151
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Identification of conserved and novel microRNAs in Catharanthus roseus by deep sequencing and computational prediction of their potential targets. Gene 2014; 554:181-95. [PMID: 25445288 DOI: 10.1016/j.gene.2014.10.046] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/08/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small endogenous non-coding RNAs of ~19-24 nucleotides and perform regulatory roles in many plant processes. To identify miRNAs involved in regulatory networks controlling diverse biological processes including secondary metabolism in Catharanthus roseus, an important medicinal plant, we employed deep sequencing of small RNA from leaf tissue. A total of 88 potential miRNAs comprising of 81 conserved miRNAs belonging to 35 families and seven novel miRNAs were identified. Precursors for 16 conserved and seven novel cro-miRNAs were identified, and their stem-loop hairpin structures were predicted. Selected cro-miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in different vegetative tissues of C. roseus. Targets were predicted for conserved and novel cro-miRNAs, which were found to be involved in diverse biological role(s) including secondary metabolism. Our study enriches available resources and information regarding miRNAs and their potential targets for better understanding of miRNA-mediated gene regulation in plants.
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152
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Vidal EA, Moyano TC, Canales J, Gutiérrez RA. Nitrogen control of developmental phase transitions in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5611-8. [PMID: 25129132 DOI: 10.1093/jxb/eru326] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Canales
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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153
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Abreu PMV, Gaspar CG, Buss DS, Ventura JA, Ferreira PCG, Fernandes PMB. Carica papaya microRNAs are responsive to Papaya meleira virus infection. PLoS One 2014; 9:e103401. [PMID: 25072834 PMCID: PMC4114745 DOI: 10.1371/journal.pone.0103401] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/30/2014] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs are implicated in the response to biotic stresses. Papaya meleira virus (PMeV) is the causal agent of sticky disease, a commercially important pathology in papaya for which there are currently no resistant varieties. PMeV has a number of unusual features, such as residence in the laticifers of infected plants, and the response of the papaya to PMeV infection is not well understood. The protein levels of 20S proteasome subunits increase during PMeV infection, suggesting that proteolysis could be an important aspect of the plant defense response mechanism. To date, 10,598 plant microRNAs have been identified in the Plant miRNAs Database, but only two, miR162 and miR403, are from papaya. In this study, known plant microRNA sequences were used to search for potential microRNAs in the papaya genome. A total of 462 microRNAs, representing 72 microRNA families, were identified. The expression of 11 microRNAs, whose targets are involved in 20S and 26S proteasomal degradation and in other stress response pathways, was compared by real-time PCR in healthy and infected papaya leaf tissue. We found that the expression of miRNAs involved in proteasomal degradation increased in response to very low levels of PMeV titre and decreased as the viral titre increased. In contrast, miRNAs implicated in the plant response to biotic stress decreased their expression at very low level of PMeV and increased at high PMeV levels. Corroborating with this results, analysed target genes for this miRNAs had their expression modulated in a dependent manner. This study represents a comprehensive identification of conserved miRNAs inpapaya. The data presented here might help to complement the available molecular and genomic tools for the study of papaya. The differential expression of some miRNAs and identifying their target genes will be helpful for understanding the regulation and interaction of PMeV and papaya.
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Affiliation(s)
- Paolla M. V. Abreu
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Clicia G. Gaspar
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - David S. Buss
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - José A. Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória, Espírito Santo, Brazil
| | - Paulo C. G. Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia M. B. Fernandes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- * E-mail:
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154
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Pashkovskiy PP, Ryazansky SS. Biogenesis, evolution, and functions of plant microRNAs. BIOCHEMISTRY (MOSCOW) 2014; 78:627-37. [PMID: 23980889 DOI: 10.1134/s0006297913060084] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review focuses on the biological role of one class of plant small RNAs, ~22-nt microRNAs (miRNAs). The majority of plant miRNA targets are genes encoding the effector factors of cell signaling pathways. The regulation of their expression is necessary for both ontogenesis and rapid response of plants to biotic and abiotic stress factors. We also summarized current views on the biogenesis and evolution of plant miRNAs as well as the techniques used for their investigation.
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Affiliation(s)
- P P Pashkovskiy
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow 127276, Russia.
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155
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Wang ST, Sun XL, Hoshino Y, Yu Y, Jia B, Sun ZW, Sun MZ, Duan XB, Zhu YM. MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in rice (Oryza sativa L.). PLoS One 2014; 9:e91357. [PMID: 24667308 PMCID: PMC3965387 DOI: 10.1371/journal.pone.0091357] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/10/2014] [Indexed: 11/19/2022] Open
Abstract
The microRNA319 (miR319) family is conserved among diverse plant species. In rice (Oryza sativa L.), the miR319 gene family is comprised of two members, Osa-miR319a and Osa-miR319b. We found that overexpressing Osa-miR319b in rice resulted in wider leaf blades and delayed development. Here, we focused on the biological function and potential molecular mechanism of the Osa-miR319b gene in response to cold stress in rice. The expression of Osa-miR319b was down-regulated by cold stress, and the overexpression of Osa-miR319b led to an enhanced tolerance to cold stress, as evidenced by higher survival rates and proline content. Also, the expression of a handful of cold stress responsive genes, such as DREB1A/B/C, DREB2A, TPP1/2, was increased in Osa-miR319b transgenic lines. Furthermore, we demonstrated the nuclear localization of the transcription factors, OsPCF6 and OsTCP21, which may be Osa-miR319b-targeted genes. We also showed that OsPCF6 and OsTCP21 expression was largely induced by cold stress, and the degree of induction was obviously repressed in plants overexpressing Osa-miR319b. As expected, the down-regulation of OsPCF6 and OsTCP21 resulted in enhanced tolerance to cold stress, partially by modifying active oxygen scavenging. Taken together, our findings suggest that Osa-miR319b plays an important role in plant response to cold stress, maybe by targeting OsPCF6 and OsTCP21.
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Affiliation(s)
- Sun-ting Wang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Xiao-li Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Yoichiro Hoshino
- Field Science Center for Northern Biosphere, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Yang Yu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Bei Jia
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Zhong-wen Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Ming-zhe Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Xiang-bo Duan
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
| | - Yan-ming Zhu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, P.R. China
- * E-mail:
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156
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Identification of microRNAs in the coral Stylophora pistillata. PLoS One 2014; 9:e91101. [PMID: 24658574 PMCID: PMC3962355 DOI: 10.1371/journal.pone.0091101] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/06/2014] [Indexed: 12/22/2022] Open
Abstract
Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral Stylophora pistillata for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 bona fide microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of S. pistillata based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in S. pistillata, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in S. pistillata suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.
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157
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Chao YT, Su CL, Jean WH, Chen WC, Chang YCA, Shih MC. Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite. PLANT MOLECULAR BIOLOGY 2014; 84:529-48. [PMID: 24173913 PMCID: PMC3920020 DOI: 10.1007/s11103-013-0150-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/24/2013] [Indexed: 05/21/2023]
Abstract
Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5' ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.
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Affiliation(s)
- Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Chun-Lin Su
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Wen-Han Jean
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Yao-Chien Alex Chang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 10617 Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
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158
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Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ. Evolutionary history of plant microRNAs. TRENDS IN PLANT SCIENCE 2014; 19:175-82. [PMID: 24405820 DOI: 10.1016/j.tplants.2013.11.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/18/2013] [Accepted: 11/28/2013] [Indexed: 05/11/2023]
Abstract
microRNAs (miRNAs) are short noncoding regulatory genes that perform important roles in plant development and physiology. With the increasing power of next generation sequencing technologies and the development of bioinformatic tools, there has been a dramatic increase in the number of studies surveying the miRNAomes of plant species, which has led to an explosion in the number of described miRNAs. Unfortunately, very many of these new discoveries have been incompletely annotated and thus fail to discriminate genuine miRNAs from small interfering RNAs (siRNAs), fragments of longer RNAs, and random sequence. We review the published repertoire of plant miRNAs, discriminating those that have been correctly annotated. We use these data to explore prevailing hypotheses on the tempo and mode of miRNA evolution within the plant kingdom.
