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Chandan K, Gupta M, Ahmad A, Sarwat M. P-type calcium ATPases play important roles in biotic and abiotic stress signaling. PLANTA 2024; 260:37. [PMID: 38922354 DOI: 10.1007/s00425-024-04462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024]
Abstract
MAIN CONCLUSION Knowledge of Ca2+-ATPases is imperative for improving crop quality/ food security, highly threatened due to global warming. Ca2+-ATPases modulates calcium, essential for stress signaling and modulating growth, development, and immune activities. Calcium is considered a versatile secondary messenger and essential for short- and long-term responses to biotic and abiotic stresses in plants. Coordinated transport activities from both calcium influx and efflux channels are required to generate cellular calcium signals. Various extracellular stimuli cause an induction in cytosolic calcium levels. To cope with such stresses, it is important to maintain intracellular Ca2+ levels. Plants need to evolve efficient efflux mechanisms to maintain Ca2+ ion homeostasis. Plant Ca2+-ATPases are members of the P-type ATPase superfamily and localized in the plasma membrane and endoplasmic reticulum (ER). They are required for various cellular processes, including plant growth, development, calcium signaling, and even retorts to environmental stress. These ATPases play an essential role in Ca2+ homeostasis and are actively involved in Ca2+ transport. Plant Ca2+-ATPases are categorized into two major classes: type IIA and type IIB. Although these two classes of ATPases share similarities in protein sequence, they differ in their structure, cellular localization, and sensitivity to inhibitors. Due to the emerging role of Ca2+-ATPase in abiotic and biotic plant stress, members of this family may help promote agricultural improvement under stress conditions. This review provides a comprehensive overview of P-type Ca2+-ATPase, and their role in Ca2+ transport, stress signaling, and cellular homeostasis focusing on their classification, evolution, ion specificities, and catalytic mechanisms. It also describes the main aspects of the role of Ca2+-ATPase in transducing signals during plant biotic and abiotic stress responses and its role in plant development and physiology.
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Affiliation(s)
- Kumari Chandan
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Meenakshi Gupta
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201313, India.
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2
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Banu MSA, Huda KMK, Harun-Ur-Rashid M, Parveen S, Shahinul Islam SM, Tuteja N. Phenotypic and microarray analysis reveals salinity stress-induced oxidative tolerance in transgenic rice expressing a DEAD-box RNA helicase, OsDB10. PLANT MOLECULAR BIOLOGY 2023; 113:19-32. [PMID: 37523054 DOI: 10.1007/s11103-023-01372-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023]
Abstract
Helicases are the motor proteins not only involved in the process of mRNA metabolism but also played a significant role in providing abiotic stresses tolerance. In this study, a DEAD-box RNA helicase OsDB10 was cloned and functionally characterized. The transcript levels of OsDB10 were increased both in shoot and root upon salt, heat, cold, and ABA application and was more prominent in shoot compared to root. Genomic integration of OsDB10 in transgenic rice was confirmed by PCR, Southern blot and qRT-PCR analysis. The transgenic plants showed quicker seed germination, reduced necrosis, higher chlorophyll, more survival rate, better seedling growth, and produced more grain yield under salinity stress. Furthermore, transgenic lines also accumulated less Na+ and high K+ ions and salinity tolerance of the transgenic were also assayed by measuring different bio-physiological indices. Moreover, the OsDB10 transgenic plants showed enhanced tolerance to salinity-induced oxidative stress by scavenging ROS and increased activity of antioxidants enzymes. Microarray analysis showed upregulation of transcriptional regulations and metabolic reprogramming as OsDB10 overexpression modulates the expression of many other genes. Altogether, our results confirmed that OsDB10 is a functional DEAD-box RNA helicase and played vital roles in plant defence response against salinity stress.
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Affiliation(s)
- Mst Sufara Akhter Banu
- Bangladesh Agricultural Research Council (BARC), Dhaka, 1215, Bangladesh
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Kazi Md Kamrul Huda
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh.
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India.
| | - Md Harun-Ur-Rashid
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - Shahanaz Parveen
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - S M Shahinul Islam
- Institute of Biological Sciences, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
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Banu MSA, Huda KMK, Harun-Ur-Rashid M, Parveen S, Tuteja N. A DEAD box helicase Psp68 positively regulates salt stress responses in marker-free transgenic rice plants. Transgenic Res 2023; 32:293-304. [PMID: 37247124 DOI: 10.1007/s11248-023-00353-x] [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: 03/15/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023]
Abstract
Helicases are the motor proteins not only involved in transcriptional and post-transcription process but also provide abiotic stress tolerance in many crops. The p68, belong to the SF2 (DEAD-box helicase) family proteins and overexpression of Psp68 providing enhanced tolerance to transgenic rice plants. In this study, salinity tolerant marker-free transgenic rice has been developed by overexpressing Psp68 gene and phenotypically characterized. The Psp68 overexpressing marker-free transgenic rice plants were initially screened in the rooting medium containing salt stress and 20% polyethylene glycol (PEG). Stable integration and overexpression of Psp68 in marker-free transgenic lines were confirmed by molecular analyses including PCR, southern, western blot, and qRT-PCR analyses. The marker-free transgenic lines showed enhanced tolerance to salinity stress as displayed by early seed germination, higher chlorophyll content, reduced necrosis, more survival rate, improved seedling growth and more grain yield per plant. Furthermore, Psp68 overexpressing marker-free transgenics also accumulated less Na+ and higher K+ ions in the presence of salinity stress. Phenotypic analyses also revealed that marker-free transgenic rice lines efficiently scavenge ROS-mediated damages as displayed by lower H2O2 and malondialdehyde content, delayed electrolyte leakage, higher photosynthetic efficiency, membrane stability, proline content and enhanced activities of antioxidants enzymes. Overall, our results confirmed that Psp68 overexpression confers salinity stress tolerance in marker-free transgenics, hence the technique could be utilized to develop genetically modified crops without any biosafety issues.
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Affiliation(s)
- Mst Sufara Akhter Banu
- Bangladesh Agricultural Research Council (BARC), Dhaka, 1215, Bangladesh
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Kazi Md Kamrul Huda
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh.
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India.
| | - Md Harun-Ur-Rashid
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - Shahanaz Parveen
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
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4
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Identification of microRNA and analysis of target genes in Panax ginseng. CHINESE HERBAL MEDICINES 2023; 15:69-75. [PMID: 36875435 PMCID: PMC9975625 DOI: 10.1016/j.chmed.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/05/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Objective Ginsenosides, polysaccharides and phenols, the main active ingredients in Panax ginseng, are not different significantly in content between 3 and 5 years old of ginsengs called Yuan ginseng and more than ten years old ones called Shizhu ginseng. The responsible chemical compounds cannot fully explain difference in efficacy between them. According to reports in Lonicerae Japonicae Flos (Jinyinhua in Chinese) and Glycyrrhizae Radix et Rhizoma (Gancao in Chinese), microRNA may play a role in efficacy, so we identified microRNAs in P. ginseng at the different growth years and analyzed their target genes. Methods Using high-throughput sequencing, the RNA-Seq, small RNA-Seq and degradome databases of P. ginseng were constructed. The differentially expressed microRNAs was identified by qRT-PCR. Results A total of 63,875 unigenes and 24,154,579 small RNA clean reads were obtained from the roots of P. ginseng. From these small RNAs, 71 miRNA families were identified by bioinformatics target prediction software, including 34 conserved miRNAs, 37 non-conserved miRNA families, as well as 179 target genes of 17 known miRNAs. Through degradome sequencing and computation, we finally verified 13 targets of eight miRNAs involved in transcription, energy metabolism, biological stress and disease resistance, suggesting the significance of miRNAs in the development of P. ginseng. Consistently, major miRNA targets exhibited tissue specificity and complexity in expression patterns. Conclusion Differential expression microRNAs were found in different growth years of ginsengs (Shizhu ginseng and Yuan ginseng), and the regulatory roles and functional annotations of miRNA targets in P. ginseng need further investigation.
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Tomato MicroRNAs and Their Functions. Int J Mol Sci 2022; 23:ijms231911979. [PMID: 36233279 PMCID: PMC9569937 DOI: 10.3390/ijms231911979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.
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6
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Qi N, Wang N, Hou X, Li Y, Liao W. Involvement of Calcium and Calmodulin in NO-Alleviated Salt Stress in Tomato Seedlings. PLANTS 2022; 11:plants11192479. [PMID: 36235348 PMCID: PMC9571744 DOI: 10.3390/plants11192479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022]
Abstract
Salt stress is an adverse impact on the growth and development of plants, leading to yield losses in crops. It has been suggested that nitric oxide (NO) and calcium ion (Ca2+) act as critical signals in regulating plant growth. However, their crosstalk remains unclear under stress condition. In this study, we demonstrate that NO and Ca2+ play positive roles in the growth of tomato (Lycopersicum esculentum) seedlings under salt stress. Our data show that Ca2+ channel inhibitor lanthanum chloride (LaCl3), Ca2+ chelator ethylene glycol-bis (2-aminoethylether)-N,N,N,N-tetraacetic acid (EGTA), or calmodulin (CaM) antagonist N-(6-aminohexyl)-5-chloro-1-naphthalenesulfona-mide hydrochloride (W-7) significantly reversed the effect of NO-promoted the growth of tomato seedlings under salt stress. We further show that NO and Ca2+ significantly decreased reactive oxygen accumulation, increased proline content, and increased the activity of antioxidant enzymes, as well as increased expression of antioxidant enzymes related genes. However, LaCl3, EGTA, and W-7 prevented the positive roles of NO. In addition, the activity of downstream target enzymes related to Ca2+/CaM was increased by NO under salt stress, while LaCl3, EGTA, and W-7 reversed this enhancement. Taken together, these results demonstrate that Ca2+/CaM might be involved in NO-alleviate salt stress.
