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Zhang J, Zhang S, Han S, Li X, Tong Z, Qi L. Deciphering small noncoding RNAs during the transition from dormant embryo to germinated embryo in Larches (Larix leptolepis). PLoS One 2013; 8:e81452. [PMID: 24339932 PMCID: PMC3858266 DOI: 10.1371/journal.pone.0081452] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022] Open
Abstract
Small RNAs (sRNAs), as a key component of molecular biology, play essential roles in plant development, hormone signaling, and stress response. However, little is known about the relationships among sRNAs, hormone signaling, and dormancy regulation in gymnosperm embryos. To investigate the roles of sRNAs in embryo dormancy maintenance and release in Larix leptolepis, we deciphered the endogenous “sRNAome” in dormant and germinated embryos. High-throughput sequencing of sRNA libraries showed that dormant embryos exhibited a length bias toward 24-nt while germinated embryos showed a bias toward 21-nt lengths. This might be associated with distinct levels of RNA-dependent RNA polymerase2 (RDR2) and/or RDR6, which is regulated by hormones. Proportions of miRNAs to nonredundant and redundant sRNAs were higher in germinated embryos than in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. We identified a total of 160 conserved miRNAs from 38 families, 3 novel miRNAs, and 16 plausible miRNA candidates, of which many were upregulated in germinated embryos relative to dormant embryos. These findings indicate that larches and possibly other gymnosperms have complex mechanisms of gene regulation involving miRNAs and other sRNAs operating transcriptionally and posttranscriptionally during embryo dormancy and germination. We propose that abscisic acid modulates embryo dormancy and germination at least in part through regulation of the expression level of sRNA-biogenesis genes, thus changing the sRNA components.
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Affiliation(s)
- Junhong Zhang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, Zhejiang, P.R. China
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Shougong Zhang
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Suying Han
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, P.R. China
| | - Xinmin Li
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Zaikang Tong
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, Zhejiang, P.R. China
- * E-mail: (ZT); (LQ)
| | - Liwang Qi
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
- * E-mail: (ZT); (LQ)
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202
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Cao S, Zhu QH, Shen W, Jiao X, Zhao X, Wang MB, Liu L, Singh SP, Liu Q. Comparative profiling of miRNA expression in developing seeds of high linoleic and high oleic safflower (Carthamus tinctorius L.) plants. FRONTIERS IN PLANT SCIENCE 2013; 4:489. [PMID: 24348492 PMCID: PMC3844856 DOI: 10.3389/fpls.2013.00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/12/2013] [Indexed: 05/20/2023]
Abstract
Vegetable oils high in oleic acid are considered to be advantageous because of their better nutritional value and potential industrial applications. The oleic acid content in the classic safflower oil is normally 10-15% while a natural mutant (ol) accumulates elevated oleic acid up to 70% in seed oil. As a part of our investigation into the molecular features of the high oleic (HO) trait in safflower we have profiled the microRNA (miRNA) populations in developing safflower seeds expressing the ol allele in comparison to the wild type high linoleic (HL) safflower using deep sequencing technology. The small RNA populations of the mid-maturity developing embryos of homozygous ol HO and wild type HL safflower had a very similar size distribution pattern, however, only ~16.5% of the unique small RNAs were overlapping in these two genotypes. From these two small RNA populations we have found 55 known miRNAs and identified two candidate novel miRNA families to be likely unique to the developing safflower seeds. Target genes with conserved as well as novel functions were predicted for the conserved miRNAs. We have also identified 13 miRNAs differentially expressed between the HO and HL safflower genotypes. The results may lay a foundation for unraveling the miRNA-mediated molecular processes that regulate oleic acid accumulation in the HO safflower mutant and developmental processes in safflower embryos in general.
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Affiliation(s)
- Shijiang Cao
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
| | - Qian-Hao Zhu
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
| | - Wanxia Shen
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Xiaoming Jiao
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
- National Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Xiaochun Zhao
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
| | - Lixia Liu
- School of Life Sciences, Northeast Normal UniversityChangchun, China
| | - Surinder P. Singh
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
| | - Qing Liu
- Commonwealth Scientific and Industrial Research Organization Plant IndustryACT, Australia
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203
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Duarte GT, Matiolli CC, Pant BD, Schlereth A, Scheible WR, Stitt M, Vicentini R, Vincentz M. Involvement of microRNA-related regulatory pathways in the glucose-mediated control of Arabidopsis early seedling development. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4301-12. [PMID: 23997203 PMCID: PMC3808316 DOI: 10.1093/jxb/ert239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In plants, sugars such as glucose act as signalling molecules that promote changes in gene expression programmes that impact on growth and development. Recent evidence has revealed the potential importance of controlling mRNA decay in some aspects of glucose-mediated regulatory responses suggesting a role of microRNAs (miRNAs) in these responses. In order to get a better understanding of glucose-mediated development modulation involving miRNA-related regulatory pathways, early seedling development of mutants impaired in miRNA biogenesis (hyl1-2 and dcl1-11) and miRNA activity (ago1-25) was evaluated. All mutants exhibited a glucose hyposensitive phenotype from germination up to seedling establishment, indicating that miRNA regulatory pathways are involved in the glucose-mediated delay of early seedling development. The expression profile of 200 miRNA primary transcripts (pri-miRs) was evaluated by large-scale quantitative real-time PCR profiling, which revealed that 38 pri-miRs were regulated by glucose. For several of them, the corresponding mature miRNAs are known to participate directly or indirectly in plant development, and their accumulation was shown to be co-regulated with the pri-miR by glucose. Furthermore, the expression of several miRNA target genes was found to be deregulated in response to glucose in the miRNA machinery mutants ago1-25, dcl1-11, and hyl1-2. Also, in these mutants, glucose promoted misexpression of genes for the three abscisic acid signalling elements ABI3, ABI4, and ABI5. Thus, miRNA regulatory pathways play a role in the adjustments of growth and development triggered by glucose signalling.
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Affiliation(s)
- Gustavo Turqueto Duarte
- Laboratório de Genética de Plantas, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CEP 13083-875, CP 6010; Campinas, São Paulo, Brazil
| | - Cleverson Carlos Matiolli
- Laboratório de Genética de Plantas, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CEP 13083-875, CP 6010; Campinas, São Paulo, Brazil
| | - Bikram Datt Pant
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Armin Schlereth
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Wolf-Rüdiger Scheible
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Mark Stitt
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Renato Vicentini
- Laboratório de Bioinformática e Biologia de Sistemas, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CEP 13083-875, CP 6010; Campinas, São Paulo, Brazil
| | - Michel Vincentz
- Laboratório de Genética de Plantas, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CEP 13083-875, CP 6010; Campinas, São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, CEP 13083-875, CP 6009; Campinas, São Paulo, Brazil
- * To whom correspondence should be addressed. E-mail:
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204
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Gu Y, Liu Y, Zhang J, Liu H, Hu Y, Du H, Li Y, Chen J, Wei B, Huang Y. Identification and characterization of microRNAs in the developing maize endosperm. Genomics 2013; 102:472-8. [PMID: 24021532 DOI: 10.1016/j.ygeno.2013.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 08/04/2013] [Accepted: 08/22/2013] [Indexed: 11/16/2022]
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that are approximately 20-22 nucleotides long. miRNAs have been shown to be important regulators that control a large variety of biological functions in eukaryotic cells. To investigate the roles of miRNAs in maize endosperm development, two small RNA libraries of maize endosperm at two developmental stages were sequenced. A total of 17,773,394 and 18,586,523 small RNA raw reads were obtained, respectively. Further analysis identified and characterized 95 known miRNAs belonging to 20 miRNA families. In addition, 18 novel miRNAs were identified and grouped into 11 families. Potential targets for 5 of the novel miRNA families were successfully predicted. We had also identified 12 corresponding miRNAs* of these novel miRNAs. In summary, we investigated expression patterns of miRNA in maize endosperm at key developmental stages and identified miRNAs that are likely to playing an important role in endosperm development.