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Affiliation(s)
- Richard S Taylor
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK; Genome Evolution Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Simon J Hiscock
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK.
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159
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Jiang J, Lv M, Liang Y, Ma Z, Cao J. Identification of novel and conserved miRNAs involved in pollen development in Brassica campestris ssp. chinensis by high-throughput sequencing and degradome analysis. BMC Genomics 2014; 15:146. [PMID: 24559317 PMCID: PMC3936892 DOI: 10.1186/1471-2164-15-146] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/07/2014] [Indexed: 11/21/2022] Open
Abstract
Background microRNAs (miRNAs) are endogenous, noncoding, small RNAs that have essential regulatory functions in plant growth, development, and stress response processes. However, limited information is available about their functions in sexual reproduction of flowering plants. Pollen development is an important process in the life cycle of a flowering plant and is a major factor that affects the yield and quality of crop seeds. Results This study aims to identify miRNAs involved in pollen development. Two independent small RNA libraries were constructed from the flower buds of the male sterile line (Bcajh97-01A) and male fertile line (Bcajh97-01B) of Brassica campestris ssp. chinensis. The libraries were subjected to high-throughput sequencing by using the Illumina Solexa system. Eight novel miRNAs on the other arm of known pre-miRNAs, 54 new conserved miRNAs, and 8 novel miRNA members were identified. Twenty-five pairs of novel miRNA/miRNA* were found. Among all the identified miRNAs, 18 differentially expressed miRNAs with over two-fold change between flower buds of male sterile line (Bcajh97-01A) and male fertile line (Bcajh97-01B) were identified. qRT-PCR analysis revealed that most of the differentially expressed miRNAs were preferentially expressed in flower buds of the male fertile line (Bcajh97-01B). Degradome analysis showed that a total of 15 genes were predicted to be the targets of seven miRNAs. Conclusions Our findings provide an overview of potential miRNAs involved in pollen development and interactions between miRNAs and their corresponding targets, which may provide important clues on the function of miRNAs in pollen development.
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Affiliation(s)
| | | | | | | | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
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160
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Jung JH, Lee S, Yun J, Lee M, Park CM. The miR172 target TOE3 represses AGAMOUS expression during Arabidopsis floral patterning. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 215-216:29-38. [PMID: 24388512 DOI: 10.1016/j.plantsci.2013.10.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/14/2013] [Accepted: 10/19/2013] [Indexed: 05/02/2023]
Abstract
microRNA172 (miR172) regulates phase transition and floral patterning in Arabidopsis by repressing targets that encode the APETALA2 (AP2) and AP2-like transcription factors. The miR172-mediated repression of the AP2 gene restricts AGAMOUS (AG) expression. In addition, most miR172 targets, including AP2, redundantly act as floral repressors, and the overexpression of the target genes causes delayed flowering. However, how miR172 targets other than AP2 regulate both of the developmental processes remains unclear. Here, we demonstrate that miR172-mediated repression of the TARGET OF EAT 3 (TOE3) gene is critical for floral patterning in Arabidopsis. Transgenic plants that overexpress a miR172-resistant TOE3 gene (rTOE3-ox) exhibit indeterminate flowers with numerous stamens and carpelloid organs, which is consistent with previous observations in transgenic plants that overexpress a miR172-resistant AP2 gene. TOE3 binds to the second intron of the AG gene. Accordingly, AG expression is significantly reduced in rTOE3-ox plants. TOE3 also interacts with AP2 in the nucleus. Given the major role of AP2 in floral patterning, miR172 likely regulates TOE3 in floral patterning, at least in part via AP2. In addition, a miR156 target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 directly activates TOE3 expression, revealing a novel signaling interaction between miR156 and miR172 in floral patterning.
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Affiliation(s)
- Jae-Hoon Jung
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sangmin Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ju Yun
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Minyoung Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Republic of Korea.
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161
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Bhogale S, Mahajan AS, Natarajan B, Rajabhoj M, Thulasiram HV, Banerjee AK. MicroRNA156: a potential graft-transmissible microRNA that modulates plant architecture and tuberization in Solanum tuberosum ssp. andigena. PLANT PHYSIOLOGY 2014; 164:1011-27. [PMID: 24351688 PMCID: PMC3912076 DOI: 10.1104/pp.113.230714] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 12/13/2013] [Indexed: 05/18/2023]
Abstract
MicroRNA156 (miR156) functions in maintaining the juvenile phase in plants. However, the mobility of this microRNA has not been demonstrated. So far, only three microRNAs, miR399, miR395, and miR172, have been shown to be mobile. We demonstrate here that miR156 is a potential graft-transmissible signal that affects plant architecture and tuberization in potato (Solanum tuberosum). Under tuber-noninductive (long-day) conditions, miR156 shows higher abundance in leaves and stems, whereas an increase in abundance of miR156 has been observed in stolons under tuber-inductive (short-day) conditions, indicative of a photoperiodic control. Detection of miR156 in phloem cells of wild-type plants and mobility assays in heterografts suggest that miR156 is a graft-transmissible signal. This movement was correlated with changes in leaf morphology and longer trichomes in leaves. Overexpression of miR156 in potato caused a drastic phenotype resulting in altered plant architecture and reduced tuber yield. miR156 overexpression plants also exhibited altered levels of cytokinin and strigolactone along with increased levels of LONELY GUY1 and StCyclin D3.1 transcripts as compared with wild-type plants. RNA ligase-mediated rapid amplification of complementary DNA ends analysis validated SQUAMOSA PROMOTER BINDING-LIKE3 (StSPL3), StSPL6, StSPL9, StSPL13, and StLIGULELESS1 as targets of miR156. Gel-shift assays indicate the regulation of miR172 by miR156 through StSPL9. miR156-resistant SPL9 overexpression lines exhibited increased miR172 levels under a short-day photoperiod, supporting miR172 regulation via the miR156-SPL9 module. Overall, our results strongly suggest that miR156 is a phloem-mobile signal regulating potato development.
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162
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Verma SS, Rahman MH, Deyholos MK, Basu U, Kav NNV. Differential expression of miRNAs in Brassica napus root following infection with Plasmodiophora brassicae. PLoS One 2014; 9:e86648. [PMID: 24497962 PMCID: PMC3909011 DOI: 10.1371/journal.pone.0086648] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/17/2013] [Indexed: 12/29/2022] Open
Abstract
Canola (oilseed rape, Brassica napus L.) is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. Two different stages of clubroot development were targeted in this miRNA profiling study: an early time of 10-dpi for disease initiation and a later 20-dpi, by which time the pathogen had colonized the roots (as evident by visible gall formation and histological observations). P. brassicae responsive miRNAs were identified and validated by qRT-PCR of miRNAs and the subsequent validation of the target mRNAs through starBase degradome analysis, and through 5' RLM-RACE. This study identifies putative miRNA-regulated genes with roles during clubroot disease initiation and development. Putative target genes identified in this study included: transcription factors (TFs), hormone-related genes, as well as genes associated with plant stress response regulation such as cytokinin, auxin/ethylene response elements. The results of our study may assist in elucidating the role of miRNAs in post-transcriptional regulation of target genes during disease development and may contribute to the development of strategies to engineer durable resistance to this important phytopathogen.
