlos Sanchez-Ferrero
- Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, SA, 5064, Australia
- Phenomics and Bioinformatics Research Centre, School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Linda Milne
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Jamil Chowdhury
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
- ARC Centre of Excellence in Plant Cell Walls, PMB1, Glen Osmond, SA, 5064, Australia
| | - Chris Brien
- Phenomics and Bioinformatics Research Centre, School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Penny J Tricker
- Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
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22
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Kim HS, Park SC, Ji CY, Park S, Jeong JC, Lee HS, Kwak SS. Molecular characterization of biotic and abiotic stress-responsive MAP kinase genes, IbMPK3 and IbMPK6, in sweetpotato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:37-48. [PMID: 27404133 DOI: 10.1016/j.plaphy.2016.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 05/18/2023]
Abstract
Plants are continually exposed to numerous environmental stresses. To decrease damage caused by these potentially detrimental factors, various stress-related signaling cascades are activated in plants. One such stress-responsive signaling pathway, the mitogen-activated protein kinase (MAPK) module, plays a critical role in diverse plant stress responses. Here, we functionally characterized biotic and abiotic stress-responsive MAPK genes, IbMPK3 and IbMPK6, from sweetpotato. IbMPK3/6 contain totally 11 MAPK conserved subdomains and the phosphorylating motif TEY. Bacterially expressed IbMPK3/6 could be autophosphorylated in vitro, and these proteins phosphorylated universal kinase substrate, such as myelin basic protein. IbMPK3/6 transcripts were expressed in leaf, stem, and root of sweetpotato cultivars with storage roots of various colors. IbMPK3 and IbMPK6 were induced by various biotic/abiotic stress treatments. Furthermore, the kinase activity of IbMPK3/6 was induced during early NaCl, SA, H2O2, and ABA treatment. IbMPK3/6 were predominantly localized to the nucleus. To determine the biological functions of IbMPK3/6, we transiently expressed the IbMPK genes in tobacco (Nicotiana benthamiana) leaves, which resulted in enhanced tolerance to bacterial pathogen and increased expression of pathogenesis-related (PR) genes. These data demonstrate that IbMPK3 and IbMPK6 play significant roles in plant responses to environmental stress.
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Affiliation(s)
- Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea
| | - Sung-Chul Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea
| | - Chang Yoon Ji
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, Republic of Korea
| | - Seyeon Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, Republic of Korea
| | - Jae Cheol Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, Republic of Korea
| | - Haeng-Soon Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, Republic of Korea.
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23
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Qu B, Qiu Y, Zhen Z, Zhao F, Wang C, Cui Y, Li Q, Zhang L. Computational identification and characterization of novel microRNA in the mammary gland of dairy goat (Capra hircus). J Genet 2016; 95:625-37. [PMID: 27659334 DOI: 10.1007/s12041-016-0674-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many studies have indicated that microRNAs (miRNAs) influence the development of the mammary gland by posttranscriptionally affecting their target genes. The objective of this research was to identify novel miRNAs in the mammary gland of dairy goats with a bioinformatics approach that was based on expressed sequence tag (EST) and genome survey sequence (GSS) analyses. We applied all known major mammals, miRNAs to search against the goat EST and GSS databases for the first time to identify new miRNAs. We, then, validated these newly predicted miRNAs with stem-loop reverse transcription followed by a SYBR Green polymerase chain reaction assay. Finally, 29 mature miRNAs were identified and verified, and of these, 14 were grouped into 13 families based on seed sequence identity and 85 potential target genes of newly verified miRNAs were subsequently predicted, most of which seemed to encode the proteins participating in regulation of metabolism, signal transduction, growth and development. The predicting accuracy of the new miRNAs was 70.37%, which confirmed that the methods used in this study were efficient and reliable. Detailed analyses of the sequence characteristics of the novel miRNAs of the goat mammary gland were performed. In conclusion, these results provide a reference for further identification of miRNAs in animals without a complete genome and thus improve the understanding of miRNAs in the caprine mammary gland.