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Affiliation(s)
| | | | | | | | - Weibiao Liao
- Correspondence: ; Tel.: +86-138-9328-7942; Fax: +86-931-7632155
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7
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Attri K, Zhang Z, Singh A, Sharrock RA, Xie Z. Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants. THE NEW PHYTOLOGIST 2022; 235:1082-1095. [PMID: 35485957 PMCID: PMC9322595 DOI: 10.1111/nph.18185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
MicroRNA (miRNA)-directed posttranscriptional gene silencing (miR-PTGS) is an integral component of gene regulatory networks governing plant development and responses to the environment. The sequence homology between Sly-miR4376, a miRNA common to Solanaceae and reported to target autoinhibited Ca2+ -ATPase 10 (ACA10) messenger RNA (mRNA) in tomato, and Arabidopsis miR391 (Ath-miR391), previously annotated as a nonconserved member of the deeply conserved miR390 family, has prompted us to revisit the function of Ath-miR391, as well as its regulatory conservation. A combination of genetic, molecular, and bioinformatic analyses revealed a hidden conservation for miR-PTGS of ACA10 homologs in spermatophytes. We found that the Arabidopsis ACA10 mRNA undergoes miR391-directed cleavage in vivo. Furthermore, transgenic overexpression of miR391 recapitulated the compact inflorescence (cif) phenotypes characteristic of ACA10 loss-of-function mutants, due to miR391-directed PTGS of ACA10. Significantly, comprehensive data mining revealed robust evidence for widespread PTGS of ACA10 homologs directed by a superfamily of related miRNAs sharing a conserved sequence core. Intriguingly, the ACA-targeting miRNAs in Poaceae also direct PTGS for calmodulin-like proteins which are putative Ca2+ sensors. The PTGS of ACA10 homologs is therefore directed by a miRNA superfamily that is of ancient origin and has undergone rapid sequence diversification associated with functional innovation.
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Affiliation(s)
- Komal Attri
- Department of Biological SciencesTexas Tech UniversityLubbockTX79409USA
| | - Zijie Zhang
- Department of Biological SciencesTexas Tech UniversityLubbockTX79409USA
| | - Atinder Singh
- Department of Biological SciencesTexas Tech UniversityLubbockTX79409USA
| | - Robert A. Sharrock
- Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanMT59717USA
| | - Zhixin Xie
- Department of Biological SciencesTexas Tech UniversityLubbockTX79409USA
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8
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Tirumalai V, Narjala A, Swetha C, Sundar GVH, Sujith TN, Shivaprasad PV. Cultivar-specific miRNA-mediated RNA silencing in grapes. PLANTA 2022; 256:17. [PMID: 35737180 DOI: 10.1007/s00425-022-03934-y] [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: 02/16/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity. However, it is not known if there are variations in miRNA-mediated targeting between subspecies and cultivars that have been subjected to vast genetic modifications through breeding and other selections. Here, we have used PAREsnip2 tool for analysis of degradome datasets derived from two contrasting domesticated grape cultivars having varied fruit color, habit and leaf shape. We identified several interesting variations in sRNA targeting using degradome and 5'RACE analysis between two contrasting grape cultivars that was further correlated using RNA-seq analysis. Several of the differences we identified are associated with secondary metabolic pathways. We propose possible means by which sRNAs might contribute to diversity in secondary metabolites and other development pathways between two domesticated cultivars of grapes.
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Affiliation(s)
- Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - G Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - T N Sujith
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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Qing Y, Zheng Y, Mlotshwa S, Smith HN, Wang X, Zhai X, van der Knaap E, Wang Y, Fei Z. Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1536-1550. [PMID: 35514123 DOI: 10.1111/tpj.15798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/23/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
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Affiliation(s)
- You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | | | - Heather N Smith
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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10
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Jyothsna S, Alagu M. Role of phasiRNAs in plant-pathogen interactions: molecular perspectives and bioinformatics tools. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:947-961. [PMID: 35722509 PMCID: PMC9203634 DOI: 10.1007/s12298-022-01189-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/01/2022] [Accepted: 05/18/2022] [Indexed: 05/03/2023]
Abstract
The genome of an organism is regulated in concert with the organized action of various genetic regulators at different hierarchical levels. Small non-coding RNAs are one of these regulators, among which microRNAs (miRNAs), a distinguished sRNA group with decisive functions in the development, growth and stress-responsive activities of both plants as well as animals, are keenly explored over a good number of years. Recent studies in plants revealed that apart from the silencing activity exhibited by miRNAs on their targets, miRNAs of specific size and structural features can direct the phasing pattern of their target loci to form phased secondary small interfering RNAs (phasiRNAs). These trigger-miRNAs were identified to target both coding and long non-coding RNAs that act as potent phasiRNA precursors or PHAS loci. The phasiRNAs produced thereby exhibit a role in enhancing further downstream regulation either on their own precursors or on those transcripts that are distinct from their genetic source of origin. Hence, these tiny regulators can stimulate an elaborative cascade of interacting RNA networks via cis and trans-regulatory mechanisms. Our review focuses on the comprehensive understanding of phasiRNAs and their trigger miRNAs, by giving much emphasis on their role in the regulation of plant defense responses, together with a summary of the computational tools available for the prediction of the same.
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Affiliation(s)
- S. Jyothsna
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
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11
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Gupta C, Salgotra RK. Epigenetics and its role in effecting agronomical traits. FRONTIERS IN PLANT SCIENCE 2022; 13:925688. [PMID: 36046583 PMCID: PMC9421166 DOI: 10.3389/fpls.2022.925688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 05/16/2023]
Abstract
Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.
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12
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Kansal S, Panwar V, Mutum RD, Raghuvanshi S. Investigations on Regulation of MicroRNAs in Rice Reveal [Ca 2+] cyt Signal Transduction Regulated MicroRNAs. FRONTIERS IN PLANT SCIENCE 2021; 12:720009. [PMID: 34733300 PMCID: PMC8558223 DOI: 10.3389/fpls.2021.720009] [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: 06/03/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs) are critical components of the multidimensional regulatory networks in eukaryotic systems. Given their diverse spectrum of function, it is apparent that the transcription, processing, and activity of the miRNAs themselves, is very dynamically regulated. One of the most important and universally implicated signaling molecules is [Ca2+]cyt. It is known to regulate a plethora of developmental and metabolic processes in both plants and animals; however, its impact on the regulation of miRNA expression is relatively less explored. The current study employed a combination of internal and external calcium channel inhibitors to establishing that [Ca2+]cyt signatures actively regulate miRNA expression in rice. Involvement of [Ca2+]cyt in the regulation of miRNA expression was further confirmed by treatment with calcimycin, the calcium ionophore. Modulation of the cytosolic calcium levels was also found to regulate the drought-responsive expression as well as ABA-mediated response of miRNA genes in rice seedlings. The study further establishes the role of calmodulins and Calmodulin-binding Transcription Activators (CAMTAs) as important components of the signal transduction schema that regulates miRNA expression. Yeast one-hybrid assay established that OsCAMTA4 & 6 are involved in the transcriptional regulation of miR156a and miR167h. Thus, the study was able to establish that [Ca2+]cyt is actively involved in regulating the expression of miRNA genes both under control and stress conditions.