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Affiliation(s)
- Shiv S. Verma
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Muhammad H. Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Michael K. Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Nat N. V. Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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163
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Zhang L, Wu B, Zhao D, Li C, Shao F, Lu S. Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:38-50. [PMID: 24112769 DOI: 10.1111/jipb.12111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/22/2013] [Indexed: 05/09/2023]
Abstract
SQUAMOSA promoter binding protein-likes (SPLs) are plant-specific transcription factors playing vital regulatory roles in plant growth and development. There is no information about SPLs in Salvia miltiorrhiza (Danshen), a significant medicinal plant widely used in Traditional Chinese medicine (TCM) for >1,700 years and an emerging model plant for TCM studies. Through genome-wide identification and subsequent molecular cloning, we identified a total 15 SmSPLs with divergent sequence features, gene structures, and motifs. Comparative analysis showed sequence conservation between SmSPLs and their Arabidopsis counterparts. A phylogenetic tree clusters SmSPLs into six groups. Many of the motifs identified commonly exist in a group/subgroup, implying their functional redundancy. Eight SmSPLs were predicted and experimentally validated to be targets of miR156/157. SmSPLs were differentially expressed in various tissues of S. milltiorrhiza. The expression of miR156/157-targeted SmSPLs was increased with the maturation of S. miltiorrhiza, whereas the expression of miR156/157 was decreased, confirming the regulatory roles of miR156/157 in SmSPLs and suggesting the functions of SmSPLs in S. miltiorrhiza development. The expression of miR156/157 was negatively correlated with miR172 during the maturation of S. miltiorrhiza. The results indicate the significance and complexity of SmSPL-, miR156-, and miR172-mediated regulation of developmental timing in S. miltiorrhiza.
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Affiliation(s)
- Linsu Zhang
- Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, 550025, China; Institute of Medicinal Plant Development, the Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; Qiannan Medical College for Nationalities, Duyun, 558003, China
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164
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Qin Z, Li C, Mao L, Wu L. Novel insights from non-conserved microRNAs in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:586. [PMID: 25389431 PMCID: PMC4211545 DOI: 10.3389/fpls.2014.00586] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Plant microRNAs (miRNAs), a class of small non-coding regulatory RNAs, are canonically 20-24 nucleotides in length and bind to complementary target RNA sequences, guiding target attenuation via mRNA degradation or translation inhibition. Of the annotated miRNA families, evolutionarily conserved families have been well known to extensively regulate analogous targets and play critical roles in plant development and adaptation to adverse environments. By contrast, majority of these families that are merely present in a specific lineage or in a few closely related species have not been well functionally explored until recently. The fast-growing progresses being made in the actions of non-conserved miRNAs nowadays in diverse plant species may represent a highly promising research field in future. This review thereby summarizes the emerging advances in our understanding of the biogenesis, associated effectors, modes to targets, and biological functions of plant non-conserved miRNAs. In addition, it outlines the regulatory units recently discovered between conserved miRNAs and their alternative targets.
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Affiliation(s)
- Zhengrui Qin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunlian Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Liang Wu and Long Mao, National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Haidian District, Beijing 100081, China e-mail: ;
| | - Liang Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Liang Wu and Long Mao, National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Haidian District, Beijing 100081, China e-mail: ;
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165
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Abstract
The computational identification of novel microRNA (miRNA) genes is a challenging task in bioinformatics. Massive amounts of data describing unknown functional RNA transcripts have to be analyzed for putative miRNA candidates with automated computational pipelines. Beyond those miRNAs that meet the classical definition, high-throughput sequencing techniques have revealed additional miRNA-like molecules that are derived by alternative biogenesis pathways. Exhaustive bioinformatics analyses on such data involve statistical issues as well as precise sequence and structure inspection not only of the functional mature part but also of the whole precursor sequence of the putative miRNA. Apart from a considerable amount of species-specific miRNAs, the majority of all those genes are conserved at least among closely related organisms. Some miRNAs, however, can be traced back to very early points in the evolution of eukaryotic species. Thus, the investigation of the conservation of newly found miRNA candidates comprises an important step in the computational annotation of miRNAs.Topics covered in this chapter include a review on the obvious problem of miRNA annotation and family definition, recommended pipelines of computational miRNA annotation or detection, and an overview of current computer tools for the prediction of miRNAs and their limitations. The chapter closes discussing how those bioinformatic approaches address the problem of faithful miRNA prediction and correct annotation.
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Affiliation(s)
- Jana Hertel
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
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166
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Li X, Hou Y, Zhang L, Zhang W, Quan C, Cui Y, Bian S. Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum). PLANT SIGNALING & BEHAVIOR 2014; 9:e29462. [PMID: 25763692 PMCID: PMC4203583 DOI: 10.4161/psb.29462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous, approximately 21nt in length, non-coding RNA, which mediate the expression of target genes primarily at post-transcriptional levels. miRNAs play critical roles in almost all plant cellular and metabolic processes. Although numerous miRNAs have been identified in the plant kingdom, the miRNAs in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNAs and their targets in blueberry. By conducting an EST-based comparative genomics approach, 9 potential vco-miRNAs were discovered from 22,402 blueberry ESTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNA and its target transcript, 34 target ESTs from blueberry and 70 targets from other species were identified for the vco-miRNAs. The targets were found to be involved in transcription, RNA splicing and binding, DNA duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNAs.
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Affiliation(s)
- Xuyan Li
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yanming Hou
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Li Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Wenhao Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Chen Quan
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Biology; Western University; London, ON Canada
| | - Shaomin Bian
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
- Correspondence to: Shaomin Bian,
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167
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Bellini C, Pacurar DI, Perrone I. Adventitious roots and lateral roots: similarities and differences. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:639-66. [PMID: 24555710 DOI: 10.1146/annurev-arplant-050213-035645] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. Adventitious roots, by comparison, display the same functions as lateral roots but develop from aerial tissues. In addition, they not only develop as an adaptive response to various stresses, such as wounding or flooding, but also are a key limiting component of vegetative propagation. Lateral and adventitious roots share key elements of the genetic and hormonal regulatory networks but are subject to different regulatory mechanisms. In this review, we discuss the developmental processes that give rise to lateral and adventitious roots and highlight knowledge acquired over the past few years about the mechanisms that regulate adventitious root formation.
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Affiliation(s)
- Catherine Bellini
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE90187 Umeå, Sweden; , ,
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168
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Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol 2013; 14:R145. [PMID: 24367943 PMCID: PMC4053937 DOI: 10.1186/gb-2013-14-12-r145] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon. RESULTS B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. CONCLUSIONS B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.
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169
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Ma Z, Axtell MJ. Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA. PLoS One 2013; 8:e83721. [PMID: 24376739 PMCID: PMC3869802 DOI: 10.1371/journal.pone.0083721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/06/2013] [Indexed: 01/08/2023] Open
Abstract
Conserved plant microRNAs (miRNAs) modulate important biological processes but little is known about conserved cis-regulatory elements (CREs) surrounding MIRNA genes. We developed a solution-based targeted genomic enrichment methodology to capture, enrich, and sequence flanking genomic regions surrounding conserved MIRNA genes with a locked-nucleic acid (LNA)-modified, biotinylated probe complementary to the mature miRNA sequence. Genomic DNA bound by the probe is captured by streptavidin-coated magnetic beads, amplified, sequenced and assembled de novo to obtain genomic DNA sequences flanking MIRNA locus of interest. We demonstrate the sensitivity and specificity of this enrichment methodology in Arabidopsis thaliana to enrich targeted regions spanning 10–20 kb surrounding known MIR166 and MIR165 loci. Assembly of the sequencing reads successfully recovered all targeted loci. While further optimization for larger, more complex genomes is needed, this method may enable determination of flanking genomic DNA sequence surrounding a known core (like a conserved mature miRNA) from multiple species that currently don't have a full genome assembly available.
