51
|
Achkar NP, Cambiagno DA, Manavella PA. miRNA Biogenesis: A Dynamic Pathway. TRENDS IN PLANT SCIENCE 2016; 21:1034-1044. [PMID: 27793495 DOI: 10.1016/j.tplants.2016.09.003] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) modulate plant homeostasis through the inactivation of specific mRNAs, especially those encoding transcription factors. A delicate spatial/temporal balance between a miRNA and its targets is central to achieving the appropriate biological outcomes. In this review we discuss our growing understanding of the dynamic regulation of miRNA biogenesis. We put special emphasis on crosstalk between miRNA biogenesis and other cellular processes such as transcription and splicing. We also discuss how the pathway is regulated in specific tissues to achieve harmonious plant development through a subtle balance between gene expression and silencing.
Collapse
Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Damián A Cambiagno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina.
| |
Collapse
|
52
|
von Arnim AG, Hellmann HA. Meeting report: processing, translation, decay - three ways to keep RNA sizzling. PLANT, CELL & ENVIRONMENT 2016; 39:2624-2628. [PMID: 27859406 DOI: 10.1111/pce.12819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/17/2016] [Accepted: 08/21/2016] [Indexed: 06/06/2023]
Abstract
This meeting report highlights key trends that emerged from a conference entitled Post-Transcriptional Gene Regulation in Plants, which was held 14-15 July 2016, as a satellite meeting of the annual meeting of the American Society of Plant Biologists in Austin, Texas. The molecular biology of RNA is emerging as an integral part of the framework for plants' responses to environmental challenges such as drought and heat, hypoxia, nutrient deprivation, light and pathogens. Moreover, the conference illustrated how a multitude of customized and pioneering omics-related technologies are being applied, more and more often in combination, to describe and dissect the complexities of gene expression at the post-transcriptional level.
Collapse
Affiliation(s)
- Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Hanjo A Hellmann
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164-4236, USA
| |
Collapse
|
53
|
Stepien A, Knop K, Dolata J, Taube M, Bajczyk M, Barciszewska-Pacak M, Pacak A, Jarmolowski A, Szweykowska-Kulinska Z. Posttranscriptional coordination of splicing and miRNA biogenesis in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1403] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 09/30/2016] [Accepted: 10/08/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Michal Taube
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Maria Barciszewska-Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| |
Collapse
|
54
|
Dolata J, Bajczyk M, Bielewicz D, Niedojadlo K, Niedojadlo J, Pietrykowska H, Walczak W, Szweykowska-Kulinska Z, Jarmolowski A. Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels. PLANT PHYSIOLOGY 2016; 172:297-312. [PMID: 27385819 PMCID: PMC5074614 DOI: 10.1104/pp.16.00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/02/2016] [Indexed: 05/03/2023]
Abstract
Plants as sessile organisms have developed prompt response mechanisms to react to rapid environmental changes. In addition to the transcriptional regulation of gene expression, microRNAs (miRNAs) are key posttranscriptional regulators of the plant stress response. We show here that the expression levels of many miRNAs were regulated under salt stress conditions. This regulation occurred at the transcriptional and posttranscriptional levels. During salinity stress, the levels of miRNA161 and miRNA173 increased, while the expression of pri-miRNA161 and pri-miRNA173 was down-regulated. Under salt stress conditions, miRNA161 and miRNA173 were stabilized in the cytoplasm, and the expressions of MIR161 and MIR173 were negatively regulated in the nucleus. ARGONAUTE1 (AGO1) participated in both processes. We demonstrated that AGO1 cotranscriptionally controlled the expression of MIR161 and MIR173 in the nucleus. Our results suggests that AGO1 interacts with chromatin at MIR161 and MIR173 loci and causes the disassembly of the transcriptional complex, releasing short and unpolyadenylated transcripts.