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Affiliation(s)
- Yong Gu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural Universities, Ya'an, Sichuan 625014, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural Universities, Ya'an, Sichuan 625014, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengd u, Sichuan 611130, China
| | - Hai Du
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yangping Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jiang Chen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Bin Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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205
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Palovaara J, Saiga S, Weijers D. Transcriptomics approaches in the early Arabidopsis embryo. TRENDS IN PLANT SCIENCE 2013; 18:514-21. [PMID: 23726727 DOI: 10.1016/j.tplants.2013.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 05/20/2023]
Abstract
Early plant embryogenesis condenses the fundamental processes underlying plant development into a short sequence of predictable steps. The main tissues, as well as stem cells for their post-embryonic maintenance, are specified through genetic control networks. A key question is how cell fates are instructed by unique cellular transcriptomes, and important insights have recently been gained through cell type-specific transcriptomics during post-embryonic development. However, the poor accessibility and small size of Arabidopsis (Arabidopsis thaliana) embryos have obstructed similar progress during embryogenesis. Here, we review the current situation in plant embryo transcriptomics, and discuss how the recent development of novel cell-specific analysis technologies will enable the identification of cellular transcriptomes in the early Arabidopsis embryo.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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206
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de Vega-Bartol JJ, Simões M, Lorenz WW, Rodrigues AS, Alba R, Dean JFD, Miguel CM. Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster. BMC PLANT BIOLOGY 2013; 13:123. [PMID: 23987738 PMCID: PMC3844413 DOI: 10.1186/1471-2229-13-123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 08/24/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND It is during embryogenesis that the plant body plan is established and the meristems responsible for all post-embryonic growth are specified. The molecular mechanisms governing conifer embryogenesis are still largely unknown. Their elucidation may contribute valuable information to clarify if the distinct features of embryo development in angiosperms and gymnosperms result from differential gene regulation. To address this issue, we have performed the first transcriptomic analysis of zygotic embryo development in a conifer species (Pinus pinaster) focusing our study in particular on regulatory genes playing important roles during plant embryo development, namely epigenetic regulators and transcription factors. RESULTS Microarray analysis of P. pinaster zygotic embryogenesis was performed at five periods of embryo development from early developing to mature embryos. Our results show that most changes in transcript levels occurred in the first and the last embryo stage-to-stage transitions, namely early to pre-cotyledonary embryo and cotyledonary to mature embryo. An analysis of functional categories for genes that were differentially expressed through embryogenesis highlighted several epigenetic regulation mechanisms. While putative orthologs of transcripts associated with mechanisms that target transposable elements and repetitive sequences were strongly expressed in early embryogenesis, PRC2-mediated repression of genes seemed more relevant during late embryogenesis. On the other hand, functions related to sRNA pathways appeared differentially regulated across all stages of embryo development with a prevalence of miRNA functions in mid to late embryogenesis. Identification of putative transcription factor genes differentially regulated between consecutive embryo stages was strongly suggestive of the relevance of auxin responses and regulation of auxin carriers during early embryogenesis. Such responses could be involved in establishing embryo patterning. Later in development, transcripts with homology to genes acting on modulation of auxin flow and determination of adaxial-abaxial polarity were up-regulated, as were putative orthologs of genes required for meristem formation and function as well as establishment of organ boundaries. Comparative analysis with A. thaliana embryogenesis also highlighted genes involved in auxin-mediated responses, as well as epigenetic regulation, indicating highly correlated transcript profiles between the two species. CONCLUSIONS This is the first report of a time-course transcriptomic analysis of zygotic embryogenesis in a conifer. Taken together our results show that epigenetic regulation and transcriptional control related to auxin transport and response are critical during early to mid stages of pine embryogenesis and that important events during embryogenesis seem to be coordinated by putative orthologs of major developmental regulators in angiosperms.
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Affiliation(s)
- José J de Vega-Bartol
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marta Simões
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - W Walter Lorenz
- Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA 30602, USA
| | - Andreia S Rodrigues
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Rob Alba
- Monsanto Company, Mailstop CC4, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Jeffrey F D Dean
- Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA 30602, USA
| | - Célia M Miguel
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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207
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Wendrich JR, Weijers D. The Arabidopsis embryo as a miniature morphogenesis model. THE NEW PHYTOLOGIST 2013; 199:14-25. [PMID: 23590679 DOI: 10.1111/nph.12267] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/12/2013] [Indexed: 05/06/2023]
Abstract
Four basic ingredients of morphogenesis, oriented cell division and expansion, cell-cell communication and cell fate specification allow plant cells to develop into a wide variety of organismal architectures. A central question in plant biology is how these cellular processes are regulated and orchestrated. Here, we present the advantages of the early Arabidopsis embryo as a model for studying the control of morphogenesis. All ingredients of morphogenesis converge during embryogenesis, and the highly predictable nature of embryo development offers unprecedented opportunities for understanding their regulation in time and space. In this review we describe the morphogenetic principles underlying embryo patterning and discuss recent advances in their regulation. Morphogenesis is under tight transcriptional control and most genes that were identified as important regulators of embryo patterning encode transcription factors or components of signaling pathways. There exists, therefore, a large gap between the transcriptional control of embryo morphogenesis and the cellular execution. We describe the first such connections, and propose future directions that should help bridge this gap and generate comprehensive understanding of the control of morphogenesis.
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Affiliation(s)
- Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
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208
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Lin YL, Lai ZX. Evaluation of suitable reference genes for normalization of microRNA expression by real-time reverse transcription PCR analysis during longan somatic embryogenesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 66:20-5. [PMID: 23454294 DOI: 10.1016/j.plaphy.2013.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 02/05/2013] [Indexed: 05/02/2023]
Abstract
Accurate profiling of microRNAs (miRNAs) is an essential step for understanding both developmental and physiological functions of miRNAs. Real-time quantitative PCR (qPCR) is being widely used in miRNA expression studies, but choosing a suitable reference gene is a crucial factor for correct analysis of results. To date, there has been no systematic evaluation of qPCR reference genes for the study of miRNAs during somatic embryogenesis (SE) in the longan tree (Dimocarpus longan). Here, the most stably expressed miRNAs in synchronized longan tree embryogenic cultures at different developmental stages were determined using the geNorm and NormFinder algorithms. Validation qPCR experiments were performed for 24 miRNAs together with a snRNA (U6 snRNA), a rRNA (5S rRNA), and three housekeeping genes. It was found that small RNAs had better expression stability than protein-coding genes, and dlo-miR24 was identified as the most reliable reference gene, followed by dlo-miR168a*, dlo-miR2089*-1 and 5S rRNA. dlo-miR24 was recommended as a normalizer if only a single reference gene was to be used, while the combination of dlo-miR156c, dlo-2089*-1 and 5S rRNA was preferred to normalize miRNA expression data during longan SE.
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Affiliation(s)
- Yu Ling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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209
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Lin Y, Lai Z. Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.). PLoS One 2013; 8:e60337. [PMID: 23593197 PMCID: PMC3623967 DOI: 10.1371/journal.pone.0060337] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/25/2013] [Indexed: 01/27/2023] Open
Abstract
Somatic embryogenesis (SE), which resembles zygotic embryogenesis, is an essential component of the process of plant cell differentiation and embryo development. Although microRNAs (miRNAs) are important regulators of many plant develop- mental processes, their roles in SE have not been thoroughly investigated. In this study, we used deep-sequencing, computational, and qPCR methods to identify, profile, and describe conserved and novel miRNAs involved in longan (Dimocarpus longan) SE. A total of 643 conserved and 29 novel miRNAs (including star strands) from more than 169 miRNA families were identified in longan embryogenic tissue using Solexa sequencing. By combining computational and degradome sequencing approaches, we were able to predict 2063 targets of 272 miRNAs and verify 862 targets of 181 miRNAs. Target annotation revealed that the putative targets were involved in a broad variety of biological processes, including plant metabolism, signal transduction, and stimulus response. Analysis of stage- and tissue-specific expressions of 20 conserved and 4 novel miRNAs indicated their possible roles in longan SE. These miRNAs were dlo-miR156 family members and dlo-miR166c* associated with early embryonic culture developmental stages; dlo-miR26, dlo-miR160a, and families dlo-miR159, dlo-miR390, and dlo-miR398b related to heart-shaped and torpedo- shaped embryo formation; dlo-miR4a, dlo-miR24, dlo-miR167a, dlo-miR168a*, dlo-miR397a, dlo-miR398b.1, dlo-miR398b.2, dlo-miR808 and dlo-miR5077 involved in cotyledonary embryonic development; and dlo-miR17 and dlo-miR2089*-1 that have regulatory roles during longan SE. In addition, dlo-miR167a, dlo-miR808, and dlo-miR5077 may be required for mature embryo formation. This study is the first reported investigation of longan SE involving large-scale cloning, characterization, and expression profiling of miRNAs and their targets. The reported results contribute to our knowledge of somatic embryo miRNAs and provide insights into miRNA biogenesis and expression in plant somatic embryo development.
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Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry, Fuzhou, Fujian, China
- * E-mail:
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210
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Preston JC, Hileman LC. Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family. FRONTIERS IN PLANT SCIENCE 2013; 4:80. [PMID: 23577017 PMCID: PMC3617394 DOI: 10.3389/fpls.2013.00080] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/19/2013] [Indexed: 05/18/2023]
Abstract
The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors is functionally diverse, controlling a number of fundamental aspects of plant growth and development, including vegetative phase change, flowering time, branching, and leaf initiation rate. In natural plant populations, variation in flowering time and shoot architecture have major consequences for fitness. Likewise, in crop species, variation in branching and developmental rate impact biomass and yield. Thus, studies aimed at dissecting how the various functions are partitioned among different SPL genes in diverse plant lineages are key to providing insight into the genetic basis of local adaptation and have already garnered attention by crop breeders. Here we use phylogenetic reconstruction to reveal nine major SPL gene lineages, each of which is described in terms of function and diversification. To assess evidence for ancestral and derived functions within each SPL gene lineage, we use ancestral character state reconstructions. Our analyses suggest an emerging pattern of sub-functionalization, neo-functionalization, and possible convergent evolution following both ancient and recent gene duplication. Based on these analyses we suggest future avenues of research that may prove fruitful for elucidating the importance of SPL gene evolution in plant growth and development.