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Affiliation(s)
- Zhaorong Ma
- Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael J. Axtell
- Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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170
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Yang C, Li D, Mao D, Liu X, Ji C, Li X, Zhao X, Cheng Z, Chen C, Zhu L. Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). PLANT, CELL & ENVIRONMENT 2013; 36:2207-18. [PMID: 23651319 DOI: 10.1111/pce.12130] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/24/2013] [Indexed: 05/20/2023]
Abstract
MicroRNA319 (miR319) family is one of the conserved microRNA (miRNA) families among diverse plant species. It has been reported that miR319 regulates plant development in dicotyledons, but little is known at present about its functions in monocotyledons. In rice (Oryza sativa L.), the MIR319 gene family comprises two members, Osa-MIR319a and Osa-MIR319b. Here, we report an expression pattern analysis and a functional characterization of the two Osa-MIR319 genes in rice. We found that overexpressing Osa-MIR319a and Osa-MIR319b in rice both resulted in wider leaf blades. Leaves of osa-miR319 overexpression transgenic plants showed an increased number of longitudinal small veins, which probably accounted for the increased leaf blade width. In addition, we observed that overexpressing osa-miR319 led to enhanced cold tolerance (4 °C) after chilling acclimation (12 °C) in transgenic rice seedlings. Notably, under both 4 and 12 °C low temperatures, Osa-MIR319a and Osa-MIR319b were down-regulated while the expression of miR319-targeted genes was induced. Furthermore, genetically down-regulating the expression of either of the two miR319-targeted genes, OsPCF5 and OsPCF8, in RNA interference (RNAi) plants also resulted in enhanced cold tolerance after chilling acclimation. Our findings in this study demonstrate that miR319 plays important roles in leaf morphogenesis and cold tolerance in rice.
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Affiliation(s)
- Chunhua Yang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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171
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Iwakawa HO, Tomari Y. Molecular insights into microRNA-mediated translational repression in plants. Mol Cell 2013; 52:591-601. [PMID: 24267452 DOI: 10.1016/j.molcel.2013.10.033] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/08/2013] [Accepted: 10/07/2013] [Indexed: 01/01/2023]
Abstract
microRNAs (miRNAs) bind Argonaute proteins in order to form RNA-induced silencing complexes (RISCs) that can silence the expression of complementary mRNAs. Plant miRNAs can mediate the cleavage of their target mRNAs as well as the repression of their translation. Here, by using an in vitro system prepared from plant culture cells, we biochemically dissect the mechanisms by which Arabidopsis thaliana ARGONAUTE1 RISC (AtAGO1-RISC) silences its mRNA targets. We find that AtAGO1-RISC has the ability to repress translation initiation without promoting deadenylation or mRNA decay. Strikingly, AtAGO1-RISC bound in the 5' untranslated region or the open reading frame can sterically block the recruitment or movement of ribosomes. These silencing effects require more extensive base pairing to the target site in comparison to typical animal miRNAs. Our data provide mechanistic insights into miRNA-mediated translational repression in plants.
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Affiliation(s)
- Hiro-oki Iwakawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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172
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Peculiar evolutionary history of miR390-guided TAS3-like genes in land plants. ScientificWorldJournal 2013; 2013:924153. [PMID: 24302881 PMCID: PMC3835848 DOI: 10.1155/2013/924153] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 08/27/2013] [Indexed: 11/17/2022] Open
Abstract
PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant moss taxa, namely, classes Bryopsida, Tetraphidopsida, Polytrichopsida, Andreaeopsida, and Sphagnopsida. We found relatives of all Physcomitrella patens miR390 and TAS3-like loci in these plant taxa excluding Sphagnopsida. Importantly, cloning and sequencing of Marchantia polymorpha genomic DNA showed miR390 and TAS3-like sequences which were also found among genomic reads of M. polymorpha at NCBI database. Our data suggest that the ancient plant miR390-dependent TAS molecular machinery firstly evolved to target AP2-like mRNAs in Marchantiophyta and only then both ARF- and AP2-specific mRNAs in mosses. The presented analysis shows that moss TAS3 families may undergone losses of tasiAP2 sites during evolution toward ferns and seed plants. These data confirm that miR390-guided genes coding for ARF- and AP2-specific ta-siRNAs have been gradually changed during land plant evolution.
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173
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Carvalho A, Paiva J, Louzada J, Lima-Brito J. The transcriptomics of secondary growth and wood formation in conifers. Mol Biol Int 2013; 2013:974324. [PMID: 24288610 PMCID: PMC3830773 DOI: 10.1155/2013/974324] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/22/2013] [Accepted: 09/09/2013] [Indexed: 11/17/2022] Open
Abstract
In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality.
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Affiliation(s)
- Ana Carvalho
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology (IBB/CGB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - Jorge Paiva
- Instituto de Investigação Científica Tropical (IICT), Centro de Florestas e Produtos Florestais (FLOR), Tapada da Ajuda, 1349-018 Lisboa, Portugal
| | - José Louzada
- Department of Forestry Sciences and Landscape (CIFAP), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - José Lima-Brito
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology (IBB/CGB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
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174
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Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PLoS One 2013; 8:e77181. [PMID: 24204767 PMCID: PMC3804510 DOI: 10.1371/journal.pone.0077181] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/06/2013] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.
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Affiliation(s)
- Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Stephanie R. Bollmann
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Kristin D. Kasschau
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Josh T. Cuperus
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Caroline M. Press
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Christopher M. Sullivan
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Elisabeth J. Chapman
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - J. Steen Hoyer
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
- * E-mail: (NJG); (JCC)
| | - James C. Carrington
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail: (NJG); (JCC)
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175
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Zhou Z, Wang Z, Li W, Fang C, Shen Y, Li C, Wu Y, Tian Z. Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:332-44. [PMID: 23876088 DOI: 10.1111/tpj.12293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 07/16/2013] [Indexed: 06/02/2023]
Abstract
miRNA genes are thought to undergo quick birth and death processes in genomes and the emergence of a MIRNA-like hairpin provides the base for functional miRNA gene formation. However, the factors affecting the formation of an active miRNA gene from a MIRNA-like hairpin within a genome remain unclear. We performed a genome-wide investigation of MIRNA-like hairpin accumulation, expression, structural changes and relationships with annotated genomic features in the paleopolyploid soybean genome. Our results showed that adjacent gene and transposable element content, rates of genetic recombination at location of emergence, along with its own gene structure divergence greatly affected miRNA gene evolution. Further investigation suggested that miRNA genes from different duplication sources followed distinct evolutionary trajectories and that the accumulation of MIRNA-like hairpins might be an important factor in causing long terminal repeat retrotransposons to lose activity during genome evolution.
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Affiliation(s)
- Zhengkui Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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176
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Zhou M, Luo H. MicroRNA-mediated gene regulation: potential applications for plant genetic engineering. PLANT MOLECULAR BIOLOGY 2013; 83:59-75. [PMID: 23771582 DOI: 10.1007/s11103-013-0089-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/05/2013] [Indexed: 05/19/2023]
Abstract
Food security is one of the most important issues challenging the world today. Any strategies to solve this problem must include increasing crop yields and quality. MicroRNA-based genetic modification technology (miRNA-based GM tech) can be one of the most promising solutions that contribute to agricultural productivity directly by developing superior crop cultivars with enhanced biotic and abiotic stress tolerance and increased biomass yields. Indirectly, the technology may increase usage of marginal soils and decrease pesticide use, among other benefits. This review highlights the most recent progress of transgenic studies utilizing various miRNAs and their targets for plant trait modifications, and analyzes the potential of miRNA-mediated gene regulation for use in crop improvement. Strategies for manipulating miRNAs and their targets in transgenic plants including constitutive, stress-induced, or tissue-specific expression of miRNAs or their targets, RNA interference, expressing miRNA-resistant target genes, artificial target mimic and artificial miRNAs were discussed. We also discussed potential risks of utilizing miRNA-based GM tech. In general, miRNAs and their targets not only provide an invaluable source of novel transgenes, but also inspire the development of several new GM strategies, allowing advances in breeding novel crop cultivars with agronomically useful characteristics.