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Affiliation(s)
| | | | | | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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13
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El-Sappah AH, Yan K, Huang Q, Islam MM, Li Q, Wang Y, Khan MS, Zhao X, Mir RR, Li J, El-Tarabily KA, Abbas M. Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:705249. [PMID: 34589097 PMCID: PMC8475493 DOI: 10.3389/fpls.2021.705249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/10/2021] [Indexed: 05/19/2023]
Abstract
Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Qiulan Huang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
- College of Tea Science, Yibin University, Yibin, China
| | | | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Muhammad Sarwar Khan
- Center of Agriculture Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Xianming Zhao
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST–K), Sopore, India
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
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Bhutia KL, Nongbri EL, Sharma TO, Rai M, Tyagi W. A 1.84-Mb region on rice chromosome 2 carrying SPL4, SPL5 and MLO8 genes is associated with higher yield under phosphorus-deficient acidic soil. J Appl Genet 2021; 62:207-222. [PMID: 33409935 DOI: 10.1007/s13353-020-00601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
Phosphorus (P) deficiency is one of the major limiting factors for rice productivity with only one locus (PSTOL1) available for field based application. A biparental mapping population (F6) derived from two P deficiency tolerant genotypes (Sahbhagi Dhan (SD) (PSTOL1+) and Chakhao Poreiton (CP) (PSTOL1-)), in which, transcriptome data generated from our lab had previously shown existence of diverse mechanisms was used to identify novel regions for better yield under lowland acidic soils. Phenotyping at F4, F5 and F6 generations revealed significant correlation between traits like tiller number at 30 days (TN 30), tiller number at 60 days (TN 60), filled grains (FG), percent spikelet fertility (SF%), panicle number (PN) and grain yield per panicle (GYPP) and also association with better yield/performance under low P acidic soil conditions. Through selected genotyping on a set of forty superior and inferior lines using SSR, candidate gene-based and SNP polymorphic markers, 5 genomic regions associated with various yield-related traits were identified. Marker trait association studies revealed 13 markers significantly associated with yield attributing traits and PUE under lowland acidic field conditions. Chi-square and regression analyses of markers run on the entire population identified seven and six markers for SF% and GYPP, respectively, and two for biological yield with positive allele derived from SD which constitute a novel 1.847-Mb region on chromosome 2 flanked by two markers RM12550 and PR9-2. Expression analysis of 7 candidate genes lying within this region across SD, CP and two low P susceptible rice genotypes has revealed that expression of four genes including SPL4, SPL5, ACA9 and MLO8 is significantly upregulated only in SD under low P conditions. In CP, there is low expression of MLO8 under low P conditions, whereas SPL4, SPL5 and Os02g08120 are downregulated. In the case of the two susceptible genotypes, there is no expression of Os02g08120 either in optimum or limiting conditions. Sequence data across a panel of 3024 rice genotypes also suggests that there is polymorphism for these differentially expressed genes. The genes and underlying markers identified on chromosome 2 will be key to imparting tolerance to low P in diverse genetic backgrounds and for marker-assisted selection for higher yield under lowland acidic conditions.
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Affiliation(s)
- Karma Landup Bhutia
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India.,CBS&H, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - Ernieca Lyngdoh Nongbri
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Takhenchangbam Oshin Sharma
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Mayank Rai
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Wricha Tyagi
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India.
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15
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Liu Y, Teng C, Xia R, Meyers BC. PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. THE PLANT CELL 2020; 32:3059-3080. [PMID: 32817252 PMCID: PMC7534485 DOI: 10.1105/tpc.20.00335] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 05/08/2023]
Abstract
Phased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
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Affiliation(s)
- Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri 65211
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16
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Malle S, Morrison M, Belzile F. Identification of loci controlling mineral element concentration in soybean seeds. BMC PLANT BIOLOGY 2020; 20:419. [PMID: 32894046 PMCID: PMC7487956 DOI: 10.1186/s12870-020-02631-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/30/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Mineral nutrients play a crucial role in the biochemical and physiological functions of biological systems. The enhancement of seed mineral content via genetic improvement is considered as the most promising and cost-effective approach compared alternative means for meeting the dietary needs. The overall objective of this study was to perform a GWAS of mineral content (Ca, K, P and S) in seeds of a core set of 137 soybean lines that are representative of the diversity of early maturing soybeans cultivated in Canada (maturity groups 000-II). RESULTS This panel of 137 soybean lines was grown in five environments (in total) and the seed mineral content was measured using a portable x-ray fluorescence (XRF) spectrometer. The association analyses were carried out using three statistical models and a set of 2.2 million SNPs obtained from a combined dataset of genotyping-by-sequencing and whole-genome sequencing. Eight QTLs significantly associated with the Ca, K, P and S content were identified by at least two of the three statistical models used (in two environments) contributing each from 17 to 31% of the phenotypic variation. A strong reproducibility of the effect of seven out these eight QTLs was observed in three other environments. In total, three candidate genes were identified involved in transport and assimilation of these mineral elements. CONCLUSIONS There have been very few GWAS studies to identify QTLs associated with the mineral element content of soybean seeds. In addition to being new, the QTLs identified in this study and candidate genes will be useful for the genetic improvement of soybean nutritional quality through marker-assisted selection. Moreover, this study also provides details on the range of phenotypic variation encountered within the Canadian soybean germplasm.
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Affiliation(s)
- Sidiki Malle
- Département de phytologie, Faculty of Agricultural and Food Sciences and Institute for Integrative and Systems Biology (IBIS), Laval University, Quebec City, Quebec, Canada
| | - Malcolm Morrison
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - François Belzile
- Département de phytologie, Faculty of Agricultural and Food Sciences and Institute for Integrative and Systems Biology (IBIS), Laval University, Quebec City, Quebec, Canada.
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17
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Esposito S, Aversano R, Bradeen JM, Di Matteo A, Villano C, Carputo D. Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22 Suppl 1:133-142. [PMID: 30597710 DOI: 10.1111/plb.12955] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.
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Affiliation(s)
- S Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - R Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - J M Bradeen
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - A Di Matteo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - C Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - D Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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18
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Yu L, Guo R, Jiang Y, Ye X, Yang Z, Meng Y, Shao C. Identification of novel phasiRNAs loci on long non-coding RNAs in Arabidopsis thaliana. Genomics 2019; 111:1668-1675. [PMID: 30458274 DOI: 10.1016/j.ygeno.2018.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/08/2018] [Accepted: 11/13/2018] [Indexed: 01/28/2023]
Abstract
Long non-coding RNAs (lncRNAs) are the "dark matters"involved in gene regulation with complex mechanisms. However, the functions of most lncRNAs remain to be determined. Our previous work revealed a massive number of degradome-supported cleavage signatures on Arabidopsis lncRNAs. Some of them have been confirmed associated with miRNAs-like sRNAs production, while others without long stem structure remain unexplored. A systematical search for phasiRNAs generating ability of these lncRNAs was conducted. Eight novel small RNA triggered lncRNA-phasiRNA pathways were discovered and three of them were found to be conserved in Arabidopsis, Oryza sativa, Glycine max and Gossypium hirsutum. Besides, Five novel ta-siRNAs derived from these lncRNAs were further identified to be involved in the regulation of plant development, stress responses and aromatic amino acids synthesis. These results substantially expanded the gene regulation mechanisms of lncRNAs.
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Affiliation(s)
- Lan Yu
- College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Rongkai Guo
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Yeqin Jiang
- College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Xinghuo Ye
- College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Zhihong Yang
- College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou 313000, PR China.
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19
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The Role of UV-B light on Small RNA Activity During Grapevine Berry Development. G3-GENES GENOMES GENETICS 2019; 9:769-787. [PMID: 30647106 PMCID: PMC6404619 DOI: 10.1534/g3.118.200805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We explored the effects of ultraviolet B radiation (UV-B) on the developmental dynamics of microRNAs and phased small-interfering-RNA (phasi-RNAs)-producing loci by sequencing small RNAs in vegetative and reproductive organs of grapevine (Vitis vinifera L.). In particular, we tested different UV-B conditions in in vitro-grown plantlets (high-fluence exposition) and in berries from field-grown (radiation filtering) and greenhouse-grown (low- and high-fluence expositions) adult plants throughout fruit development and ripening. The functional significance of the observed UV-coordinated miRNA responses was supported by degradome evidences of ARGONAUTE (AGO)-programmed slicing of mRNAs. Co-expression patterns of the up-regulated miRNAs miR156, miR482, miR530, and miR828 with cognate target gene expressions in response to high-fluence UV-B was tested by q-RT-PCR. The observed UV-response relationships were also interrogated against two published UV-stress and developmental transcriptome datasets. Together, the dynamics observed between miRNAs and targets suggest that changes in target abundance are mediated transcriptionally and, in some cases, modulated post-transcriptionally by miRNAs. Despite the major changes in target abundance are being controlled primarily by those developmental effects that are similar between treatments, we show evidence for novel miRNA-regulatory networks in grape. A model is proposed where high-fluence UV-B increases miR168 and miR530 that target ARGONAUTE 1 (AGO1) and a Plus-3 domain mRNA, respectively, while decreasing miR403 that targets AGO2, thereby coordinating post-transcriptional gene silencing activities by different AGOs. Up-regulation of miR3627/4376 could facilitate anthocyanin accumulation by antagonizing a calcium effector, whereas miR395 and miR399, induced by micronutrient deficiencies known to trigger anthocyanin accumulation, respond positively to UV-B radiation. Finally, increases in the abundance of an anthocyanin-regulatory MYB-bHLH-WD40 complex elucidated in Arabidopsis, mediated by UV-B-induced changes in miR156/miR535, could contribute to the observed up-regulation of miR828. In turn, miR828 would regulate the AtMYB113-ortologues MYBA5, A6 and A7 (and thereby anthocyanins) via a widely conserved and previously validated auto-regulatory loop involving miR828 and phasi TAS4abc RNAs.
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20
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An integrated analysis of mRNA and sRNA transcriptional profiles in tomato root: Insights on tomato wilt disease. PLoS One 2018; 13:e0206765. [PMID: 30395631 PMCID: PMC6218063 DOI: 10.1371/journal.pone.0206765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/18/2018] [Indexed: 11/19/2022] Open
Abstract
Tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a worldwide destructive disease of tomato. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed RNA-seq and sRNA-seq analysis to investigate the transcriptome of tomato root under FOL infection. Differentially expressed (DE) protein-coding gene and miRNA gene profiles upon inoculation with FOL were presented at twenty-four hours post-inoculation in four treatments. A total of more than 182.6 million and 132.2 million high quality clean reads were obtained by RNA-seq and sRNA-seq, respectively. A large overlap was found in DE mRNAs between susceptible cultivar Moneymaker and resistant cultivar Motelle. Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. Combining with qRT-PCR and Northern blot, we validated the transcriptional profile of five genes and five miRNAs conferred to FOL infection. Our work allowed comprehensive understanding of different transcriptional reaction of genes/miRNAs between the susceptible and resistant cultivars tomato to the FOL challenge, which could offer us with a future direction to generate models of mediated resistance responses.