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Affiliation(s)
- Bo Qu
- Faculty of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of
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24
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Mondal TK, Ganie SA, Debnath AB. Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice. PLoS One 2015; 10:e0140675. [PMID: 26506249 PMCID: PMC4623511 DOI: 10.1371/journal.pone.0140675] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/29/2015] [Indexed: 01/25/2023] Open
Abstract
Oryza coarctata, a halophyte and wild relative of rice, is grown normally in saline water. MicroRNAs (miRNAs) are non-coding RNAs that play pivotal roles in every domain of life including stress response. There are very few reports on the discovery of salt-responsive miRNAs from halophytes. In this study, two small RNA libraries, one each from the control and salt-treated (450 mM NaCl for 24 h) leaves of O. coarctata were sequenced, which yielded 338 known and 95 novel miRNAs. Additionally, we used publicly available transcriptomics data of O. coarctata which led to the discovery of additional 48 conserved miRNAs along with their pre-miRNA sequences through in silico analysis. In total, 36 known and 7 novel miRNAs were up-regulated whereas, 12 known and 7 novel miRNAs were down-regulated under salinity stress. Further, 233 and 154 target genes were predicted for 48 known and 14 novel differentially regulated miRNAs respectively. These targets with the help of gene ontology analysis were found to be involved in several important biological processes that could be involved in salinity tolerance. Relative expression trends of majority of the miRNAs as detected by real time-PCR as well as predicted by Illumina sequencing were found to be coherent. Additionally, expression of most of the target genes was negatively correlated with their corresponding miRNAs. Thus, the present study provides an account of miRNA-target networking that is involved in salinity adaption of O. coarctata.
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Affiliation(s)
- Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi-4, 110012, India
| | - Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi-4, 110012, India
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi-4, 110012, India
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25
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Sun Y, Qiu Y, Zhang X, Chen X, Shen D, Wang H, Li X. Genome-wide identification of microRNAs associated with taproot development in radish (Raphanus sativus L.). Gene 2015; 569:118-26. [PMID: 26013046 DOI: 10.1016/j.gene.2015.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/07/2015] [Accepted: 05/17/2015] [Indexed: 11/29/2022]
Abstract
MicroRNAs (miRNAs) are small, endogenous, non-coding RNAs that play vital regulatory roles in plant growth and development. To identify the miRNAs associated with taproot development at the whole genome level, we sequenced five RNA libraries constructed from radish taproots at different developmental stages and generated a total of 148M clean reads. Using an integrative bioinformatics analysis, 494 known miRNAs belonging to 434 families and 220 putative novel miRNAs were identified. Combining the differential expression analysis and target prediction, we found that 77 miRNAs were potentially associated with taproot development. Target transcripts generated significant GO terms relating to cell proliferation, root development and hormone-mediated signaling. The KEGG analyses revealed that plant hormone signal transduction, zeatin biosynthesis, biosynthesis of secondary metabolites, cell cycle, MAPK signaling and p53 signaling were closely associated with taproot development. These findings will provide valuable information for further functional verification of miRNAs and their targets in radish taproot development.
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Affiliation(s)
- Yuyan Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China
| | - Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China
| | - Xiaohua Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China
| | - Di Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
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26
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Li X, Hou Y, Zhang L, Zhang W, Quan C, Cui Y, Bian S. Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum). PLANT SIGNALING & BEHAVIOR 2014; 9:e29462. [PMID: 25763692 PMCID: PMC4203583 DOI: 10.4161/psb.29462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous, approximately 21nt in length, non-coding RNA, which mediate the expression of target genes primarily at post-transcriptional levels. miRNAs play critical roles in almost all plant cellular and metabolic processes. Although numerous miRNAs have been identified in the plant kingdom, the miRNAs in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNAs and their targets in blueberry. By conducting an EST-based comparative genomics approach, 9 potential vco-miRNAs were discovered from 22,402 blueberry ESTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNA and its target transcript, 34 target ESTs from blueberry and 70 targets from other species were identified for the vco-miRNAs. The targets were found to be involved in transcription, RNA splicing and binding, DNA duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNAs.
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Affiliation(s)
- Xuyan Li
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yanming Hou
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Li Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Wenhao Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Chen Quan
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Biology; Western University; London, ON Canada
| | - Shaomin Bian
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
- Correspondence to: Shaomin Bian,
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