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MESH Headings
- Adaptation, Biological
- Crops, Agricultural/genetics
- Crops, Agricultural/immunology
- Crops, Agricultural/metabolism
- Disease Resistance
- Food Supply
- Food, Genetically Modified
- Gene Expression Regulation, Plant
- Genes, Plant
- Genetic Engineering/methods
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/immunology
- Plants, Genetically Modified/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Risk Factors
- Transgenes
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Affiliation(s)
- Man Zhou
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
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177
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Galla G, Volpato M, Sharbel TF, Barcaccia G. Computational identification of conserved microRNAs and their putative targets in the Hypericum perforatum L. flower transcriptome. PLANT REPRODUCTION 2013; 26:209-29. [PMID: 23846415 DOI: 10.1007/s00497-013-0227-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/28/2013] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) have recently emerged as important regulators of gene expression in plants. Many miRNA families and their targets have been extensively studied in model species and major crops. We have characterized mature miRNAs along with their precursors and potential targets in Hypericum to generate a comprehensive list of conserved miRNA families and to investigate the regulatory role of selected miRNAs in biological processes that occur in the flower. St. John's wort (Hypericum perforatum L., 2n = 4x = 32), a medicinal plant that produces pharmaceutically important metabolites with therapeutic activities, was chosen because it is regarded as an attractive model system for the study of apomixis. A computational in silico prediction of structure, in combination with an in vitro validation, allowed us to identify 7 pre-miRNAs, including miR156, miR166, miR390, miR394, miR396, and miR414. We demonstrated that H. perforatum flowers share highly conserved miRNAs and that these miRNAs potentially target dozens of genes with a wide range of molecular functions, including metabolism, response to stress, flower development, and plant reproduction. Our analysis paves the way toward identifying flower-specific miRNAs that may differentiate the sexual and apomictic reproductive pathways.
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Affiliation(s)
- Giulio Galla
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Italy
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178
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Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik JF. Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res 2013; 23:1675-89. [PMID: 23990609 PMCID: PMC3787264 DOI: 10.1101/gr.153387.112] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) derive from longer precursors with fold-back structures. While animal miRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionarily conserved miRNAs present in Arabidopsis thaliana. We found that plant miRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionarily young sequences and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide an explanation for the structural diversity of miRNA precursors in plants and new insights toward the understanding of the biogenesis of small RNAs.
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Affiliation(s)
- Nicolás G Bologna
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
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179
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Identification of tissue-preferential expression patterns of rice miRNAs. J Cell Biochem 2013; 114:2071-81. [DOI: 10.1002/jcb.24552] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 03/14/2013] [Indexed: 11/07/2022]
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180
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Higashi Y, Takechi K, Takano H, Takio S. Involvement of MicroRNA in Copper Deficiency-Induced Repression of Chloroplastic CuZn-Superoxide Dismutase Genes in the Moss Physcomitrella patens. ACTA ACUST UNITED AC 2013; 54:1345-55. [DOI: 10.1093/pcp/pct084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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181
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Pei H, Ma N, Chen J, Zheng Y, Tian J, Li J, Zhang S, Fei Z, Gao J. Integrative analysis of miRNA and mRNA profiles in response to ethylene in rose petals during flower opening. PLoS One 2013; 8:e64290. [PMID: 23696879 PMCID: PMC3655976 DOI: 10.1371/journal.pone.0064290] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 04/11/2013] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs play an important role in plant development and plant responses to various biotic and abiotic stimuli. As one of the most important ornamental crops, rose (Rosa hybrida) possesses several specific morphological and physiological features, including recurrent flowering, highly divergent flower shapes, colors and volatiles. Ethylene plays an important role in regulating petal cell expansion during rose flower opening. Here, we report the population and expression profiles of miRNAs in rose petals during flower opening and in response to ethylene based on high throughput sequencing. We identified a total of 33 conserved miRNAs, as well as 47 putative novel miRNAs were identified from rose petals. The conserved and novel targets to those miRNAs were predicted using the rose floral transcriptome database. Expression profiling revealed that expression of 28 known (84.8% of known miRNAs) and 39 novel (83.0% of novel miRNAs) miRNAs was substantially changed in rose petals during the earlier opening period. We also found that 28 known and 22 novel miRNAs showed expression changes in response to ethylene treatment. Furthermore, we performed integrative analysis of expression profiles of miRNAs and their targets. We found that ethylene-caused expression changes of five miRNAs (miR156, miR164, miR166, miR5139 and rhy-miRC1) were inversely correlated to those of their seven target genes. These results indicate that these miRNA/target modules might be regulated by ethylene and were involved in ethylene-regulated petal growth.
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Affiliation(s)
- Haixia Pei
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Nan Ma
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Jiwei Chen
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yi Zheng
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America
| | - Ji Tian
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Jing Li
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Shuai Zhang
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
| | - Junping Gao
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
- * E-mail:
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182
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Gu W, Wang X, Zhai C, Zhou T, Xie X. Biological basis of miRNA action when their targets are located in human protein coding region. PLoS One 2013; 8:e63403. [PMID: 23671676 PMCID: PMC3646042 DOI: 10.1371/journal.pone.0063403] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/30/2013] [Indexed: 01/09/2023] Open
Abstract
Recent analyses have revealed many functional microRNA (miRNA) targets in mammalian protein coding regions. But, the mechanisms that ensure miRNA function when their target sites are located in protein coding regions of mammalian mRNA transcripts are largely unknown. In this paper, we investigate some potential biological factors, such as target site accessibility and local translation efficiency. We computationally analyze these two factors using experimentally identified miRNA targets in human protein coding region. We find site accessibility is significantly increased in miRNA target region to facilitate miRNA binding. At the mean time, local translation efficiency is also selectively decreased near miRNA target region. GC-poor codons are preferred in the flank region of miRNA target sites to ease the access of miRNA targets. Within-genome analysis shows substantial variations of site accessibility and local translation efficiency among different miRNA targets in the genome. Further analyses suggest target gene’s GC content and conservation level could explain some of the differences in site accessibility. On the other hand, target gene’s functional importance and conservation level can affect local translation efficiency near miRNA target region. We hence propose both site accessibility and local translation efficiency are important in miRNA action when miRNA target sites are located in mammalian protein coding regions.