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21
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Thibaut O, Claude B. Innate Immunity Activation and RNAi Interplay in Citrus Exocortis Viroid-Tomato Pathosystem. Viruses 2018; 10:E587. [PMID: 30373191 PMCID: PMC6266551 DOI: 10.3390/v10110587] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/18/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Although viroids are the smallest and simplest plant pathogens known, the molecular mechanisms underlying their pathogenesis remain unclear. To unravel these mechanisms, a dual approach was implemented consisting of in silico identification of potential tomato silencing targets of pospiviroids, and the experimental validation of these targets through the sequencing of small RNAs and RNA ends extracted from tomatoes infected with a severe isolate of Citrus exocortis viroid (CEVd). The generated RNA ends were also used to monitor the differentially-expressed genes. These analyses showed that when CEVd symptoms are well established: (i) CEVd are degraded by at least three Dicer-like (DCL) proteins and possibly by RNA-induced silencing complex (RISC), (ii) five different mRNAs are partially degraded through post-transcriptional gene silencing (PTGS), including argonaute 2a, which is further degraded in phasiRNAs, (iii) Dicer-like 2b and 2d are both upregulated and degraded in phasiRNAs, and (iv) CEVd infection induced a significant shift in gene expression allowing to explain the usual symptoms of pospiviroids on tomato and to demonstrate the constant activation of host innate immunity and systemic acquired resistance (SAR) by these pathogenic RNAs. Finally, based on in silico analysis, potential immunity receptor candidates of viroid-derived RNAs are suggested.
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Affiliation(s)
- Olivier Thibaut
- Life Sciences Department, Walloon agricultural research Centre, Rue de Liroux 4, 5030 Gembloux, Belgium.
- UCLouvain, Earth&Life Institute, Croix du Sud 2bte L7.05.03, 1348 Louvain-la-Neuve, Belgium.
| | - Bragard Claude
- UCLouvain, Earth&Life Institute, Croix du Sud 2bte L7.05.03, 1348 Louvain-la-Neuve, Belgium.
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22
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Deng P, Muhammad S, Cao M, Wu L. Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:965-975. [PMID: 29327403 PMCID: PMC5902766 DOI: 10.1111/pbi.12882] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 05/02/2023]
Abstract
Several varieties of small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are generated in plants to regulate development, genome stability and response to adverse environments. Phased siRNA (phasiRNA) is a type of secondary siRNA that is processed from a miRNA-mediated cleavage of RNA transcripts, increasing silencing efficiency or simultaneously suppressing multiple target genes. Trans-acting siRNAs (ta-siRNAs) are a particular class of phasiRNA produced from noncoding transcripts that silence targets in trans. It was originally thought that 'one-hit' and 'two-hit' models were essential for processing distinct TAS precursors; however, a single hit event was recently shown to be sufficient at triggering all types of ta-siRNAs. This review discusses the findings about biogenesis, targeting modes and regulatory networks of plant ta-siRNAs. We also summarize recent advances in the generation of other phasiRNAs and their possible biological benefits to plants.
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Affiliation(s)
- Pingchuan Deng
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Sajid Muhammad
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Min Cao
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Liang Wu
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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23
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Liu H, Yu H, Tang G, Huang T. Small but powerful: function of microRNAs in plant development. PLANT CELL REPORTS 2018; 37:515-528. [PMID: 29318384 DOI: 10.1007/s00299-017-2246-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/15/2017] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a group of endogenous noncoding small RNAs frequently 21 nucleotides long. miRNAs act as negative regulators of their target genes through sequence-specific mRNA cleavage, translational repression, or chromatin modifications. Alterations of the expression of a miRNA or its targets often result in a variety of morphological and physiological abnormalities, suggesting the strong impact of miRNAs on plant development. Here, we review the recent advances on the functional studies of plant miRNAs. We will summarize the regulatory networks of miRNAs in a series of developmental processes, including meristem development, establishment of lateral organ polarity and boundaries, vegetative and reproductive organ growth, etc. We will also conclude the conserved and species-specific roles of plant miRNAs in evolution and discuss the strategies for further elucidating the functional mechanisms of miRNAs during plant development.
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Affiliation(s)
- Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hongyang Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Guiliang Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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24
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Yang X, Liu F, Zhang Y, Wang L, Cheng YF. Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum. BMC Genomics 2017; 18:1000. [PMID: 29287583 PMCID: PMC5747154 DOI: 10.1186/s12864-017-4341-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance. Results Here, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association. Conclusions In summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12864-017-4341-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Fei Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Lu Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu-Fu Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
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25
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Tang J, Chu C. MicroRNAs in crop improvement: fine-tuners for complex traits. NATURE PLANTS 2017; 3:17077. [PMID: 28665396 DOI: 10.1038/nplants.2017.77] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/28/2017] [Indexed: 05/20/2023]
Abstract
One of the most common challenges for both conventional and modern crop improvement is that the appearance of one desirable trait in a new crop variety is always balanced by the impairment of one or more other beneficial characteristics. The best way to overcome this problem is the flexible utilization of regulatory genes, especially genes that provide more efficient and precise regulation in a targeted manner. MicroRNAs (miRNAs), a type of short non-coding RNA, are promising candidates in this area due to their role as master modulators of gene expression at the post-transcriptional level, targeting messenger RNAs for cleavage or directing translational inhibition in eukaryotes. We herein highlight the current understanding of the biological role of miRNAs in orchestrating distinct agriculturally important traits by summarizing recent functional analyses of 65 miRNAs in 9 major crops worldwide. The integration of current miRNA knowledge with conventional and modern crop improvement strategies is also discussed.
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Affiliation(s)
- Jiuyou Tang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Liu D, Mewalal R, Hu R, Tuskan GA, Yang X. New technologies accelerate the exploration of non-coding RNAs in horticultural plants. HORTICULTURE RESEARCH 2017; 4:17031. [PMID: 28698797 PMCID: PMC5496985 DOI: 10.1038/hortres.2017.31] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 05/06/2023]
Abstract
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
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Liberatore KL, Dukowic-Schulze S, Miller ME, Chen C, Kianian SF. The role of mitochondria in plant development and stress tolerance. Free Radic Biol Med 2016; 100:238-256. [PMID: 27036362 DOI: 10.1016/j.freeradbiomed.2016.03.033] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 01/03/2023]
Abstract
Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.
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Affiliation(s)
- Katie L Liberatore
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States.
| | | | - Marisa E Miller
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Shahryar F Kianian
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States
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Palma-Martínez I, Guerrero-Mandujano A, Ruiz-Ruiz MJ, Hernández-Cortez C, Molina-López J, Bocanegra-García V, Castro-Escarpulli G. Active Shiga-Like Toxin Produced by Some Aeromonas spp., Isolated in Mexico City. Front Microbiol 2016; 7:1552. [PMID: 27757103 PMCID: PMC5048074 DOI: 10.3389/fmicb.2016.01552] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/16/2016] [Indexed: 12/29/2022] Open
Abstract
RNA silencing is a conserved mechanism that utilizes small RNAs (sRNAs) to direct the regulation of gene expression at the transcriptional or post-transcriptional level. Plants utilizing RNA silencing machinery to defend pathogen infection was first identified in plant–virus interaction and later was observed in distinct plant–pathogen interactions. RNA silencing is not only responsible for suppressing RNA accumulation and movement of virus and viroid, but also facilitates plant immune responses against bacterial, oomycete, and fungal infection. Interestingly, even the same plant sRNA can perform different roles when encounters with different pathogens. On the other side, pathogens counteract by generating sRNAs that directly regulate pathogen gene expression to increase virulence or target host genes to facilitate pathogen infection. Here, we summarize the current knowledge of the characterization and biogenesis of host- and pathogen-derived sRNAs, as well as the different RNA silencing machineries that plants utilize to defend against different pathogens. The functions of these sRNAs in defense and counter-defense and their mechanisms for regulation during different plant–pathogen interactions are also discussed.