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Affiliation(s)
| | - Lena C. Hileman
- Ecology and Evolutionary Biology, The University of KansasLawrence, KS, USA
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211
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Yang X, Wang L, Yuan D, Lindsey K, Zhang X. Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1521-36. [PMID: 23382553 PMCID: PMC3617824 DOI: 10.1093/jxb/ert013] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide RNAs that regulate gene expression at the transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress, and pathogen responses. miRNAs with their targets have been widely studied in model plants, but limited knowledge is available on the small RNA population of cotton (Gossypium hirsutum)-an important economic crop, and global identification of related targets through degradome sequencing has not been developed previously. In this study, small RNAs and their targets were identified during cotton somatic embryogenesis (SE) through high-throughput small RNA and degradome sequencing, comparing seedling hypocotyl and embryogenic callus (EC) of G. hirsutum YZ1. A total of 36 known miRNA families were found to be differentially expressed, of which 19 miRNA families were represented by 29 precursors. Twenty-five novel miRNAs were identified. A total of 234 transcripts in EC and 322 transcripts in control (CK) were found to be the targets of 23 and 30 known miRNA families, respectively, and 16 transcripts were targeted by eight novel miRNAs. Interestingly, four trans-acting small interfering RNAs (tas3-siRNAs) were also found in degradome libraries, three of which perfectly matched their precursors. Several targets were further validated via RNA ligase-mediated rapid amplification of 5' cDNA ends (RLM 5'-RACE). The profiling of the miRNAs and their target genes provides new information on the miRNAs network during cotton SE.
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Affiliation(s)
- Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
- These authors contributed equally to this work
| | - Lichen Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
- These authors contributed equally to this work
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Keith Lindsey
- Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
- To whom correspondence should be addressed. E-mail:
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212
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MicroRNAs and their cross-talks in plant development. J Genet Genomics 2013; 40:161-70. [PMID: 23618399 DOI: 10.1016/j.jgg.2013.02.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 01/10/2023]
Abstract
Plant development is a complex process influenced by exogenous and endogenous elements. A series of postembryonic developmental events is involved to form the final architecture and contend with the changing environment. MicroRNA (miRNA) is one of endogenous non-coding RNAs, which plays an important role in plant developmental regulation. In this review, we summarized 34 miRNA families that are closely associated with plant development. Among these families, nine are expressed only in specific organs, whereas 20 families are expressed in at least two different organs. It is known that some miRNAs are expressed across most processes of plant growth, while some appear only at particular developmental stages or under special environmental conditions such as drought, waterlogging and short-day time. These miRNAs execute their diverse functions by regulating developmental gene expression levels, interacting with phytohormone signaling response, participating in the biogenesis of ta-siRNAs and affecting the production of miRNAs.
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213
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Wang F, Perry SE. Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development. PLANT PHYSIOLOGY 2013; 161:1251-64. [PMID: 23314941 PMCID: PMC3585594 DOI: 10.1104/pp.112.212282] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/10/2013] [Indexed: 05/18/2023]
Abstract
FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box-binding factor. LEC1, LEC2, and FUS3 are essential for plant embryo development. All three loss-of-function mutants in Arabidopsis (Arabidopsis thaliana) prematurely exit embryogenesis and enter seedling developmental programs. When ectopically expressed, these genes promote embryo programs in seedlings. We report on chromatin immunoprecipitation-tiling array experiments to globally map binding sites for FUS3 that, along with other published work to assess transcriptomes in response to FUS3, allow us to determine direct from indirect targets. Many transcription factors associated with embryogenesis are direct targets of FUS3, as are genes involved in the seed maturation program. FUS3 regulates genes encoding microRNAs that, in turn, control transcripts encoding transcription factors involved in developmental phase changes. Examination of direct targets of FUS3 reveals that FUS3 acts primarily or exclusively as a transcriptional activator. Regulation of microRNA-encoding genes is one mechanism by which FUS3 may repress indirect target genes. FUS3 also directly up-regulates VP1/ABI3-LIKE1 (VAL1), encoding a B3 domain protein that functions as a repressor of transcription. VAL1, along with VAL2 and VAL3, is involved in the transition from embryo to seedling development. Many genes are responsive to FUS3 and to VAL1/VAL2 but with opposite regulatory consequences. The emerging picture is one of complex cross talk and interactions among embryo transcription factors and their target genes.
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214
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Huang D, Koh C, Feurtado JA, Tsang EWT, Cutler AJ. MicroRNAs and their putative targets in Brassica napus seed maturation. BMC Genomics 2013; 14:140. [PMID: 23448243 PMCID: PMC3602245 DOI: 10.1186/1471-2164-14-140] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 02/21/2013] [Indexed: 01/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) are 20–21 nucleotide RNA molecules that suppress the transcription of target genes and may also inhibit translation. Despite the thousands of miRNAs identified and validated in numerous plant species, only small numbers have been identified from the oilseed crop plant Brassica napus (canola) – especially in seeds. Results Using next-generation sequencing technologies, we performed a comprehensive analysis of miRNAs during seed maturation at 9 time points from 10 days after flowering (DAF) to 50 DAF using whole seeds and included separate analyses of radicle, hypocotyl, cotyledon, embryo, endosperm and seed coat tissues at 4 selected time points. We identified more than 500 conserved miRNA or variant unique sequences with >300 sequence reads and also found 10 novel miRNAs. Only 27 of the conserved miRNA sequences had been previously identified in B. napus (miRBase Release 18). More than 180 MIRNA loci were identified/annotated using the B. rapa genome as a surrogate for the B.napus A genome. Numerous miRNAs were expressed in a stage- or tissue-specific manner suggesting that they have specific functions related to the fine tuning of transcript abundance during seed development. miRNA targets in B. napus were predicted and their expression patterns profiled using microarray analyses. Global correlation analysis of the expression patterns of miRNAs and their targets revealed complex miRNA-target gene regulatory networks during seed development. The miR156 family was the most abundant and the majority of the family members were primarily expressed in the embryo. Conclusions Large numbers of miRNAs with diverse expression patterns, multiple-targeting and co-targeting of many miRNAs, and complex relationships between expression of miRNAs and targets were identified in this study. Several key miRNA-target expression patterns were identified and new roles of miRNAs in regulating seed development are suggested. miR156, miR159, miR172, miR167, miR158 and miR166 are the major contributors to the network controlling seed development and maturation through their pivotal roles in plant development. miR156 may regulate the developmental transition to germination.
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Affiliation(s)
- Daiqing Huang
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon S7N 0W9, Canada
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215
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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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216
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Grant-Downton R, Rodriguez-Enriquez J. Emerging Roles for Non-Coding RNAs in Male Reproductive Development in Flowering Plants. Biomolecules 2012; 2:608-21. [PMID: 24970151 PMCID: PMC4030863 DOI: 10.3390/biom2040608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/19/2012] [Accepted: 11/23/2012] [Indexed: 01/07/2023] Open
Abstract
Knowledge of sexual reproduction systems in flowering plants is essential to humankind, with crop fertility vitally important for food security. Here, we review rapidly emerging new evidence for the key importance of non-coding RNAs in male reproductive development in flowering plants. From the commitment of somatic cells to initiating reproductive development through to meiosis and the development of pollen—containing the male gametes (sperm cells)—in the anther, there is now overwhelming data for a diversity of non-coding RNAs and emerging evidence for crucial roles for them in regulating cellular events at these developmental stages. A particularly exciting development has been the association of one example of cytoplasmic male sterility, which has become an unparalleled breeding tool for producing new crop hybrids, with a non-coding RNA locus.
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Affiliation(s)
- Robert Grant-Downton
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Josefina Rodriguez-Enriquez
- Instituto de Bioorgánica Antonio González (IUBO) University of La Laguna, Avenida Astrofísico Francisco Sánchez, 38206 La Laguna Tenerife, Spain.
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217
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Körbes AP, Machado RD, Guzman F, Almerão MP, de Oliveira LFV, Loss-Morais G, Turchetto-Zolet AC, Cagliari A, dos Santos Maraschin F, Margis-Pinheiro M, Margis R. Identifying conserved and novel microRNAs in developing seeds of Brassica napus using deep sequencing. PLoS One 2012; 7:e50663. [PMID: 23226347 PMCID: PMC3511302 DOI: 10.1371/journal.pone.0050663] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/24/2012] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. Members of 59 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally 29 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. Assembled mRNA-seq contigs allowed for a search of putative new precursors and led to the identification of 13 novel miRNA families. Analysis of miRNA population between libraries reveals that several miRNAs and isomiRNAs have different abundance in developing stages compared to mature seeds. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comparative study of the miRNA transcriptome of mature and developing B. napus seeds and provides a basis for future research on individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus.