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Affiliation(s)
- Wanjun Gu
- Research Center of Learning Sciences, Southeast University, Nanjing, Jiangsu, China
- * E-mail: (WG); (TZ); (XX)
| | - Xiaofei Wang
- Research Center of Learning Sciences, Southeast University, Nanjing, Jiangsu, China
| | - Chuanying Zhai
- Research Center of Learning Sciences, Southeast University, Nanjing, Jiangsu, China
| | - Tong Zhou
- Institute for Personalized Respiratory Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- Section of Pulmonary, Critical Care, Sleep & Allergy, Department of Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (WG); (TZ); (XX)
| | - Xueying Xie
- Research Center of Learning Sciences, Southeast University, Nanjing, Jiangsu, China
- * E-mail: (WG); (TZ); (XX)
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183
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Mohanan S, Gowda K, Kandukuri SV, Chandrashekar A. Involvement of a novel intronic microRNA in cross regulation of N-methyltransferase genes involved in caffeine biosynthesis in Coffea canephora. Gene 2013; 519:107-12. [PMID: 23376454 DOI: 10.1016/j.gene.2013.01.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/11/2013] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
Abstract
There are numerous reports on intronic miRNAs from plants, most of which are involved in the regulation of unrelated genes. Some of the target genes are antagonistic to the host genes. Intronic miRNAs in animal systems, however, are known to have synergistic effects. This article is the first to report a similar regulatory effect of a miRNA originating from an intron in plants. NMT genes involved in caffeine biosynthesis were silenced to obtain transformants with reduced caffeine. Transcript analysis revealed the accumulation of transcripts for a related NMT gene (CaMTL1) in transformants bearing either antisense or RNAi constructs. The altered expression was assumed to relate to the silencing of the NMT genes. Bioinformatics analysis of the genes involved in biosynthesis revealed the presence of an intronic miRNA originating from the intron of the theobromine synthase gene targeting CaMTL1. The putative miRNA was cloned and sequenced. Modified 5'-RLM-RACE mapping of the cleavage site and subsequent Northern blotting experimentally demonstrated the presence and activity of such a miRNA in Coffea canephora. This novel regulatory mechanism previously unreported in plants will shed more light onto the evolution of multigene families and the role of introns in this process.
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Affiliation(s)
- Shibin Mohanan
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka 570020, India
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184
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Wu HJ, Wang ZM, Wang M, Wang XJ. Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. PLANT PHYSIOLOGY 2013; 161:1875-84. [PMID: 23429259 PMCID: PMC3613462 DOI: 10.1104/pp.113.215962] [Citation(s) in RCA: 286] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 02/19/2013] [Indexed: 05/18/2023]
Abstract
Target mimicry is a recently identified regulatory mechanism for microRNA (miRNA) functions in plants in which the decoy RNAs bind to miRNAs via complementary sequences and therefore block the interaction between miRNAs and their authentic targets. Both endogenous decoy RNAs (miRNA target mimics) and engineered artificial RNAs can induce target mimicry effects. Yet until now, only the Induced by Phosphate Starvation1 RNA has been proven to be a functional endogenous microRNA target mimic (eTM). In this work, we developed a computational method and systematically identified intergenic or noncoding gene-originated eTMs for 20 conserved miRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). The predicted miRNA binding sites were well conserved among eTMs of the same miRNA, whereas sequences outside of the binding sites varied a lot. We proved that the eTMs of miR160 and miR166 are functional target mimics and identified their roles in the regulation of plant development. The effectiveness of eTMs for three other miRNAs was also confirmed by transient agroinfiltration assay.
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185
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Zhang H, Li L. SQUAMOSA promoter binding protein-like7 regulated microRNA408 is required for vegetative development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:98-109. [PMID: 23289771 DOI: 10.1111/tpj.12107] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/11/2012] [Accepted: 12/20/2012] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs repressing target gene expression post-transcriptionally and are critically involved in various development processes and responses to environmental stresses. MiR408 is highly conserved in land plants and targets several transcripts encoding copper proteins. Although it has been well documented that expression level of miR408 is strongly influenced by a variety of environmental conditions including copper availability, the biological function of this miRNA is still unknown. Here we show that constitutive expression of miR408 results in enhanced growth of seedling and adult plant while knocking down miR408 level by T-DNA insertions or the artificial miRNA technique causes impaired growth. Further, we found that constitutively activated miR408 is able to complement the growth defects of the T-DNA lines. Regarding the molecular mechanism governing miR408 expression, we found that the transcription factors SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) binds to the GTAC motifs in the MIR408 promoter in response to copper deficiency. Interestingly, constitutive activation of miR408 in the spl7 background could partially rescue the severe growth defects of the mutant. Together these results demonstrate that miR408 is a powerful modulator of vegetative growth. Our finding thus reveals a novel control mechanism for vegetative development based on calculated miR408 expression in response to environmental cues.
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Affiliation(s)
- Huiyong Zhang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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186
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Yang L, Xu M, Koo Y, He J, Poethig RS. Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C. eLife 2013; 2:e00260. [PMID: 23538384 PMCID: PMC3608266 DOI: 10.7554/elife.00260] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 02/05/2013] [Indexed: 11/15/2022] Open
Abstract
Nutrients shape the growth, maturation, and aging of plants and animals. In plants, the juvenile to adult transition (vegetative phase change) is initiated by a decrease in miR156. In Arabidopsis, we found that exogenous sugar decreased the abundance of miR156, whereas reduced photosynthesis increased the level of this miRNA. This effect was correlated with a change in the timing of vegetative phase change, and was primarily attributable to a change in the expression of two genes, MIR156A and MIR156C, which were found to play dominant roles in this transition. The glucose-induced repression of miR156 was dependent on the signaling activity of HEXOKINASE1. We also show that the defoliation-induced increase in miR156 levels can be suppressed by exogenous glucose. These results provide a molecular link between nutrient availability and developmental timing in plants, and suggest that sugar is a component of the leaf signal that mediates vegetative phase change. DOI:http://dx.doi.org/10.7554/eLife.00260.001.
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Affiliation(s)
- Li Yang
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Yeonjong Koo
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jia He
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, United States
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187
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Yu S, Cao L, Zhou CM, Zhang TQ, Lian H, Sun Y, Wu J, Huang J, Wang G, Wang JW. Sugar is an endogenous cue for juvenile-to-adult phase transition in plants. eLife 2013; 2:e00269. [PMID: 23543845 PMCID: PMC3610343 DOI: 10.7554/elife.00269] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 01/30/2013] [Indexed: 01/17/2023] Open
Abstract
The transition from the juvenile to adult phase in plants is controlled by diverse exogenous and endogenous cues such as age, day length, light, nutrients, and temperature. Previous studies have shown that the gradual decline in microRNA156 (miR156) with age promotes the expression of adult traits. However, how age temporally regulates the abundance of miR156 is poorly understood. We show here that the expression of miR156 responds to sugar. Sugar represses miR156 expression at both the transcriptional level and post-transcriptional level through the degradation of miR156 primary transcripts. Defoliation and photosynthetic mutant assays further demonstrate that sugar from the pre-existing leaves acts as a mobile signal to repress miR156, and subsequently triggers the juvenile-to-adult phase transition in young leaf primordia. We propose that the gradual increase in sugar after seed germination serves as an endogenous cue for developmental timing in plants. DOI:http://dx.doi.org/10.7554/eLife.00269.001.
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Affiliation(s)
- Sha Yu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Li Cao
- Graduate School of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Heng Lian
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Yue Sun
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, China
| | - Jirong Huang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
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188
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Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, Inzé D, Pè ME, Mica E. Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. MOLECULAR PLANT 2013; 6:423-43. [PMID: 23264558 PMCID: PMC3603004 DOI: 10.1093/mp/sss160] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/15/2012] [Indexed: 05/04/2023]
Abstract
Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth. miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium distachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expanding the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miRNAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. Proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed conditions and demonstrate that drought triggers a genetic reprogramming of leaf growth in which miRNAs are deeply involved.
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Affiliation(s)
- Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Wim Verelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - David Stephen Horner
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Luca Gianfranceschi
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Viviana Piccolo
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Erica Mica
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
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189
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Liu N, Yang J, Guo S, Xu Y, Zhang M. Genome-wide identification and comparative analysis of conserved and novel microRNAs in grafted watermelon by high-throughput sequencing. PLoS One 2013; 8:e57359. [PMID: 23468976 PMCID: PMC3582568 DOI: 10.1371/journal.pone.0057359] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stresses response. However less is known about miRNAs involvement in grafting behaviors, especially with the watermelon (Citrullus lanatus L.) crop, which is one of the most important agricultural crops worldwide. Grafting method is commonly used in watermelon production in attempts to improve its adaptation to abiotic and biotic stresses, in particular to the soil-borne fusarium wilt disease. In this study, Solexa sequencing has been used to discover small RNA populations and compare miRNAs on genome-wide scale in watermelon grafting system. A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known miRNA families and 15 novel miRNAs) and 47 (17 known miRNA families and 30 novel miRNAs) miRNAs were expressed significantly different in watermelon grafted on to bottle gourd and squash, respectively. MiRNAs expressed differentially when watermelon was grafted onto different rootstocks, suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expressions to regulate plant growth and development as well as adaptation to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular aspects of miRNA-mediated regulation in grafted watermelon. Obviously, this result would provide a basis for further unravelling the mechanism on how miRNAs information is exchanged between scion and rootstock in grafted watermelon, and its relevance to diverse biological processes and environmental adaptation.