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Affiliation(s)
- Ingrid Palma-Martínez
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Andrea Guerrero-Mandujano
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Manuel J Ruiz-Ruiz
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio Central de Análisis Clínicos Unidad Médica de Alta Especialidad Hospital de Pediatría "Silvestre Frenk Freund," Centro Médico Nacional Siglo XXIMexico City, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico
| | - José Molina-López
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | | | - Graciela Castro-Escarpulli
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
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Shchennikova AV, Beletsky AV, Shulga OA, Mazur AM, Prokhortchouk EB, Kochieva EZ, Ravin NV, Skryabin KG. Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys. PLANT MOLECULAR BIOLOGY 2016; 91:441-458. [PMID: 27097902 DOI: 10.1007/s11103-016-0478-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Myco-heterotroph Monotropa hypopitys is a widely spread perennial herb used to study symbiotic interactions and physiological mechanisms underlying the development of non-photosynthetic plant. Here, we performed, for the first time, transcriptome-wide characterization of M. hypopitys miRNA profile using high throughput Illumina sequencing. As a result of small RNA library sequencing and bioinformatic analysis, we identified 55 members belonging to 40 families of known miRNAs and 17 putative novel miRNAs unique for M. hypopitys. Computational screening revealed 206 potential mRNA targets for known miRNAs and 31 potential mRNA targets for novel miRNAs. The predicted target genes were described in Gene Ontology terms and were found to be involved in a broad range of metabolic and regulatory pathways. The identification of novel M. hypopitys-specific miRNAs, some with few target genes and low abundances, suggests their recent evolutionary origin and participation in highly specialized regulatory mechanisms fundamental for non-photosynthetic biology of M. hypopitys. This global analysis of miRNAs and their potential targets in M. hypopitys provides a framework for further investigation of miRNA role in the evolution and establishment of non-photosynthetic myco-heterotrophs.
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Affiliation(s)
- Anna V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Olga A Shulga
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexander M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Egor B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Elena Z Kochieva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Nikolay V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Konstantin G Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071.
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Damodharan S, Zhao D, Arazi T. A common miRNA160-based mechanism regulates ovary patterning, floral organ abscission and lamina outgrowth in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:458-71. [PMID: 26800988 DOI: 10.1111/tpj.13127] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/07/2016] [Accepted: 01/14/2016] [Indexed: 05/04/2023]
Abstract
Plant microRNAs play vital roles in auxin signaling via the negative regulation of auxin response factors (ARFs). Studies have shown that targeting of ARF10/16/17 by miR160 is indispensable for various aspects of development, but its functions in the model crop tomato (Solanum lycopersicum) are unknown. Here we knocked down miR160 (sly-miR160) using a short tandem target mimic (STTM160), and investigated its roles in tomato development. Northern blot analysis showed that miR160 is abundant in developing ovaries. In line with this, its down-regulation perturbed ovary patterning as indicated by the excessive elongation of the proximal ends of mutant ovaries and thinning of the placenta. Following fertilization, these morphological changes led to formation of elongated, pear-shaped fruits reminiscent of those of the tomato ovate mutant. In addition, STTM160-expressing plants displayed abnormal floral organ abscission, and produced leaves, sepals and petals with diminished blades, indicating a requirement for sly-miR160 for these auxin-mediated processes. We found that sly-miR160 depletion was always associated with the up-regulation of SlARF10A, SlARF10B and SlARF17, of which the expression of SlARF10A increased the most. Despite the sly-miR160 legitimate site of SlARF16A, its mRNA levels did not change in response to sly-miR160 down-regulation, suggesting that it may be regulated by a mechanism other than mRNA cleavage. SlARF10A and SlARF17 were previously suggested to function as inhibiting ARFs. We propose that by adjusting the expression of a group of ARF repressors, of which SlARF10A is a primary target, sly-miR160 regulates auxin-mediated ovary patterning as well as floral organ abscission and lateral organ lamina outgrowth.
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Affiliation(s)
- Subha Damodharan
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan, 50250, Israel
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Lapham Hall S181, 3209 N. Maryland Avenue, Milwaukee, WI, 53201-0413, USA
| | - Tzahi Arazi
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan, 50250, Israel
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Bai S, Saito T, Ito A, Tuan PA, Xu Y, Teng Y, Moriguchi T. Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui'). BMC Genomics 2016; 17:230. [PMID: 26976036 PMCID: PMC4791883 DOI: 10.1186/s12864-016-2514-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/23/2016] [Indexed: 01/12/2023] Open
Abstract
Background In woody perennial plants, including deciduous fruit trees, such as pear, endodormancy is a strategy for surviving the cold winter. A better understanding of the mechanism underlying the endodormancy phase transition is necessary for developing countermeasures against the effects of global warming. In this study, we analyzed the sRNAome of Japanese pear flower buds in endodormant and ecodormant stages over two seasons by implementing of RNA-seq and degradome-sequencing. Results We identified 137 conserved or less conserved miRNAs and 50 pear-specific miRNAs. However, none of the conserved microRNAs or pear-specific miRNAs was differentially expressed between endodormancy and ecodormancy stages. On the contrast, 1540 of 218,050 loci that produced sRNAs were differentially expressed between endodormancy and ecodormancy, suggesting their potential roles on the phase transition from endodormancy to ecodomancy. We also characterized a multifunctional miRNA precursor MIR168, which produces two functional miR168 transcripts, namely miR168.1 and miR168.2; cleavage events were predominantly mediated by the non-conserved variant miR168.2 rather than the conserved variant miR168.1. Finally, we showed that a TAS3 trans-acting siRNA triggered phased siRNA within the ORF of one of its target genes, AUXIN RESPONSE FACTOR 4, via the analysis of phased siRNA loci, indicating that siRNAs are able to trigger phased siRNAs in pear. Conclusion We analyzed the sRNAome of pear flower bud during dormant phase transition. Our work described the sRNA profiles of pear winter buds during dormant phase transition, showing that dormancy release is a highly coordinated physiological process involving the regulation of sRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2514-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Songling Bai
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan. .,Department of Horticulture, The State Agricultural Ministry's Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China.
| | - Takanori Saito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan.,Present address: Graduate School of Horticulture, Chiba University, Matsudo-shi, Chiba, 271-8510, Japan
| | - Akiko Ito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan
| | - Pham Anh Tuan
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan
| | - Ying Xu
- Department of Horticulture, The State Agricultural Ministry's Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yuanwen Teng
- Department of Horticulture, The State Agricultural Ministry's Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Takaya Moriguchi
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan.
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Chen H, Arsovski AA, Yu K, Wang A. Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection. PLoS One 2016; 11:e0150582. [PMID: 26963095 PMCID: PMC4786119 DOI: 10.1371/journal.pone.0150582] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 02/16/2016] [Indexed: 11/25/2022] Open
Abstract
MicroRNAs (miRNAs) play key roles in a variety of cellular processes through regulation of their target gene expression. Accumulated experimental evidence has demonstrated that infections by viruses are associated with the altered expression profile of miRNAs and their mRNA targets in the host. However, the regulatory network of miRNA-mRNA interactions during viral infection remains largely unknown. In this study, we performed small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis to profile the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain). sRNA-seq analyses revealed a total of 253 soybean miRNAs with a two-fold or greater change in abundance compared with the mock-inoculated control. 125 transcripts were identified as the potential cleavage targets of 105 miRNAs and validated by degradome-seq analyses. Genome-wide transcriptome analysis showed that total 2679 genes are differentially expressed in response to SMV infection including 71 genes predicted as involved in defense response. Finally, complex miRNA-mRNA regulatory networks were derived using the RNAseq, small RNAseq and degradome data. This work represents a comprehensive, global approach to examining virus-host interactions. Genes responsive to SMV infection are identified as are their potential miRNA regulators. Additionally, regulatory changes of the miRNAs themselves are described and the regulatory relationships were supported with degradome data. Taken together these data provide new insights into molecular SMV-soybean interactions and offer candidate miRNAs and their targets for further elucidation of the SMV infection process.
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Affiliation(s)
- Hui Chen
- Agriculture and Agri-Food Canada, 1391 Sandford ST. London, Ontario, N5T 4T3, Canada
- Dept of Biology, The University of Western Ontario, 1151 Richmond ST N. London, Ontario, N6A 5B7, Canada
| | - Andrej Adam Arsovski
- Agriculture and Agri-Food Canada, 1391 Sandford ST. London, Ontario, N5T 4T3, Canada
| | - Kangfu Yu
- Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, 2585 County Rd. 20, Harrow, Ontario, N0R 1G0, Canada
| | - Aiming Wang
- Agriculture and Agri-Food Canada, 1391 Sandford ST. London, Ontario, N5T 4T3, Canada
- Dept of Biology, The University of Western Ontario, 1151 Richmond ST N. London, Ontario, N6A 5B7, Canada
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Baksa I, Nagy T, Barta E, Havelda Z, Várallyay É, Silhavy D, Burgyán J, Szittya G. Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics 2015; 16:1025. [PMID: 26626050 PMCID: PMC4667520 DOI: 10.1186/s12864-015-2209-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. RESULTS We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. CONCLUSIONS The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.
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Affiliation(s)
- Ivett Baksa
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Tibor Nagy
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Endre Barta
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Zoltán Havelda
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Éva Várallyay
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - Dániel Silhavy
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - József Burgyán
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
| | - György Szittya
- Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary.