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Affiliation(s)
- Ana Paula Körbes
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ronei Dorneles Machado
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Frank Guzman
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mauricio Pereira Almerão
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luiz Felipe Valter de Oliveira
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Guilherme Loss-Morais
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Andreia Carina Turchetto-Zolet
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Alexandro Cagliari
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Felipe dos Santos Maraschin
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marcia Margis-Pinheiro
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rogerio Margis
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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Meng Y, Shao C, Ma X, Wang H, Chen M. Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis. PLoS One 2012; 7:e50870. [PMID: 23226412 PMCID: PMC3511311 DOI: 10.1371/journal.pone.0050870] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/25/2012] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in plant development. The expression patterns of the miRNA genes significantly influence their regulatory activities. By utilizing small RNA (sRNA) high-throughput sequencing (HTS) data, the miRNA expression patterns were investigated in four organs (flowers, leaves, roots and seedlings) of Arabidopsis. Based on a set of criteria, dozens of organ-specific miRNAs were discovered. A dominant portion of the organ-specific miRNAs identified from the ARGONAUTE 4-enriched sRNA HTS libraries were highly expressed in flowers. Additionally, the expression of the precursors of the organ-specific miRNAs was analyzed. Degradome sequencing data-based approach was employed to identify the targets of the organ-specific miRNAs. The miRNA–target interactions were used for network construction. Subnetwork analysis unraveled some novel regulatory cascades, such as the feedback regulation mediated by miR161, the potential self-regulation of the genes miR172, miR396, miR398 and miR860, and the miR863-guided cleavage of the SERRATE transcript. Our bioinformatics survey expanded the organ-specific miRNA–target list in Arabidopsis, and could deepen the biological view of the miRNA expression and their regulatory roles.
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Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People’s Republic of China
- * E-mail: (YM); (HW); (MC)
| | - Chaogang Shao
- College of Life Sciences, Huzhou Teachers College, Huzhou, People’s Republic of China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People’s Republic of China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People’s Republic of China
- * E-mail: (YM); (HW); (MC)
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- * E-mail: (YM); (HW); (MC)
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219
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Tang X, Bian S, Tang M, Lu Q, Li S, Liu X, Tian G, Nguyen V, Tsang EWT, Wang A, Rothstein SJ, Chen X, Cui Y. MicroRNA-mediated repression of the seed maturation program during vegetative development in Arabidopsis. PLoS Genet 2012; 8:e1003091. [PMID: 23209442 PMCID: PMC3510056 DOI: 10.1371/journal.pgen.1003091] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 09/30/2012] [Indexed: 11/19/2022] Open
Abstract
The seed maturation program only occurs during late embryogenesis, and repression of the program is pivotal for seedling development. However, the mechanism through which this repression is achieved in vegetative tissues is poorly understood. Here we report a microRNA (miRNA)–mediated repression mechanism operating in leaves. To understand the repression of the embryonic program in seedlings, we have conducted a genetic screen using a seed maturation gene reporter transgenic line in Arabidopsis (Arabidopsis thaliana) for the isolation of mutants that ectopically express seed maturation genes in leaves. One of the mutants identified from the screen is a weak allele of ARGONAUTE1 (AGO1) that encodes an effector protein for small RNAs. We first show that it is the defect in the accumulation of miRNAs rather than other small RNAs that causes the ectopic seed gene expression in ago1. We then demonstrate that overexpression of miR166 suppresses the derepression of the seed gene reporter in ago1 and that, conversely, the specific loss of miR166 causes ectopic expression of seed maturation genes. Further, we show that ectopic expression of miR166 targets, type III homeodomain-leucine zipper (HD-ZIPIII) genes PHABULOSA (PHB) and PHAVOLUTA (PHV), is sufficient to activate seed maturation genes in vegetative tissues. Lastly, we show that PHB binds the promoter of LEAFY COTYLEDON2 (LEC2), which encodes a master regulator of seed maturation. Therefore, this study establishes a core module composed of a miRNA, its target genes (PHB and PHV), and the direct target of PHB (LEC2) as an underlying mechanism that keeps the seed maturation program off during vegetative development. Seed development can be conceptually divided into two phases: namely the morphogenesis phase, in which cell division is active and all the major organs are formed, and the maturation phase, in which cells enlarge and storage reserves are synthesized and accumulated. Expression of the seed maturation program is tightly controlled such that it only occurs during the late phase of seed development. To uncover the molecular mechanisms underlying the repression of seed genes during vegetative development, we performed a reporter-assisted genetic screen, and one mutant identified is a weak allele of ARGONAUTE1 (AGO1) that displays ectopic seed gene expression. We then performed a series of transgenic and genetic analyses to search for the molecular mechanisms underlying the mutant phenotype. We first demonstrate that the decrease in miR166 in ago1 is a major cause of the mutant phenotype. Further, we show that the targets of miR166, type III HD-ZIP transcription factors PHB and PHV, are sufficient for derepressing seed maturation genes in seedlings, likely by binding directly to the promoter of a master regulator gene of maturation. Thus, this work establishes a miRNA–mediated pathway that represses the embryonic program and also establishes PHB/PHV as direct activators of the maturation program.
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Affiliation(s)
- Xurong Tang
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Shaomin Bian
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Mingjuan Tang
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
| | - Qing Lu
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
| | - Shengben Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Xigang Liu
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Gang Tian
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
| | - Edward W. T. Tsang
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - Aiming Wang
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America
- * E-mail: (YC); (XC)
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
- * E-mail: (YC); (XC)
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220
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Arif MA, Fattash I, Ma Z, Cho SH, Beike AK, Reski R, Axtell MJ, Frank W. DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility. MOLECULAR PLANT 2012; 5:1281-94. [PMID: 22511605 PMCID: PMC3506028 DOI: 10.1093/mp/sss036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 02/27/2012] [Indexed: 05/18/2023]
Abstract
Trans-acting small interfering RNAs (ta-siRNAs) are plant-specific siRNAs released from TAS precursor transcripts after microRNA-dependent cleavage, conversion into double-stranded RNA, and Dicer-dependent phased processing. Like microRNAs (miRNAs), ta-siRNAs direct site-specific cleavage of target RNAs at sites of extensive complementarity. Here, we show that the DICER-LIKE 4 protein of Physcomitrella patens (PpDCL4) is essential for the biogenesis of 21 nucleotide (nt) ta-siRNAs. In ΔPpDCL4 mutants, off-sized 23 and 24-nt ta-siRNAs accumulated as the result of PpDCL3 activity. ΔPpDCL4 mutants display severe abnormalities throughout Physcomitrella development, including sterility, that were fully reversed in ΔPpDCL3/ΔPpDCL4 double-mutant plants. Therefore, PpDCL3 activity, not loss of PpDCL4 function per se, is the cause of the ΔPpDCL4 phenotypes. Additionally, we describe several new Physcomitrella trans-acting siRNA loci, three of which belong to a new family, TAS6. TAS6 loci are typified by sliced miR156 and miR529 target sites and are in close proximity to PpTAS3 loci.
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Affiliation(s)
- M. Asif Arif
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestraβe 1, D-79104 Freiburg, Germany
| | - Isam Fattash
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestraβe 1, D-79104 Freiburg, Germany
| | - Zhaorong Ma
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sung Hyun Cho
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Anna K. Beike
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestraβe 1, D-79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestraβe 1, D-79104 Freiburg, Germany
- FRISYS Freiburg Initiative for Systems Biology, D-79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, D-79104 Freiburg, Germany
- FRIAS Freiburg Institute for Advanced Studies, D-79104 Freiburg, Germany
| | - Michael J. Axtell
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Wolfgang Frank
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestraβe 1, D-79104 Freiburg, Germany
- FRISYS Freiburg Initiative for Systems Biology, D-79104 Freiburg, Germany
- To whom correspondence should be addressed. E-mail , tel. +49 761 203 2820, fax +49 761 203 6945
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221
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Yamaguchi A, Abe M. Regulation of reproductive development by non-coding RNA in Arabidopsis: to flower or not to flower. JOURNAL OF PLANT RESEARCH 2012; 125:693-704. [PMID: 22836383 PMCID: PMC3485539 DOI: 10.1007/s10265-012-0513-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/06/2012] [Indexed: 05/18/2023]
Abstract
Plants monitor environmental factors, such as temperature and day length, and also endogenous factors, such as their age and phytohormones, to decide when to flower. These cues are utilized to control expression levels of genes required for flowering. Thus, flowering time control is a unique model for understanding how gene activity is precisely regulated at the transcriptional level. In Arabidopsis, a remarkable number of non-coding RNA molecules have been identified by advanced sequencing technology. Recent progress in the flowering field has revealed several non-coding RNAs that play a major role in determining flowering time. Here, we introduce how two types of non-coding RNA species, microRNA (miRNA) and long noncoding RNA (lncRNA), contribute to flowering via regulation of target gene activity involved in this vital developmental transition.