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Affiliation(s)
- Na Liu
- Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant, Department of Horticulture, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Jinghua Yang
- Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant, Department of Horticulture, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Shaogui Guo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, People’s Republic of China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, People’s Republic of China
- * E-mail: (YX); (MZ)
| | - Mingfang Zhang
- Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant, Department of Horticulture, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, People’s Republic of China
- * E-mail: (YX); (MZ)
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190
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Lelandais-Brière C, Sorin C, Crespi M, Hartmann C. [Non-coding RNAs involved in plant responses to environmental constraints]. Biol Aujourdhui 2013; 206:313-22. [PMID: 23419258 DOI: 10.1051/jbio/2012032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Indexed: 12/20/2022]
Abstract
In recent years, in addition to mRNAs, the non-protein-coding RNAs (or ncRNAs) have emerged as a major part of the eukaryotic transcriptome. New genomic approaches allowed the discovery of many novel long and small ncRNAs that may be linked to the generation of evolutionary complexity in multicellular organisms. Many long ncRNAs are regulated by abiotic stresses although only very few long ncRNAs have been functionally analyzed. On the other hand, small RNAs act in the regulation of gene expression at transcriptional or post-transcriptional level and several among them have been linked to abiotic stress responses. Here we describe various ncRNAs associated with environmental stress responses such as to salt, cold or nutrient deprivation. The understanding of these RNA networks may reveal novel mechanisms involved in plant adaptation to changing environmental conditions.
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Affiliation(s)
- Christine Lelandais-Brière
- Université Paris-Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France - Institut des Sciences du Végétal ISV, CNRS, UPR2355, 91198 Gif-sur-Yvette Cedex, France
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191
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Zhao X, Zhang H, Li L. Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis. Genomics 2013; 101:187-94. [PMID: 23295247 DOI: 10.1016/j.ygeno.2012.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/22/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022]
Abstract
Endogenous microRNAs (miRNAs) modulate gene expression at the post-transcription level. In plants, a vast majority of MIR genes are thought to be transcribed by RNA Polymerase II (Pol II). However, promoter organization is currently unknown for most plant MIR genes. This deficiency prevents a comprehensive understanding of miRNA-mediated gene networks. In this study, we performed Pol II chromatin immunoprecipitation (ChIP) analysis in Arabidopsis using a genome tiling microarray. Distinct Pol II binding was found at most MIR loci, which allowed prediction of the transcription start sites (TSSs) for 167 MIR genes in Arabidopsis that was validated by average free energy profiling. By employing 99 position weight matrices (PWM), we systematically scanned the regulatory regions upstream of the TSSs. We discovered eleven and ten cis-elements that are statistically over- and under-represented in MIR promoters, respectively. Thus, analysis of Pol II binding provides a new perspective for studying miRNAs in plants.
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Affiliation(s)
- Xin Zhao
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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192
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Davies KM, Deroles SC, Boase MR, Hunter DA, Schwinn KE. Biolistics-based gene silencing in plants using a modified particle inflow gun. Methods Mol Biol 2013; 940:63-74. [PMID: 23104334 DOI: 10.1007/978-1-62703-110-3_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RNA interference (RNAi) is one of the most commonly used techniques for examining the function of genes of interest. In this chapter we present two examples of RNAi that use the particle inflow gun for delivery of the DNA constructs. In one example transient RNAi is used to show the function of an anthocyanin regulatory gene in flower petals. In the second example stably transformed cell cultures are produced with an RNAi construct that results in a change in the anthocyanin hydroxylation pattern.
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Affiliation(s)
- Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand.
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193
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Calviño M, Messing J. Discovery of MicroRNA169 gene copies in genomes of flowering plants through positional information. Genome Biol Evol 2013; 5:402-17. [PMID: 23348041 PMCID: PMC3590774 DOI: 10.1093/gbe/evt015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2013] [Indexed: 12/02/2022] Open
Abstract
Expansion and contraction of microRNA (miRNA) families can be studied in sequenced plant genomes through sequence alignments. Here, we focused on miR169 in sorghum because of its implications in drought tolerance and stem-sugar content. We were able to discover many miR169 copies that have escaped standard genome annotation methods. A new miR169 cluster was found on sorghum chromosome 1. This cluster is composed of the previously annotated sbi-MIR169o together with two newly found MIR169 copies, named sbi-MIR169t and sbi-MIR169u. We also found that a miR169 cluster on sorghum chr7 consisting of sbi-MIR169l, sbi-MIR169m, and sbi-MIR169n is contained within a chromosomal inversion of at least 500 kb that occurred in sorghum relative to Brachypodium, rice, foxtail millet, and maize. Surprisingly, synteny of chromosomal segments containing MIR169 copies with linked bHLH and CONSTANS-LIKE genes extended from Brachypodium to dictotyledonous species such as grapevine, soybean, and cassava, indicating a strong conservation of linkages of certain flowering and/or plant height genes and microRNAs, which may explain linkage drag of drought and flowering traits and would have consequences for breeding new varieties. Furthermore, alignment of rice and sorghum orthologous regions revealed the presence of two additional miR169 gene copies (miR169r and miR169s) on sorghum chr7 that formed an antisense miRNA gene pair. Both copies are expressed and target different set of genes. Synteny-based analysis of microRNAs among different plant species should lead to the discovery of new microRNAs in general and contribute to our understanding of their evolution.
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194
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Global identification of small RNA targets in plants by sequencing sliced ends of messenger RNAs. Methods Mol Biol 2013; 956:119-29. [PMID: 23135849 DOI: 10.1007/978-1-62703-194-3_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Small RNAs (microRNAs and other classes of endogenous small interfering RNAs) play important roles in a wide variety of biological processes. However, integration of small RNAs in diverse biological networks relies on the confirmation of their RNA targets. In plants, miRNAs negatively regulate mRNA targets by guiding a cleavage in the complementary site that leaves a 3' polyadenylated RNA possessing monophosphate at its 5' end. This chapter describes a detailed step-by-step protocol for cloning such sliced 3' products in order to identify small RNA targets. Using this protocol, we have identified more than 150 small RNA targets in rice; some are conserved and others are non-conserved targets for rice small RNAs.
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195
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Geuten K, Coenen H. Heterochronic genes in plant evolution and development. FRONTIERS IN PLANT SCIENCE 2013; 4:381. [PMID: 24093023 PMCID: PMC3782661 DOI: 10.3389/fpls.2013.00381] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/06/2013] [Indexed: 05/05/2023]
Abstract
Evolution of morphology includes evolutionary shifts of developmental processes in space or in time. Heterochronic evolution is defined as a temporal shift. The concept of heterochrony has been very rewarding to investigators of both animal and plant developmental evolution, because it has strong explanatory power when trying to understand morphological diversity. While for animals, extensive literature on heterochrony developed along with the field of evolution of development, in plants the concept has been applied less often and is less elaborately developed. Yet novel genetic findings highlight heterochrony as a developmental and evolutionary process in plants. Similar to what has been found for the worm Caenorhabditis, a heterochronic gene pathway controlling developmental timing has been elucidated in flowering plants. Two antagonistic microRNA's miR156 and miR172 target two gene families of transcription factors, SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE and APETALA2-like, respectively. Here, we propose that this finding now allows the molecular investigation of cases of heterochronic evolution in plants. We illustrate this point by examining microRNA expression patterns in the Antirrhinum majus incomposita and choripetala heterochronic mutants. Some of the more beautiful putative cases of heterochronic evolution can be found outside flowering plants, but little is known about the extent of conservation of this flowering plant pathway in other land plants. We show that the expression of an APETALA2-like gene decreases with age in a fern species. This contributes to the idea that ferns share some heterochronic gene functions with flowering plants.