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Xia R, Xu J, Arikit S, Meyers BC. Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants. Mol Biol Evol 2015; 32:2905-18. [PMID: 26318183 PMCID: PMC4651229 DOI: 10.1093/molbev/msv164] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In eudicot plants, the miR482/miR2118 superfamily regulates and instigates the production of phased secondary small interfering RNAs (siRNAs) from NB-LRR (nucleotide binding leucine-rich repeat) genes that encode disease resistance proteins. In grasses, this miRNA family triggers siRNA production specifically in reproductive tissues from long noncoding RNAs. To understand this functional divergence, we examined the small RNA population in the ancient gymnosperm Norway spruce (Picea abies). As many as 41 miRNA families in spruce were found to trigger phasiRNA (phased, secondary siRNAs) production from diverse PHAS loci, with a remarkable 19 miRNA families capable of targeting over 750 NB-LRR genes to generate phasiRNAs. miR482/miR2118, encoded in spruce by at least 24 precursor loci, targets not only NB-LRR genes to trigger phasiRNA production (as in eudicots) but also noncoding PHAS loci, generating phasiRNAs preferentially in male or female cones, reminiscent of its role in the grasses. These data suggest a dual function of miR482/miR2118 present in gymnosperms that was selectively yet divergently retained in flowering plants. A few MIR482/MIR2118 precursors possess an extremely long stem-loop structure, one arm of which shows significant sequence similarity to spruce NB-LRR genes, suggestive of an evolutionary origin from NB-LRR genes through gene duplication. We also characterized an expanded miR390-TAS3 (TRANS-ACTING SIRNA GENE 3)-ARF (AUXIN RESPONSIVE FACTOR) pathway, comprising 18 TAS3 genes of diverse features. Finally, we annotated spruce miRNAs and their targets. Taken together, these data expand our understanding of phasiRNA network in plants and the evolution of plant miRNAs, particularly miR482/miR2118 and its functional diversification.
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Affiliation(s)
- Rui Xia
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
| | - Jing Xu
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
| | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Nakhon Pathom, Thailand
| | - Blake C Meyers
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
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Computational Identification, Target Prediction, and Validation of Conserved miRNAs in Insulin Plant (Costus pictus D. Don). Appl Biochem Biotechnol 2015; 178:513-26. [PMID: 26490377 DOI: 10.1007/s12010-015-1891-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Insulin plant (Costus pictus D. Don) is an economically important medicinal plant for the content of its high value secondary metabolites, bioactive compounds, and remarkable flowering features. MicroRNAs are a class of short (∼21 nucleotides), endogenous, noncoding RNA molecules that play a vital role in regulating gene expression. Here, we used a computer-based homology approach to identify conserved miRNAs in Transcribed Sequence Assemblies (TSA) of C. pictus. It led us to identify 42 miRNAs of 13 different families in C. pictus for the first time. Using quantitative polymerase chain reaction (qPCR) assays, we further confirmed the expression of 8 miRNAs (miR394, miR159b, miR166k, miR172, miR159f, miR166, miR144, and miR858) in young and mature leaf tissues. A total of 109 potential target genes of the identified miRNAs were subsequently predicted in rice (Oryza sativa L.) genome. The target genes encode transcription factors, enzymes, and various functional proteins involved in the regulation of several metabolic pathways. The findings in the present study lay the foundation for further research on miRNAs and miRNA-mediated gene regulation in this important medicinal plant.
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36
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Xu T, Wang Y, Liu X, Lv S, Feng C, Qi M, Li T. Small RNA and degradome sequencing reveals microRNAs and their targets involved in tomato pedicel abscission. PLANTA 2015; 242:963-984. [PMID: 26021606 DOI: 10.1007/s00425-015-2318-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/01/2015] [Indexed: 06/04/2023]
Abstract
We constructed small RNA and degradome sequencing libraries to identify miRNAs and targets involved in tomato pedicel abscission, and confirmed their roles via quantitative real-time PCR. MicroRNAs (miRNAs) are endogenous small RNAs which play crucial negatively regulatory roles at both the transcriptional and post-transcriptional levels in plants; however, limited knowledge is available on the expression profiles of miRNAs and their target genes during tomato pedicel abscission. Taking advantage of small RNA (sRNA) and degradome sequencing technology, a total of 56 known and 11 novel candidate miRNAs targeting 223 mRNA genes were confirmed during pedicel abscission. Gene ontology annotation and KEGG pathway analysis showed that these target genes were significantly enriched in intracellular, membrane-bounded organelle-related biological processes as well as in metabolic, plant-pathogen interaction and hormone signaling pathways. We screened 17 miRNA/target pairs for further analysis and performed quantitative real-time PCR to identify the roles. Cluster analysis of selected miRNAs revealed that the expression profiles of miRNAs varied in different stages of abscission and could be impacted by ethylene treatment. In the present study, the correlations between miRNAs and targets suggested a complex regulatory network of miRNA-mediated target interaction during pedicel abscission. Additionally, the expression profiles of miRNAs and their targets changed by ethylene might be a considerable reason why ethylene promotes pedicel abscission. Our study provides new insights into the expression and regulatory profiles of miRNAs during tomato pedicel abscission.
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Affiliation(s)
- Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, People's Republic of China,
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Bokszczanin KL, Krezdorn N, Fragkostefanakis S, Müller S, Rycak L, Chen Y, Hoffmeier K, Kreutz J, Paupière MJ, Chaturvedi P, Iannacone R, Müller F, Bostan H, Chiusano ML, Scharf KD, Rotter B, Schleiff E, Winter P. Identification of novel small ncRNAs in pollen of tomato. BMC Genomics 2015; 16:714. [PMID: 26385469 PMCID: PMC4575465 DOI: 10.1186/s12864-015-1901-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/09/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The unprecedented role of sncRNAs in the regulation of pollen biogenesis on both transcriptional and epigenetic levels has been experimentally proven. However, little is known about their global regulation, especially under stress conditions. We used tomato pollen in order to identify pollen stage-specific sncRNAs and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing as well as Massive Analysis of cDNA Ends (MACE) were performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions. RESULTS Using the omiRas analysis pipeline we identified known and predicted novel miRNAs as well as sncRNAs from other classes, responsive or not to heat. Differential expression analysis revealed that post-meiotic and mature pollen react most strongly by regulation of the expression of coding and non-coding genomic regions in response to heat. To gain insight to the function of these miRNAs, we predicted targets and annotated them to Gene Ontology terms. This approach revealed that most of them belong to protein binding, transcription, and Serine/Threonine kinase activity GO categories. Beside miRNAs, we observed differential expression of both tRNAs and snoRNAs in tetrad, post-meiotic, and mature pollen when comparing normal and heat stress conditions. CONCLUSIONS Thus, we describe a global spectrum of sncRNAs expressed in pollen as well as unveiled those which are regulated at specific time-points during pollen biogenesis. We integrated the small RNAs into the regulatory network of tomato heat stress response in pollen.
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Affiliation(s)
| | | | - Sotirios Fragkostefanakis
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | | | | | | | | | - Marine J Paupière
- Department of Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Palak Chaturvedi
- Department for Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Rina Iannacone
- ALSIA Research Center Metapontum Agrobios Metaponto (MT), Metaponto, Italy
| | - Florian Müller
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Klaus-Dieter Scharf
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | - Enrico Schleiff
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
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Fei Q, Li P, Teng C, Meyers BC. Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:451-65. [PMID: 26042408 DOI: 10.1111/tpj.12900] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/23/2015] [Accepted: 05/28/2015] [Indexed: 05/04/2023]
Abstract
Small RNAs are a class of non-coding RNAs that are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and (typically) a microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasi-RNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3' terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3' terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this might be due to target inaccessibility determined by sequences flanking target sites. Our results suggest that target accessibility is an important component in miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA-target sites may be impacted.
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Affiliation(s)
- Qili Fei
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Pingchuan Li
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Chong Teng
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Blake C Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
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Itaya A, Lucas WJ, Qi Y, Qu F, Wang Y, Zhong X, Liu CM. In memory of Professor Biao Ding (1960-2015). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:730-731. [PMID: 26182880 DOI: 10.1111/jipb.12381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Asuka Itaya
- Agriculture and Agri-Food Canada, Ottawa, Canada
| | - William J Lucas
- Department of Plant Biology, University of California, Davis, USA
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Feng Qu
- Department of Plant Pathology, Ohio State University, Columbus, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, USA
| | - Xuehua Zhong
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin, Madison, USA
| | - Chun-Ming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
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40
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Zheng Y, Wang Y, Wu J, Ding B, Fei Z. A dynamic evolutionary and functional landscape of plant phased small interfering RNAs. BMC Biol 2015; 13:32. [PMID: 25980406 PMCID: PMC4457045 DOI: 10.1186/s12915-015-0142-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Secondary, phased small interfering RNAs (phasiRNAs) derived from protein-coding or noncoding loci (PHAS) are emerging as a new type of regulators of gene expression in plants. However, the evolution and function of these novel siRNAs in plant species remain largely unexplored. Results We systematically analyzed PHAS loci in 23 plant species covering major phylogenetic groups spanning alga, moss, gymnosperm, basal angiosperm, monocot, and dicot. We identified over 3,300 PHAS loci, among which ~1,600 were protein-coding genes. Most of these PHAS loci were novel and clade- or species-specific and showed distinct expression patterns in association with particular development stages, viral infection, or abiotic stresses. Unexpectedly, numerous PHAS loci produced phasiRNAs from introns or exon–intron junction regions. Our comprehensive analysis suggests that phasiRNAs predominantly regulate protein-coding genes from which they are derived and genes from the same families of the phasiRNA-deriving genes, in contrast to the dominant trans-regulatory mode of miRNAs. The stochastic occurrence of many PHAS loci in the plant kingdom suggests their young evolutionary origins. Conclusions Our study discovered an unprecedented diversity of protein-coding genes that produce phasiRNAs in a wide variety of plants, and set a kingdom-wide foundation for investigating the novel roles of phasiRNAs in shaping phenotype diversities of plants. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0142-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
| | - Ying Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA. .,The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Jian Wu
- The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. .,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43210, USA.
| | - Biao Ding
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA. .,The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. .,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43210, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. .,USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY, 14853, USA.