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Affiliation(s)
- Ayako Yamaguchi
- Laboratory of Plant Science, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present Address: Graduate School of Biostudies, Kyoto University, Yoshida Konoecho, Sakyo-ku, Kyoto, 606-8501 Japan
| | - Mitsutomo Abe
- Laboratory of Plant Science, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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222
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Wang QM, Wang L. An evolutionary view of plant tissue culture: somaclonal variation and selection. PLANT CELL REPORTS 2012; 31:1535-47. [PMID: 22610486 DOI: 10.1007/s00299-012-1281-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 04/30/2012] [Accepted: 04/30/2012] [Indexed: 05/20/2023]
Abstract
Plants regenerated from in vitro cultures possess an array of genetic and epigenetic changes. This phenomenon is known as 'somaclonal variation' and the frequency of somaclonal variation (SV) is usually elevated far beyond that expected in nature. Initially, the relationship between time in culture and detected SV was found to support the widespread belief that SV accumulates with culture age. However, a few studies indicated that older cultures yielded regenerants with less SV. What leads to this seemed contradiction? In this article, we have proposed a novel in vitro callus selection hypothesis, differentiation bottleneck (D-bottleneck) and dedifferentiation bottleneck (Dd-bottleneck), which consider natural selection theory to be fit for cell population in vitro. The results of multiplication races between the cells with the true-to-type phenotype and the deleterious cells determine the increase/decrease of SV frequencies in calli or regenerants as in vitro culture time goes on. The possibility of interpreting the complex situation of time-related SV by the evolutionary theory is discussed in this paper. In addition, the SV threshold, space-determined hypothesis and D-bottleneck are proposed to interpret the loss of the regenerability through a long period of plant tissue culture (PTC).
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Affiliation(s)
- Qin-Mei Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, People's Republic of China.
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223
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Jones-Rhoades MW. Conservation and divergence in plant microRNAs. PLANT MOLECULAR BIOLOGY 2012; 80:3-16. [PMID: 21996939 DOI: 10.1007/s11103-011-9829-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 09/15/2011] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression in eukaryotic cells. The past decade has seen an explosion in our understanding of the sets of miRNA genes encoded in the genomes in different species of plants and the mechanisms by which miRNAs interact with target RNAs. A subset of miRNA families (and their binding sites in target RNAs) are conserved between angiosperms and basal plants, suggesting they predate the divergence of existing lineages of plants. However, the majority of miRNA families expressed by any given plant species have a narrow phylogenetic distribution. As a group, these "young" miRNAs genes appear to be evolutionarily fluid and lack clearly understood biological function. The goal of this review is to summarize our understanding of the sets of miRNA genes and miRNA targets that exist in various plant species and to discuss hypotheses that explain the patterns of conservation and divergence observed among microRNAs in plants.
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Hwan Lee J, Joon Kim J, Ahn JH. Role of SEPALLATA3 (SEP3) as a downstream gene of miR156-SPL3-FT circuitry in ambient temperature-responsive flowering. PLANT SIGNALING & BEHAVIOR 2012; 7:1151-4. [PMID: 22899051 PMCID: PMC3489649 DOI: 10.4161/psb.21366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
SEPALLATA3 (SEP3) is important in determining flowering time as well as floral organ identity. Although much is known about the regulation of floral organ identity by SEP3, its role as a downstream gene of FLOWERING LOCUS T (FT) for the regulation of ambient temperature-responsive flowering is poorly understood. Here, we show that SEP3 as a downstream gene of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (SPL3) and FT modulates the flowering time in response to different ambient temperatures. SEP3 overexpression showed temperature-insensitive flowering at 23°C and 16°C. This suggests that altered SEP3 activity affects ambient temperature-responsive flowering. However, a lesion in SEP3 did not obviously affect ambient temperature-responsive flowering. SEP3 expression was affected by altered SPL3 and FT activities in the leaf and shoot apical regions at different temperatures. These results suggest that the miR156-SPL3-FT circuitry directly or indirectly regulates SEP3 expression for the regulation of ambient temperature-responsive flowering in Arabidopsis.
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Affiliation(s)
| | | | - Ji Hoon Ahn
- Creative Research Initiatives; Division of Life Sciences; Korea University; Seoul, South Korea
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225
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Li T, Chen J, Qiu S, Zhang Y, Wang P, Yang L, Lu Y, Shi J. Deep sequencing and microarray hybridization identify conserved and species-specific microRNAs during somatic embryogenesis in hybrid yellow poplar. PLoS One 2012; 7:e43451. [PMID: 22952685 PMCID: PMC3430688 DOI: 10.1371/journal.pone.0043451] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 07/20/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND To date, several studies have indicated a major role for microRNAs (miRNAs) in regulating plant development, but miRNA-mediated regulation of the developing somatic embryo is poorly understood, especially during early stages of somatic embryogenesis in hardwood plants. In this study, Solexa sequencing and miRNA microfluidic chips were used to discover conserved and species-specific miRNAs during somatic embryogenesis of hybrid yellow poplar (Liriodendron tulipifera×L. chinense). METHODOLOGY/PRINCIPAL FINDINGS A total of 17,214,153 reads representing 7,421,623 distinct sequences were obtained from a short RNA library generated from small RNAs extracted from all stages of somatic embryos. Through a combination of deep sequencing and bioinformatic analyses, we discovered 83 sequences with perfect matches to known miRNAs from 33 conserved miRNA families and 273 species-specific candidate miRNAs. MicroRNA microarray results demonstrated that many conserved and species-specific miRNAs were expressed in hybrid yellow poplar embryos. In addition, the microarray also detected another 149 potential miRNAs, belonging to 29 conserved families, which were not discovered by deep sequencing analysis. The biological processes and molecular functions of the targets of these miRNAs were predicted by carrying out BLAST search against Arabidopsis thaliana GenBank sequences and then analyzing the results with Gene Ontology. CONCLUSIONS Solexa sequencing and microarray hybridization were used to discover 232 candidate conserved miRNAs from 61 miRNA families and 273 candidate species-specific miRNAs in hybrid yellow poplar. In these predicted miRNAs, 64 conserved miRNAs and 177 species-specific miRNAs were detected by both sequencing and microarray hybridization. Our results suggest that miRNAs have wide-ranging characteristics and important roles during all stages of somatic embryogenesis in this economically important species.
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Affiliation(s)
- Tingting Li
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Shuai Qiu
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Yanjuan Zhang
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Liwei Yang
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China
- * E-mail:
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226
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Zhang J, Zhang S, Han S, Wu T, Li X, Li W, Qi L. Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis. PLANTA 2012; 236:647-57. [PMID: 22526500 DOI: 10.1007/s00425-012-1643-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 03/28/2012] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are emerging as essential regulators of biological processes. Somatic embryogenesis is one of the most important techniques for gymnosperm-breeding programs, but there is little understanding of its underlying mechanism. To investigate the roles of miRNAs during somatic embryogenesis in larch, we constructed a small RNA library from somatic embryos. High-throughput sequencing of the library identified 83 conserved miRNAs from 35 families, 16 novel miRNAs, and 14 plausible miRNA candidates, with a high proportion specific to larch or gymnosperms. qRT-PCR analysis demonstrated that both the conserved and novel or candidate miRNAs were expressed in larch. Several miRNA precursor sequences were obtained via RACE. We predicted 110 target genes using bioinformatics, and validated 9 of them by 5' RACE. 11 conserved miRNA families including 17 miRNAs with critical functions in plant development and six target mRNAs were detected by qRT-PCR in the larch SE. Stage-specific expression of miRNAs and their targets indicate their possible modulation on SE of larch: miR171a/b might exert function on PEMs, while miR171c acts in the induction process of larch SE; miR397 and miR398 mainly involved in modulation of PEM propagation and transition to single embryo; miR162 and miR168 exert their regulatory function during total SE process, especially during stages 5-8; miR156, miR159, miR160, miR166, miR167, and miR390 might play regulatory roles during cotyledonary embryo development. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving specific and common miRNAs operating post-transcriptionally during embryogenesis.
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Affiliation(s)
- Junhong Zhang
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
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227
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Characterization of microRNAs expression during maize seed development. BMC Genomics 2012; 13:360. [PMID: 22853295 PMCID: PMC3468377 DOI: 10.1186/1471-2164-13-360] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 07/09/2012] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are approximately 20-22 nt non-coding RNAs that play key roles in many biological processes in both animals and plants. Although a number of miRNAs were identified in maize, the function of miRNA in seed development was merely discussed. Results In this study, two small RNA libraries were sequenced, and a total reads of 9,705,761 and 9,005,563 were generated from developing seeds and growing leaves, respectively. Further analysis identified 125 known miRNAs in seeds and 127 known miRNAs in leaves. 54 novel miRNAs were identified and they were not reported in other plants. Additionally, some miRNA*s of these novel miRNAs were detected. Potential targets of all novel miRNAs were predicted based on our strict criteria. In addition to deep-sequencing, miRNA microarray study confirmed the higher expression of several miRNAs in seeds. In summary, our results indicated the distinct expression of miRNAs during seed development. Conclusions We had identified 125 and 127 known miRNAs from seeds and leaves in maize, and a total of 54 novel miRNAs were discovered. The different miRNA expression profile in developing seeds were revealed by both sequencing and microarray studies.