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Affiliation(s)
- Koen Geuten
- *Correspondence: Koen Geuten, Department of Biology, Laboratory of Molecular Plant Biology, University of Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium e-mail:
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196
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Abstract
As a plant shoot develops, it produces different types of leaves, buds, and internodes, and eventually acquires the capacity to produce structures involved in sexual reproduction. Morphological and anatomical traits that change in coordinated fashion at a predictable time in vegetative development allow this process to be divided into several more-or-less discrete phases; the transition between these phases is termed "vegetative phase change." Vegetative phase change is regulated by a decrease in the expression of the related microRNAs, miR156, and miR157, which act by repressing the expression of squamosa promoter binding protein/SBP-like (SBP/SPL) transcription factors. SBP/SPL proteins regulate a wide variety of processes in shoot development, including flowering time and inflorescence development. Answers to long-standing questions about the relationship between vegetative and reproductive maturation have come from genetic analyses of the transcriptional and posttranscriptional regulatory networks in which these proteins are involved. Studies conducted over several decades indicate that carbohydrates have a significant effect on phase-specific leaf traits, and recent research suggests that sugar may be the leaf signal that promotes vegetative phase change.
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Affiliation(s)
- R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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197
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Regulation of flowering time by microRNAs. J Genet Genomics 2012; 40:211-5. [PMID: 23706296 DOI: 10.1016/j.jgg.2012.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 12/14/2012] [Accepted: 12/14/2012] [Indexed: 11/21/2022]
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198
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Aryal R, Yang X, Yu Q, Sunkar R, Li L, Ming R. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya. BMC Genomics 2012; 13:682. [PMID: 23216749 PMCID: PMC3582581 DOI: 10.1186/1471-2164-13-682] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 11/29/2012] [Indexed: 11/10/2022] Open
Abstract
Background The small RNAs (sRNA) are a regulatory class of RNA mainly represented by the 21 and 24-nucleotide size classes. The cellular sRNAs are processed by RNase III family enzyme dicer (Dicer like in plant) from a self-complementary hairpin loop or other type of RNA duplexes. The papaya genome has been sequenced, but its microRNAs and other regulatory RNAs are yet to be analyzed. Results We analyzed the genomic features of the papaya sRNA population from three sRNA deep sequencing libraries made from leaves, flowers, and leaves infected with Papaya Ringspot Virus (PRSV). We also used the deep sequencing data to annotate the micro RNA (miRNA) in papaya. We identified 60 miRNAs, 24 of which were conserved in other species, and 36 of which were novel miRNAs specific to papaya. In contrast to the Chargaff’s purine-pyrimidine equilibrium, cellular sRNA was significantly biased towards a purine rich population. Of the two purine bases, higher frequency of adenine was present in 23nt or longer sRNAs, while 22nt or shorter sRNAs were over represented by guanine bases. However, this bias was not observed in the annotated miRNAs in plants. The 21nt species were expressed from fewer loci but expressed at higher levels relative to the 24nt species. The highly expressed 21nt species were clustered in a few isolated locations of the genome. The PRSV infected leaves showed higher accumulation of 21 and 22nt sRNA compared to uninfected leaves. We observed higher accumulation of miRNA* of seven annotated miRNAs in virus-infected tissue, indicating the potential function of miRNA* under stressed conditions. Conclusions We have identified 60 miRNAs in papaya. Our study revealed the asymmetric purine-pyrimidine distribution in cellular sRNA population. The 21nt species of sRNAs have higher expression levels than 24nt sRNA. The miRNA* of some miRNAs shows higher accumulation in PRSV infected tissues, suggesting that these strands are not totally functionally redundant. The findings open a new avenue for further investigation of the sRNA silencing pathway in plants.
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Affiliation(s)
- Rishi Aryal
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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199
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Cho SH, Coruh C, Axtell MJ. miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens. THE PLANT CELL 2012; 24:4837-49. [PMID: 23263766 PMCID: PMC3556961 DOI: 10.1105/tpc.112.103176] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/07/2012] [Accepted: 12/10/2012] [Indexed: 05/18/2023]
Abstract
microRNA156 (miR156) affects developmental timing in flowering plants. miR156 and its target relationships with members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family appear universally conserved in land plants, but the specific functions of miR156 outside of flowering plants are unknown. We find that miR156 promotes a developmental change from young filamentous protonemata to leafy gametophores in the moss Physcomitrella patens, opposite to its role as an inhibitor of development in flowering plants. P. patens miR156 also influences accumulation of trans-acting small interfering RNAs (tasiRNAs) dependent upon a second ancient microRNA, miR390. Both miR156 and miR390 directly target a single major tasiRNA primary transcript. Inhibition of miR156 function causes increased miR390-triggered tasiRNA accumulation and decreased accumulation of tasiRNA targets. Overexpression of miR390 also caused a slower formation of gametophores, elevated miR390-triggered tasiRNA accumulation, and reduced level of tasiRNA targets. We conclude that a gene regulatory network controlled by miR156, miR390, and their targets controls developmental change in P. patens. The broad outlines and regulatory logic of this network are conserved in flowering plants, albeit with some modifications. Partially conserved small RNA networks thus influence developmental timing in plants with radically different body plans.
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Affiliation(s)
- Sung Hyun Cho
- Department of Biology, Penn State University, University Park, Pennsylvania 16802
| | - Ceyda Coruh
- Department of Biology, Penn State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802
| | - Michael J. Axtell
- Department of Biology, Penn State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802
- Address correspondence to
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Romanel E, Silva TF, Corrêa RL, Farinelli L, Hawkins JS, Schrago CEG, Vaslin MFS. Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection. PLANT MOLECULAR BIOLOGY 2012; 80:443-60. [PMID: 22987114 DOI: 10.1007/s11103-012-9959-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 05/13/2023]
Abstract
Small RNAs (sRNAs) are a class of non-coding RNAs ranging from 20- to 40-nucleotides (nts) that are present in most eukaryotic organisms. In plants, sRNAs are involved in the regulation of development, the maintenance of genome stability and the antiviral response. Viruses, however, can interfere with and exploit the silencing-based regulatory networks, causing the deregulation of sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). To understand the impact of viral infection on the plant sRNA pathway, we deep sequenced the sRNAs in cotton leaves infected with Cotton leafroll dwarf virus (CLRDV), which is a member of the economically important virus family Luteoviridae. A total of 60 putative conserved cotton miRNAs were identified, including 19 new miRNA families that had not been previously described in cotton. Some of these miRNAs were clearly misregulated during viral infection, and their possible role in symptom development and disease progression is discussed. Furthermore, we found that the 24-nt heterochromatin-associated siRNAs were quantitatively and qualitatively altered in the infected plant, leading to the reactivation of at least one cotton transposable element. This is the first study to explore the global alterations of sRNAs in virus-infected cotton plants. Our results indicate that some CLRDV-induced symptoms may be correlated with the deregulation of miRNA and/or epigenetic networks.
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Affiliation(s)
- Elisson Romanel
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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