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41
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Gao C, Ju Z, Cao D, Zhai B, Qin G, Zhu H, Fu D, Luo Y, Zhu B. MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:370-82. [PMID: 25516062 DOI: 10.1111/pbi.12297] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/04/2014] [Accepted: 10/20/2014] [Indexed: 05/18/2023]
Abstract
The development and ripening of tomato fruit are complex processes involving many gene regulatory pathways at the transcriptional and post-transcriptional level. Ripening inhibitor (RIN) is a vital transcription factor, which targets numerous ripening-related genes at the transcriptional level during tomato fruit ripening. MicroRNAs (miRNAs) are a class of short noncoding RNAs that play important roles in post-transcriptional gene regulation. To elucidate the potential regulatory relationship between rin and miRNAs during fruit development and ripening, we identified known miRNAs and profiled their expression in wild-type tomato and rin mutant using a deep sequencing approach combined with quantitative RT-PCR. A total of 33 known miRNA families were identified, of which 14 miRNA families were differently accumulated. Subsequent promoter analysis showed that possible RIN-binding motifs (CArG-box) tended to occur frequently in the promoter regions of partial differently expressed miRNAs. In addition, ethylene may participate in the regulation of miRNAs accumulation during tomato fruit ripening. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assay confirmed the direct binding of RIN to the promoter of MIR172a. Collectively, these results showed a close correlation between miRNA expression and RIN as well as ethylene, which further elucidated the regulatory roles of miRNAs during fruit development and ripening and enriched the regulatory network of RIN in tomato fruit.
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Affiliation(s)
- Chao Gao
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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42
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Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC, Ma J. Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near-Isogenic Lines. THE PLANT GENOME 2015; 8:eplantgenome2014.09.0044. [PMID: 33228285 DOI: 10.3835/plantgenome2014.09.0044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/14/2014] [Indexed: 06/11/2023]
Abstract
Disease-related genes, particularly the nucleotide binding site (NB)-leucine-rich repeat (LRR) class of R plant genes can be triggered by microRNAs (miRNAs) to generate phased small interfering RNAs (phasiRNAs), which could reduce the transcript levels of their targets. However, how global changes in NB-LRR transcript levels coordinate with changes in miRNA and phasiRNA levels in defense responses remains largely unknown. Here, we investigated changes in the relative abundance of small RNAs (sRNAs), with a focus on miRNAs and phasiRNAs and their potential targets in response to the pathogen Phytophthora sojae in the susceptible soybean [Glycine max (L.) Merr.] 'Williams' and nine resistant near-isogenic lines (NILs), each carrying a unique resistance to P. sojae (Rps) gene. In total, 369 distinct miRNAs, including 78 new ones, were identified in the 10 soybean lines. The majority of miRNAs were downregulated by the pathogen. Of the 525 NB-LRR genes found in the soybean reference genome, 257 were predicted to be the targets of eight abundant miRNA families and 126 (dubbed phasi-NB-LRRs or pNLs) were predicted to have produced phasiRNAs. Upregulation of 15 phasi-NB-LRRs was associated with downregulation of their corresponding phasiRNAs in the NILs; these phasiRNAs were predicted to regulate 75 additional NB-LRRs in trans. In addition, we identified putative 24-nucleotide (nt) phasiRNAs from transposons, possibly representing a novel general epigenetic mechanism for regulation of transposon activity under biotic stresses. Together, these observations suggest that miRNAs and phasiRNAs play an important role in response to plant pathogens through complex, multiple layers of post-transcriptional regulation.
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Affiliation(s)
- Meixia Zhao
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
| | - Jixian Zhai
- Dep. of Plant and Soil Sciences, and Delaware Biotechnology Institute, Univ. of Delaware, Newark, DE, 19716
| | - Feng Lin
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
| | - Linghong Li
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue Univ., West Lafayette, IN, 47907
| | | | - Teresa J Hughes
- USDA-ARS, Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907
- Monsanto Company, St. Louis, MO, 63167
| | - Blake C Meyers
- Dep. of Plant and Soil Sciences, and Delaware Biotechnology Institute, Univ. of Delaware, Newark, DE, 19716
| | - Jianxin Ma
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
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Li J, Reichel M, Li Y, Millar AA. The functional scope of plant microRNA-mediated silencing. TRENDS IN PLANT SCIENCE 2014; 19:750-6. [PMID: 25242049 DOI: 10.1016/j.tplants.2014.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 08/05/2014] [Accepted: 08/23/2014] [Indexed: 05/26/2023]
Abstract
Deep sequencing has identified a complex set of plant miRNAs that potentially regulates many target genes of high complementarity. Furthermore, the discovery that many plant miRNAs work through a translational repression mechanism, along with the identification of noncanonical targets, has encouraged bioinformatic searches with less stringent parameters, identifying an even wider range of potential targets. Together, these findings suggest that any given plant miRNA family may regulate a highly diverse set of mRNAs. Here we present evolutionary, genetic, and mechanistic evidence that opposes this idea but instead suggests that families of sequence-related miRNAs regulate very few functionally related targets. We propose that complexities beyond complementarity impact plant miRNA target recognition, possibly explaining the current disparity between bioinformatic prediction and functional evidence.
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Affiliation(s)
- Junyan Li
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia
| | - Marlene Reichel
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia
| | - Yanjiao Li
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia
| | - Anthony A Millar
- Plant Science Division, Research School of Biology, Australian National University, 0200 ACT, Australia.
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44
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Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S. Identification of miRNAs involved in pear fruit development and quality. BMC Genomics 2014; 15:953. [PMID: 25366381 PMCID: PMC4233070 DOI: 10.1186/1471-2164-15-953] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/23/2014] [Indexed: 01/16/2023] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs. Results Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor. Conclusion Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-953) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA. MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum. PLoS Pathog 2014; 10:e1004464. [PMID: 25330340 PMCID: PMC4199772 DOI: 10.1371/journal.ppat.1004464] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/11/2014] [Indexed: 02/02/2023] Open
Abstract
MicroRNAs (miRNAs) suppress the transcriptional and post-transcriptional expression of genes in plants. Several miRNA families target genes encoding nucleotide-binding site–leucine-rich repeat (NB-LRR) plant innate immune receptors. The fungus Fusarium oxysporum f. sp. lycopersici causes vascular wilt disease in tomato. We explored a role for miRNAs in tomato defense against F. oxysporum using comparative miRNA profiling of susceptible (Moneymaker) and resistant (Motelle) tomato cultivars. slmiR482f and slmiR5300 were repressed during infection of Motelle with F. oxysporum. Two predicted mRNA targets each of slmiR482f and slmiR5300 exhibited increased expression in Motelle and the ability of these four targets to be regulated by the miRNAs was confirmed by co-expression in Nicotiana benthamiana. Silencing of the targets in the resistant Motelle cultivar revealed a role in fungal resistance for all four genes. All four targets encode proteins with full or partial nucleotide-binding (NB) domains. One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen. The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs. Fusarium oxysporum is a fungal pathogen that represents a species complex, with members that infect numerous crops. In spite of its importance to agriculture, very little is known about roles of small RNAs in plant immunity against F. oxysporum. In this study, we set up a screen for tomato microRNAs (miRNAs) that correlate with resistance to F. oxysporum f.sp. lycopersici by performing deep sequencing of small RNAs from a resistant and susceptible tomato cultivar. We focused on two miRNAs that are uniquely down-regulated in the resistant cultivar during fungal infection. All predicted targets of these miRNAs encode proteins with NB domains, a motif associated with pathogen resistance in plants. Using a heterologous system, we validated that the miRNAs could regulate expression of four targets. Silencing of the target genes in tomato resulted in decreased immunity to F. oxysporum in the normally resistant cultivar. The finding that none of our targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Our results suggest that the potential resistance of the susceptible cultivar is insufficiently expressed due to the action of miRNAs.