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228
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Liu C, Axtell MJ, Fedoroff NV. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis. PLANT PHYSIOLOGY 2012; 159:748-58. [PMID: 22474216 PMCID: PMC3406889 DOI: 10.1104/pp.112.193508] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/30/2012] [Indexed: 05/18/2023]
Abstract
Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 null mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher K(cat) and lower K(m) values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 null mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates.
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229
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Salinas M, Xing S, Höhmann S, Berndtgen R, Huijser P. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. PLANTA 2012; 235:1171-84. [PMID: 22160465 DOI: 10.1007/s00425-011-1565-y] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/25/2011] [Indexed: 05/07/2023]
Abstract
SBP-box genes represent transcription factors ubiquitously found in the plant kingdom and recognized as important regulators of many different aspects of plant development. In this study, 15 SBP-box gene family members were identified in tomato and analyzed with respect to their genomic organization and other structural features. Phylogenetic reconstruction based on the DNA-binding SBP-domain, allowed the classification of the SlySBP proteins into eight groups representing clear orthologous relationships to family members of other flowering plants and the moss Physcomitrella. In order to have a better understanding of their possible function in the development of a fleshy-fruit species like tomato, the mRNA expression levels of all SlySBP genes were quantified in vegetative and reproductive organs of plants, at different stages of growth. As transcripts of ten SlySBP genes were found to carry putative miR156- and miR157-response elements, the expression levels of the corresponding microRNAs were determined as well, revealing different patterns of expression. In addition, eight putative miR156 and four miR157 encoding loci could be identified in the tomato genome, four of them forming a polycistronic cluster. Whereas miR156 and miR157 levels were highest in seedlings, leaves and anthers of young flowers, most miR156-targeted SlySBP genes were found to be expressed in young inflorescences and during fruit development and ripening, suggesting a particularly important role during tomato reproductive growth. The data presented provide a basis for future clarification of the various functions that SBP-box gene family members play in tomato growth and development.
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Affiliation(s)
- María Salinas
- Department of Molecular Plant Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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230
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Chen X. Small RNAs in development - insights from plants. Curr Opin Genet Dev 2012; 22:361-7. [PMID: 22578318 DOI: 10.1016/j.gde.2012.04.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 03/30/2012] [Accepted: 04/11/2012] [Indexed: 10/28/2022]
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs), which constitute two major classes of endogenous small RNAs in plants, impact a multitude of developmental and physiological processes by imparting sequence specificity to gene and genome regulation. Although lacking the third major class of small RNAs found in animals, Piwi-interacting RNAs (piRNAs), plants have expanded their repertoire of endogenous siRNAs, some of which fulfill similar molecular and developmental functions as piRNAs in animals. Research on plant miRNAs and siRNAs has contributed invaluable insights into small RNA biology, thanks to the highly conserved molecular logic behind the biogenesis and actions of small RNAs. Here, I review progress in the plant small RNA field in the past two years, with an emphasis on recent findings related to plant development. I do not recount the numerous developmental processes regulated by small RNAs; instead, I focus on major principles that have been derived from recent studies and draw parallels, when applicable, between plants and animals.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, United States.
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231
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Kim JJ, Lee JH, Kim W, Jung HS, Huijser P, Ahn JH. The microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis. PLANT PHYSIOLOGY 2012; 159:461-78. [PMID: 22427344 PMCID: PMC3375978 DOI: 10.1104/pp.111.192369] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 03/13/2012] [Indexed: 05/18/2023]
Abstract
The flowering time of plants is affected by modest changes in ambient temperature. However, little is known about the regulation of ambient temperature-responsive flowering by small RNAs. In this study, we show that the microRNA156 (miR156)-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (SPL3) module directly regulates FLOWERING LOCUS T (FT) expression in the leaf to control ambient temperature-responsive flowering. Overexpression of miR156 led to more delayed flowering at a lower ambient temperature (16°C), which was associated with down-regulation of FT and FRUITFULL expression. Among miR156 target genes, SPL3 mRNA levels were mainly reduced, probably because miR156-mediated cleavage of SPL3 mRNA was higher at 16°C. Overexpression of miR156-resistant SPL3 [SPL3(-)] caused early flowering, regardless of the ambient temperature, which was associated with up-regulation of FT and FRUITFULL expression. Reduction of miR156 activity by target mimicry led to a phenotype similar to that of SUC2::rSPL3 plants. FT up-regulation was observed after dexamethasone treatment in GVG-rSPL3 plants. Misexpression and artificial microRNA-mediated suppression of FT in the leaf dramatically altered the ambient temperature-responsive flowering of plants overexpressing miR156 and SPL3(-). Chromatin immunoprecipitation assay showed that the SPL3 protein directly binds to GTAC motifs within the FT promoter. Lesions in TERMINAL FLOWER1, SHORT VEGETATIVE PHASE, and EARLY FLOWERING3 did not alter the expression of miR156 and SPL3. Taken together, our data suggest that the interaction between the miR156-SPL3 module and FT is part of the regulatory mechanism controlling flowering time in response to ambient temperature.
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232
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Bozorov TA, Pandey SP, Dinh ST, Kim SG, Heinrich M, Gase K, Baldwin IT. DICER-like proteins and their role in plant-herbivore interactions in Nicotiana attenuata. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:189-206. [PMID: 22313877 DOI: 10.1111/j.1744-7909.2012.01104.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DICER-like (DCL) proteins produce small RNAs that silence genes involved in development and defenses against viruses and pathogens. Which DCLs participate in plant-herbivore interactions remains unstudied. We identified and stably silenced four distinct DCL genes by RNAi in Nicotiana attenuata (Torrey ex. Watson), a model for the study of plant-herbivore interactions. Silencing DCL1 expression was lethal. Manduca sexta larvae performed significantly better on ir-dcl3 and ir-dcl4 plants, but not on ir-dcl2 plants compared to wild type plants. Phytohormones, defense metabolites and microarray analyses revealed that when DCL3 and DCL4 were silenced separately, herbivore resistance traits were regulated in distinctly different ways. Crossing of the lines revealed complex interactions in the patterns of regulation. Single ir-dcl4 and double ir-dcl2 ir-dcl3 plants were impaired in JA accumulation, while JA-Ile was increased in ir-dcl3 plants. Ir-dcl3 and ir-dcl4 plants were impaired in nicotine accumulation; silencing DCL2 in combination with either DCL3 or DCL4 restored nicotine levels to those of WT. Trypsin proteinase inhibitor activity and transcripts were only silenced in ir-dcl3 plants. We conclude that DCL2/3/4 interact in a complex manner to regulate anti-herbivore defenses and that these interactions significantly complicate the already challenging task of understanding smRNA function in the regulation of biotic interactions.
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233
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Xie K, Shen J, Hou X, Yao J, Li X, Xiao J, Xiong L. Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. PLANT PHYSIOLOGY 2012; 158:1382-94. [PMID: 22271747 PMCID: PMC3291253 DOI: 10.1104/pp.111.190488] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 01/17/2012] [Indexed: 05/18/2023]
Abstract
The highly conserved plant microRNA, miR156, is an essential regulator for plant development. In Arabidopsis (Arabidopsis thaliana), miR156 modulates phase changing through its temporal expression in the shoot. In contrast to the gradual decrease over time in the shoot (or whole plant), we found that the miR156 level in rice (Oryza sativa) gradually increased from young leaf to old leaf after the juvenile stage. However, the miR156-targeted rice SQUAMOSA-promoter binding-like (SPL) transcription factors were either dominantly expressed in young leaves or not changed over the time of leaf growth. A comparison of the transcriptomes of early-emerged old leaves and later-emerged young leaves from wild-type and miR156 overexpression (miR156-OE) rice lines found that expression levels of 3,008 genes were affected in miR156-OE leaves. Analysis of temporal expression changes of these genes suggested that miR156 regulates gene expression in a leaf age-dependent manner, and miR156-OE attenuated the temporal changes of 2,660 genes. Interestingly, seven conserved plant microRNAs also showed temporal changes from young to old leaves, and miR156-OE also attenuated the temporal changes of six microRNAs. Consistent with global gene expression changes, miR156-OE plants resulted in dramatic changes including precocious leaf maturation and rapid leaf/tiller initiation. Our results indicate that another gradient of miR156 is present over time, a gradual increase during leaf growth, in addition to the gradual decrease during shoot growth. Gradually increased miR156 expression in the leaf might be essential for regulating the temporal expression of genes involved in leaf development.
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MESH Headings
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genes, Plant
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Microscopy, Electron, Scanning
- Oryza/genetics
- Oryza/growth & development
- Oryza/metabolism
- Plant Epidermis/genetics
- Plant Epidermis/metabolism
- Plant Epidermis/ultrastructure
- Plant Leaves/genetics
- Plant Leaves/growth & development
- Plant Leaves/metabolism
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Shoots/genetics
- Plant Shoots/growth & development
- Plant Shoots/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Plants, Genetically Modified/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Time Factors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptome
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234
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Barr MS, Willmann MR, Jenik PD. Is there a role for trihelix transcription factors in embryo maturation? PLANT SIGNALING & BEHAVIOR 2012; 7:205-9. [PMID: 22353863 PMCID: PMC3405702 DOI: 10.4161/psb.18893] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The development of the angiosperm seed includes the accumulation of storage products, the loss of most of its water and the establishment of dormancy. While much is known about the pathways that initiate maturation during mid-embryogenesis or repress it after germination, only recently has it been shown that other mechanisms repress the program during early embryogenesis.Two recent reports have shown that microRNAs are critical regulators of maturation in Arabidopsis early embryogenesis. Two closely related trihelix transcription factors, ASIL1 and ASIL2, were identified as probable partially redundant repressors of early maturation downstream of the microRNA-synthesizing enzyme DICER-LIKE1. An overlap between the genes upregulated in asil1-1 and dcl1-15 mutants support this conclusion. ASIL2 orthologs are found across seed plants, indicating that their role in maturation might be conserved. ASIL1 arose from the ancestral ASIL2 clade by a gene duplication event in the Brassicaceae, although it is not clear whether its function has diverged.
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Affiliation(s)
| | | | - Pablo D. Jenik
- Department of Biology; Franklin & Marshall College; Lancaster, PA USA
- * Correspondence to: Pablo D. Jenik;
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235
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Jeong S, Volny M, Lukowitz W. Axis formation in Arabidopsis - transcription factors tell their side of the story. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:4-9. [PMID: 22079785 PMCID: PMC4629246 DOI: 10.1016/j.pbi.2011.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 10/05/2011] [Accepted: 10/19/2011] [Indexed: 05/06/2023]
Abstract
Apical-to-basal auxin flux is a defining feature of land plants and determines their main body axis. How is the axis first set up in the embryo? Recent studies reveal that the establishment of embryonic polarity with the asymmetric first division as well as the separation of shoot and root fates within the proembryo depend on transcriptional regulation in the zygote and early embryo. Although the functional connections need to be better defined, this transcriptional network likely provides the positional information required for initiating the machinery capable of processing the systemic signal auxin in a context-dependent manner.
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Affiliation(s)
- Sangho Jeong
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
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236
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Schmid MW, Schmidt A, Klostermeier UC, Barann M, Rosenstiel P, Grossniklaus U. A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. PLoS One 2012; 7:e29685. [PMID: 22291893 PMCID: PMC3266888 DOI: 10.1371/journal.pone.0029685] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 12/01/2011] [Indexed: 11/18/2022] Open
Abstract
The acquisition of distinct cell fates is central to the development of multicellular organisms and is largely mediated by gene expression patterns specific to individual cells and tissues. A spatially and temporally resolved analysis of gene expression facilitates the elucidation of transcriptional networks linked to cellular identity and function. We present an approach that allows cell type-specific transcriptional profiling of distinct target cells, which are rare and difficult to access, with unprecedented sensitivity and resolution. We combined laser-assisted microdissection (LAM), linear amplification starting from <1 ng of total RNA, and RNA-sequencing (RNA-Seq). As a model we used the central cell of the Arabidopsis thaliana female gametophyte, one of the female gametes harbored in the reproductive organs of the flower. We estimated the number of expressed genes to be more than twice the number reported previously in a study using LAM and ATH1 microarrays, and identified several classes of genes that were systematically underrepresented in the transcriptome measured with the ATH1 microarray. Among them are many genes that are likely to be important for developmental processes and specific cellular functions. In addition, we identified several intergenic regions, which are likely to be transcribed, and describe a considerable fraction of reads mapping to introns and regions flanking annotated loci, which may represent alternative transcript isoforms. Finally, we performed a de novo assembly of the transcriptome and show that the method is suitable for studying individual cell types of organisms lacking reference sequence information, demonstrating that this approach can be applied to most eukaryotic organisms.
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Affiliation(s)
- Marc W. Schmid
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Anja Schmidt
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | - Matthias Barann
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- * E-mail:
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237
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Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 2012; 482:94-7. [PMID: 22266940 DOI: 10.1038/nature10756] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 12/01/2011] [Indexed: 01/28/2023]
Abstract
In animals, maternal gene products deposited into eggs regulate embryonic development before activation of the zygotic genome. In plants, an analogous period of prolonged maternal control over embryogenesis is thought to occur based on some gene-expression studies. However, other gene-expression studies and genetic analyses show that some transcripts must derive from the early zygotic genome, implying that the prevailing model does not fully explain the nature of zygotic genome activation in plants. To determine the maternal, paternal and zygotic contributions to the early embryonic transcriptome, we sequenced the transcripts of hybrid embryos from crosses between two polymorphic inbred lines of Arabidopsis thaliana and used single-nucleotide polymorphisms diagnostic of each parental line to quantify parental contributions. Although some transcripts seemed to be either inherited from primarily one parent or transcribed from imprinted loci, the vast majority of transcripts were produced in near-equal amounts from both maternal and paternal alleles, even during the initial stages of embryogenesis. Results of reporter experiments and analyses of transcripts from genes that are not expressed in sperm and egg indicate early and widespread zygotic transcription. Thus, in contrast to early animal embryogenesis, early plant embryogenesis is mostly under zygotic control.
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238
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Schwab R. The Roles of miR156 and miR172 in Phase Change Regulation. MICRORNAS IN PLANT DEVELOPMENT AND STRESS RESPONSES 2012. [DOI: 10.1007/978-3-642-27384-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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239
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Lau S, Slane D, Herud O, Kong J, Jürgens G. Early embryogenesis in flowering plants: setting up the basic body pattern. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:483-506. [PMID: 22224452 DOI: 10.1146/annurev-arplant-042811-105507] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Early embryogenesis is the critical developmental phase during which the basic features of the plant body are established: the apical-basal axis of polarity, different tissue layers, and both the root pole and the shoot pole. Polarization of the zygote correlates with the generation of apical and basal (embryonic and extraembryonic) cell fates. Whereas mechanisms of zygote polarization are still largely unknown, distinct expression domains of WOX family transcription factors as well as directional auxin transport and local auxin response are known to be involved in early apical-basal patterning. Radial patterning of tissue layers appears to be mediated by cell-cell communication involving both peptide signaling and transcription factor movement. Although the initiation of the shoot pole is still unclear, the apical organization of the embryo depends on both the proper establishment of transcription factor expression domains and, for cotyledon initiation, upward auxin flow in the protoderm. Here we focus on the essential patterning processes, drawing mainly on data from Arabidopsis thaliana and also including relevant data from other species if available.
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Affiliation(s)
- Steffen Lau
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Gu XL, Wang H, Huang H, Cui XF. SPT6L encoding a putative WG/GW-repeat protein regulates apical-basal polarity of embryo in Arabidopsis. MOLECULAR PLANT 2012; 5:249-259. [PMID: 21948524 DOI: 10.1093/mp/ssr073] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In eukaryotes, a protein motif consisting of WG/GW repeats, also called the Argonaute (AGO) hook, is thought to be essential for binding AGO proteins to fulfill their functions in RNA-mediated gene silencing. Although a number of WG/GW-containing proteins have been computationally identified in Arabidopsis, their roles in plant growth and development are unknown. Here, we show that the Arabidopsis Suppressor of Ty insertion 6-like (SPT6L) gene, which encodes a protein with C-terminal WG/GW repeats, plays critical roles in embryonic development. SPT6L is evolutionarily conserved only in vascular plants, with varying numbers of C-terminal WG/GW repeats, which are plant-species specific. spt6l mutants formed embryos with an aberrant apical-basal axis, showing insufficient development of the basal domain and embryonic lethality. Expression domains of the class-III homeodomain-leucine zipper (HD-ZIP III) genes PHABULOSA (PHB) and PHAVOLUTA (PHV) were expanded in the spt6l embryo. In contrast, the PLETHORA1 (PLT1) gene, which acts antagonistically to the HD-ZIP III genes in specification of basal fate, was severely down-regulated in the spt6l mutant. Furthermore, the phb phv double mutations partially rescued aberrant basal development in the spt6l background and restored PLT1 expression. Collectively, our results indicate that SPT6L is essential for specification of the apical-basal axis, partly by controlling the HD-ZIP III genes in embryos.