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Affiliation(s)
- Shouqiang Ouyang
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Gyungsoon Park
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Hagop S. Atamian
- Department of Nematology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Cliff S. Han
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jason E. Stajich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Isgouhi Kaloshian
- Department of Nematology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Katherine A. Borkovich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
- * E-mail:
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Shukla D, Huda KMK, Banu MSA, Gill SS, Gill SS, Tuteja R, Tuteja N. OsACA6, a P-type 2B Ca(2+) ATPase functions in cadmium stress tolerance in tobacco by reducing the oxidative stress load. PLANTA 2014; 240:809-24. [PMID: 25074587 DOI: 10.1007/s00425-014-2133-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/18/2014] [Indexed: 06/03/2023]
Abstract
MAIN CONCLUSION The present study demonstrates the first direct evidence of the novel role of OsACA6 in providing Cd (2+) stress tolerance in transgenic tobacco by maintaining cellular ion homeostasis and modulating ROS-scavenging pathway. Cadmium, a non-essential toxic heavy metal, interferes with the plant growth and development. It reaches the leaves through xylem and may become part of the food chain, thus causing detrimental effects to human health. Therefore, there is an urgent need to develop strategies for engineering plants for Cd(2+) tolerance and less accumulation. The members of P-type ATPases family transport metal ions including Cd(2+), and thus play important role an ion homeostasis. The present study elucidates the role of P-type 2B Ca(2+) ATPase (OsACA6) in Cd(2+) stress tolerance. The transcript levels of OsACA6 were up-regulated upon Cd(2+), Zn(2+) and Mn(2+) exposure. Transgenic tobacco expressing OsACA6 showed tolerance towards Cd(2+) stress as demonstrated by several physiological indices including root length, biomass, chlorophyll, malondialdehyde and hydrogen peroxide content. The roots of the transgenic lines accumulated more Cd(2+) as compared to shoot. Further, confocal laser scanning microscopy showed that Cd(2+) exposure altered Ca(2+) uptake in OsACA6 transgenic plants. OsACA6 expression in tobacco also protected the transgenic plants from oxidative stress by enhancing the activity of enzymatic (SOD, CAT, APX, GR) and non-enzymatic (GSH and AsA) antioxidant machinery. Transgenic lines also tolerated Zn(2+) and Mn(2+) stress; however, tolerance for these ions was not as significant as observed for Cd(2+) exposure. Thus, overexpression of OsACA6 confers Cd(2+) stress tolerance in transgenic lines by maintaining cellular ion homeostasis and modulating reactive oxygen species (ROS)-scavenging pathway. The results of the present study will help to develop strategies for engineering Cd(2+) stress tolerance in economically important crop plants.
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Affiliation(s)
- Devesh Shukla
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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47
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Shukla D, Huda KMK, Banu MSA, Gill SS, Tuteja R, Tuteja N. OsACA6, a P-type 2B Ca(2+) ATPase functions in cadmium stress tolerance in tobacco by reducing the oxidative stress load. PLANTA 2014; 240:809-824. [PMID: 25074587 DOI: 10.1007/s00425-014-2145-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/18/2014] [Indexed: 05/20/2023]
Abstract
The present study demonstrates the first direct evidence of the novel role of OsACA6 in providing Cd (2+) stress tolerance in transgenic tobacco by maintaining cellular ion homeostasis and modulating ROS-scavenging pathway. Cadmium, a non-essential toxic heavy metal, interferes with the plant growth and development. It reaches the leaves through xylem and may become part of the food chain, thus causing detrimental effects to human health. Therefore, there is an urgent need to develop strategies for engineering plants for Cd(2+) tolerance and less accumulation. The members of P-type ATPases family transport metal ions including Cd(2+), and thus play important role an ion homeostasis. The present study elucidates the role of P-type 2B Ca(2+) ATPase (OsACA6) in Cd(2+) stress tolerance. The transcript levels of OsACA6 were up-regulated upon Cd(2+), Zn(2+) and Mn(2+) exposure. Transgenic tobacco expressing OsACA6 showed tolerance towards Cd(2+) stress as demonstrated by several physiological indices including root length, biomass, chlorophyll, malondialdehyde and hydrogen peroxide content. The roots of the transgenic lines accumulated more Cd(2+) as compared to shoot. Further, confocal laser scanning microscopy showed that Cd(2+) exposure altered Ca(2+) uptake in OsACA6 transgenic plants. OsACA6 expression in tobacco also protected the transgenic plants from oxidative stress by enhancing the activity of enzymatic (SOD, CAT, APX, GR) and non-enzymatic (GSH and AsA) antioxidant machinery. Transgenic lines also tolerated Zn(2+) and Mn(2+) stress; however, tolerance for these ions was not as significant as observed for Cd(2+) exposure. Thus, overexpression of OsACA6 confers Cd(2+) stress tolerance in transgenic lines by maintaining cellular ion homeostasis and modulating reactive oxygen species (ROS)-scavenging pathway. The results of the present study will help to develop strategies for engineering Cd(2+) stress tolerance in economically important crop plants.
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Affiliation(s)
- Devesh Shukla
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Kamrul Huda KM, Akhter Banu MS, Yadav S, Sahoo RK, Tuteja R, Tuteja N. Salinity and drought tolerant OsACA6 enhances cold tolerance in transgenic tobacco by interacting with stress-inducible proteins. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:229-38. [PMID: 24992889 DOI: 10.1016/j.plaphy.2014.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/03/2014] [Indexed: 05/04/2023]
Abstract
Plant Ca(2+)ATPases regulate many signalling pathways which are important for plant growth, development and abiotic stress responses. Our previous work identified that overexpression of OsACA6 confers salinity and drought tolerance in tobacco. In the present work we report, the function of OsACA6 in cold stress tolerance in transgenic tobacco plants. The expression of OsACA6 was induced by cold stress. The promoter-GUS fusion analyses in the different tissues of transgenic tobacoco confirmed that OsACA6 promoter is cold stress-inducible. Transgenic tobacco plants overexpressing OsACA6 exhibited cold tolerance compared to the wild type (WT) controls. The enhanced tolerance was confirmed by phenotypic analyses as well as by measuring germination, survival rate, chlorophyll content, cell membrane stability, malondialdehyde and proline content. Compared to the WT, the expression of catalase, ascorbate peroxidase and superoxide dismutase increased in the OsACA6 overexpressing plants, which was inversely correlated with the levels of H2O2 in the transgenic lines. We also identified interacting proteins of OsACA6 by using yeast two-hybrid screening assay. Most of the interacting partners of OsACA6 are associated with the widespread biological processes including plant growth, development, signalling and stress adaptation. Furthermore, we also confirmed that OsACA6 is able to self-interact. Overall, these results suggest that OsACA6 plays an important role in cold tolerance at least in part, by regulating antioxidants-mediated removal of reactive oxygen species or by interacting with different calcium signal decoders including calmodulin-like proteins (CaM) calcium/calmodulin dependent protein kinases (CDPKs) and receptor-like protein kinases (RLKs).
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Affiliation(s)
- Kazi Md Kamrul Huda
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mst Sufara Akhter Banu
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sandep Yadav
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ranjan Kumar Sahoo
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Renu Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Wei C, Kuang H, Li F, Chen J. The I2 resistance gene homologues in Solanum have complex evolutionary patterns and are targeted by miRNAs. BMC Genomics 2014; 15:743. [PMID: 25178990 PMCID: PMC4161772 DOI: 10.1186/1471-2164-15-743] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/26/2014] [Indexed: 11/10/2022] Open
Abstract
Background Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. Results Comparative analysis showed that the structure and evolutionary patterns of the I2 locus vary considerably between potato and tomato. The I2 homologues from different Solanaceae species usually do not have orthologous relationship, due to duplication, deletion and frequent sequence exchanges. At least 154 sequence exchanges were detected among 76 tomato I2 homologues, but sequence exchanges between I2 homologues in potato is less frequent. Previous study showed that I2 homologues in potato were targeted by miR482. However, our data showed that I2 homologues in tomato were targeted by miR6024 rather than miR482. Furthermore, miR6024 triggers phasiRNAs from I2 homologues in tomato. Sequence analysis showed that miR6024 was originated after the divergence of Solanaceae. We hypothesized that miR6024 and miR482 might have facilitated the expansion of the I2 family in Solanaceae species, since they can minimize their potential toxic effects by down-regulating their expression. Conclusions The I2 locus represents a most divergent resistance gene cluster in Solanum. Its high divergence was partly due to frequent sequence exchanges between homologues. We propose that the successful expansion of I2 homologues in Solanum was at least partially attributed to miRNA mediated regulation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-743) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Jiongjiong Chen
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange. BMC Genomics 2014; 15:695. [PMID: 25142253 PMCID: PMC4158063 DOI: 10.1186/1471-2164-15-695] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated gene silencing pathways play vital roles in plant development. Here, we used a high-throughput sequencing approach to characterize the miRNAs and their targeted transcripts in the leaf, flower and fruit of sweet orange. RESULTS A total of 183 known miRNAs and 38 novel miRNAs were identified. An in-house script was used to identify all potential secondary siRNAs derived from miRNA-targeted transcripts using sRNA and degradome sequencing data. Genome mapping revealed that these miRNAs were evenly distributed across the genome with several small clusters, and 69 pre-miRNAs were co-localized with simple sequence repeats (SSRs). Noticeably, the loop size of pre-miR396c was influenced by the repeat number of CUU unit. The expression pattern of miRNAs among different tissues and developmental stages were further investigated by both qRT-PCR and RNA gel blotting. Interestingly, Csi-miR164 was highly expressed in fruit ripening stage, and was validated to target a NAC transcription factor. This study depicts a global picture of miRNAs and their target genes in the genome of sweet orange, and focused on the comparison among leaf, flower and fruit tissues. CONCLUSIONS This study provides a global view of miRNAs and their target genes in different tissue of sweet orange, and focused on the identification of miRNA involved in the regulation of fruit ripening. The results of this study lay a foundation for unraveling key regulators of orange fruit development and ripening on post-transcriptional level.
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