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Affiliation(s)
- Xiao-Lu Gu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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242
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Lozada-Chávez I, Stadler PF, Prohaska SJ. "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity. ORIGINS LIFE EVOL B 2011; 41:587-607. [PMID: 22322874 DOI: 10.1007/s11084-011-9262-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/12/2011] [Indexed: 02/06/2023]
Abstract
The transitions to multicellularity mark the most pivotal and distinctive events in life's history on Earth. Although several transitions to "simple" multicellularity (SM) have been recorded in both bacterial and eukaryotic clades, transitions to complex multicellularity (CM) have only happened a few times in eukaryotes. A large number of cell types (associated with large body size), increased energy consumption per gene expressed, and an increment of non-protein-coding DNA positively correlate with CM. These three factors can indeed be understood as the causes and consequences of the regulation of gene expression. Here, we discuss how a vast expansion of non-protein-coding RNA (ncRNAs) regulators rather than large numbers of novel protein regulators can easily contribute to the emergence of CM. We also propose that the evolutionary advantage of RNA-based gene regulation derives from the robustness of the RNA structure that makes it easy to combine genetic drift with functional exploration. We describe a model which aims to explain how the evolutionary dynamic of ncRNAs becomes dominated by the accessibility of advantageous mutations to innovate regulation in complex multicellular organisms. The information and models discussed here outline the hypothesis that pervasive ncRNA-based regulatory systems, only capable of being expanded and explored in higher eukaryotes, are prerequisite to complex multicellularity. Thereby, regulatory RNA molecules in Eukarya have allowed intensification of morphological complexity by stabilizing critical phenotypes and controlling developmental precision. Although the origin of RNA on early Earth is still controversial, it is becoming clear that once RNA emerged into a protocellular system, its relevance within the evolution of biological systems has been greater than we previously thought.
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Affiliation(s)
- Irma Lozada-Chávez
- Computational EvoDevo Group, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany.
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243
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Abstract
Plant development progresses through distinct phases: vegetative growth, followed by a reproductive phase and eventually seed set and senescence. The transitions between these phases are controlled by distinct genetic circuits that integrate endogenous and environmental cues. In recent years, however, it has become evident that the genetic networks that underlie these phase transitions share some common factors. Here, we review recent advances in the field of plant phase transitions, highlighting the role of two microRNAs - miR156 and miR172 - and their respective targets during these transitions. In addition, we discuss the evolutionary conservation of the functions of these miRNAs in regulating the control of plant developmental phase transitions.
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Affiliation(s)
- Peter Huijser
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
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244
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Tingting L, Jinhui C, Jisen S, Jin X. Deep sequencing combined with microarray hybridization to identify novel and conserved microRNAs during somatic embryogenesis of hybrid yellow-poplar (Liriodendron chinense (Hemsl.) Sarg. X L. tulipiferaLinn.). BMC Proc 2011. [PMCID: PMC3240098 DOI: 10.1186/1753-6561-5-s7-p74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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245
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Miguel C, Marum L. An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3713-25. [PMID: 21617249 DOI: 10.1093/jxb/err155] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Epigenetic mechanisms are highly dynamic events that modulate gene expression. As more accurate and powerful tools for epigenetic analysis become available for application in a broader range of plant species, analysis of the epigenetic landscape of plant cell cultures may turn out to be crucial for understanding variant phenotypes. In vitro plant cell and tissue culture methodologies are important for many ongoing plant propagation and breeding programmes as well as for cutting-edge research in several plant model species. Although it has long been known that in vitro conditions induce variation at several levels, most studies using such conditions rely on the assumption that in vitro cultured plant cells/tissues mostly conform genotypically and phenotypically. However, when large-scale clonal propagation is the aim, there has been a concern in confirming true-to-typeness using molecular markers for evaluating stability. While in most reports genetic variation has been found to occur at relatively modest frequencies, variation in DNA methylation patterns seems to be much more frequent and in some cases it has been directly implicated in phenotypic variation. Recent advances in the field of epigenetics have uncovered highly dynamic mechanisms of chromatin remodelling occurring during cell dedifferentiation and differentiation processes on which in vitro adventitious plant regeneration systems are based. Here, an overview of recent findings related to developmental switches occurring during in vitro culture is presented. Additionally, an update on the detection of epigenetic variation in plant cell cultures will be provided and discussed in the light of recent progress in the plant epigenetics field.
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Affiliation(s)
- Célia Miguel
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa, Oeiras, Portugal.
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246
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Xing S, Salinas M, Huijser P. New players unveiled in early anther development. PLANT SIGNALING & BEHAVIOR 2011; 6:934-8. [PMID: 21633200 PMCID: PMC3257765 DOI: 10.4161/psb.6.7.15668] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 05/08/2023]
Abstract
Anther development is an important process for the successful sexual reproduction in plants. Whereas the regulation of the late stages of anther development is quite well described in A. thaliana, little is known about the regulation of the early stages of this process. Two novel groups of factors involved in these early stages have recently been described, namely ROXYs, members of the Glutaredoxin (GRX) family of small and ubiquitous oxidoreductases involved in various cellular and stress-related responses, and SBP-box Genes. ROXYs belong to the CC-type of GRXs with a CCXC active motif and are specific for higher plants. SBP-box genes encode for SQUAMOSA PROMOTER BINDING PROTEIN transcription factors, many of which are targeted by miR156 and miR157. Strikingly, both the enzymes and the transcription factors represent evolutionary conserved gene families and loss-of-function of these genes exhibits similar anther phenotypes, e.g. arresting sporogenous cell formation and missing pollen sacs. This mini-review gives an overview of how these factors affect early anther development and discusses a possible relationship between these factors and other known early anther genes.
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Affiliation(s)
- Shuping Xing
- Department of Molecular Plant Genetics; Max Planck Institute for Plant Breeding Research; Cologne, Germany
| | - María Salinas
- Department of Molecular Plant Genetics; Max Planck Institute for Plant Breeding Research; Cologne, Germany
- Área de Genética; Departamento de Biología Aplicada; Universidad de Almería; Almería, Spain
| | - Peter Huijser
- Department of Molecular Plant Genetics; Max Planck Institute for Plant Breeding Research; Cologne, Germany
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247
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Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. THE PLANT CELL 2011; 23:1512-22. [PMID: 21487097 PMCID: PMC3101539 DOI: 10.1105/tpc.111.084525] [Citation(s) in RCA: 602] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 03/21/2011] [Accepted: 03/29/2011] [Indexed: 05/18/2023]
Abstract
Flavonoids are synthesized through an important metabolic pathway that leads to the production of diverse secondary metabolites, including anthocyanins, flavonols, flavones, and proanthocyanidins. Anthocyanins and flavonols are derived from Phe and share common precursors, dihydroflavonols, which are substrates for both flavonol synthase and dihydroflavonol 4-reductase. In the stems of Arabidopsis thaliana, anthocyanins accumulate in an acropetal manner, with the highest level at the junction between rosette and stem. We show here that this accumulation pattern is under the regulation of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, which are deeply conserved and known to have important roles in regulating phase change and flowering. Increased miR156 activity promotes accumulation of anthocyanins, whereas reduced miR156 activity results in high levels of flavonols. We further provide evidence that at least one of the miR156 targets, SPL9, negatively regulates anthocyanin accumulation by directly preventing expression of anthocyanin biosynthetic genes through destabilization of a MYB-bHLH-WD40 transcriptional activation complex. Our results reveal a direct link between the transition to flowering and secondary metabolism and provide a potential target for manipulation of anthocyanin and flavonol content in plants.
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Affiliation(s)
- Jin-Ying Gou
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Felipe F. Felippes
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany
| | - Jia-Wei Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tuebingen, Germany
- Address correspondence to
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248
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Willmann MR, Mehalick AJ, Packer RL, Jenik PD. MicroRNAs regulate the timing of embryo maturation in Arabidopsis. PLANT PHYSIOLOGY 2011; 155:1871-84. [PMID: 21330492 PMCID: PMC3091098 DOI: 10.1104/pp.110.171355] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/15/2011] [Indexed: 05/18/2023]
Abstract
The seed is a key evolutionary adaptation of land plants that facilitates dispersal and allows for germination when the environmental conditions are adequate. Mature seeds are dormant and desiccated, with accumulated storage products that are to be used by the seedling after germination. These properties are imposed on the developing embryo by a maturation program, which operates during the later part of embryogenesis. A number of "master regulators" (the "LEC genes") required for the induction of the maturation program have been described, but it is not known what prevents this program from being expressed during early embryogenesis. Here, we report that Arabidopsis (Arabidopsis thaliana) embryos mutant for strong alleles of DICER-LIKE1, the enzyme responsible for the biosynthesis of microRNAs (miRNAs), mature earlier than their wild-type counterparts. This heterochronic phenotype indicates that miRNAs are key regulators of the timing of the maturation program. We demonstrate that miRNAs operate in part by repressing the master regulators LEAFY COTYLEDON2 and FUSCA3 and identify the trihelix transcription factors ARABIDOPSIS 6B-INTERACTING PROTEIN1-LIKE1 (ASIL1) and ASIL2 and the histone deacetylase HDA6/SIL1 as components that act downstream of miRNAs to repress the maturation program early in embryogenesis. Both ASIL1 and HDA6/SIL1 are known to act to prevent the expression of embryonic maturation genes after germination, but to our knowledge, this is the first time they have been shown to have a role during embryogenesis. Our data point to a common negative regulatory module of maturation during early embryogenesis and seedling development.
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249
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Abstract
Zygotic microRNAs coordinate the clearance of maternal mRNA in animals to facilitate developmental transitions. In a recent issue of Genes and Development, Nodine and Bartel (2010) uncover a reciprocal function in plants, where miRNA-156 preemptively represses genes that function later in development to prevent premature developmental transitions.
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