Collapse
Affiliation(s)
- Jakub Dolata
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Mateusz Bajczyk
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Katarzyna Niedojadlo
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Janusz Niedojadlo
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Halina Pietrykowska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Weronika Walczak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| |
Collapse
|
55
|
miRNA863-3p sequentially targets negative immune regulator ARLPKs and positive regulator SERRATE upon bacterial infection. Nat Commun 2016; 7:11324. [PMID: 27108563 PMCID: PMC4848489 DOI: 10.1038/ncomms11324] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/15/2016] [Indexed: 12/21/2022] Open
Abstract
Plant small RNAs play important roles in gene regulation during pathogen infection. Here we show that miR863-3p is induced by the bacterial pathogen Pseudomonas syringae carrying various effectors. Early during infection, miR863-3p silences two negative regulators of plant defence, atypical receptor-like pseudokinase1 (ARLPK1) and ARLPK2, both lacking extracellular domains and kinase activity, through mRNA degradation to promote immunity. ARLPK1 associates with, and may function through another negative immune regulator ARLPK1-interacting receptor-like kinase 1 (AKIK1), an active kinase with an extracellular domain. Later during infection, miR863-3p silences SERRATE, which is essential for miRNA accumulation and positively regulates defence, through translational inhibition. This results in decreased miR863-3p levels, thus forming a negative feedback loop to attenuate immune responses after successful defence. This is an example of a miRNA that sequentially targets both negative and positive regulators of immunity through two modes of action to fine-tune the timing and amplitude of defence responses. Small RNA plays an important role in regulating the plant defence against bacterial pathogens. Here the authors propose that miR863-3p acts to fine-tune the timing of defence responses by sequentially silencing negative and positive regulators of the plant immune response.
Collapse
|
56
|
Abstract
The use of artificial microRNAs (amiRNAs) is still a relatively new technique in molecular biology with a wide range of applications in life sciences. Here, we describe the silencing of the CBP80/ABH1 gene in Solanum tuberosum with the use of amiRNA. The CBP80/ABH1 protein is part of the Cap Binding Complex (CBC), which is involved in plant responses to drought stress conditions. Transformed plants with a decreased level of CBP80/ABH1 display increased tolerance to water shortage conditions. We describe how to design amiRNA with the Web MicroRNA Designer platform in detail. Additionally, we explain how to perform all steps of a procedure aiming to obtain transgenic potato plants with the use of designed amiRNA, through callus tissue regeneration and Agrobacterium tumefaciens strain LBA4404 as a transgene carrier.
Collapse
|
57
|
Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
Collapse
|
58
|
Chen T, Cui P, Xiong L. The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2015; 43:8283-98. [PMID: 26227967 PMCID: PMC4787832 DOI: 10.1093/nar/gkv751] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/11/2015] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs are a class of small regulatory RNAs that are generated from primary miRNA (pri-miRNA) transcripts with a stem-loop structure. Accuracy of the processing of pri-miRNA into mature miRNA in plants can be enhanced by SERRATE (SE) and HYPONASTIC LEAVES 1 (HYL1). HYL1 activity is regulated by the FIERY2 (FRY2)/RNA polymerase II C-terminal domain phosphatase-like 1 (CPL1). Here, we discover that HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5) and two serine/arginine-rich splicing factors RS40 and RS41, previously shown to be involved in pre-mRNA splicing, affect the biogenesis of a subset of miRNA. These proteins are required for correct miRNA strand selection and the maintenance of miRNA levels. FRY2 dephosphorylates HOS5 whose phosphorylation status affects its subnuclear localization. HOS5 and the RS proteins bind both intronless and intron-containing pri-miRNAs. Importantly, all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles. Our results indicate that these splicing factors are directly involved in the biogenesis of a group of miRNA.
Collapse
Affiliation(s)
- Tao Chen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Peng Cui
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
59
|
Abstract
Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. A suite of splicing factors has been identified in the model plant Arabidopsis thaliana. Here we summarize recent insights on how defects in these splicing factors impair plant performance.
Collapse
|
60
|
Zielezinski A, Dolata J, Alaba S, Kruszka K, Pacak A, Swida-Barteczka A, Knop K, Stepien A, Bielewicz D, Pietrykowska H, Sierocka I, Sobkowiak L, Lakomiak A, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM. mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs. BMC PLANT BIOLOGY 2015; 15:144. [PMID: 26141515 PMCID: PMC4490709 DOI: 10.1186/s12870-015-0533-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/23/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. DESCRIPTION The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation (e.g., tooltips, exemplary videos and presentations). All data contained within the mirEX 2.0 database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page. CONCLUSIONS The mirEX 2.0 portal provides the plant research community with easily accessible data and powerful tools for application in multi-conditioned analyses of miRNA expression from important plant species in different biological and developmental backgrounds.
Collapse
Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Sylwia Alaba
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Lukasz Sobkowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Alicja Lakomiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| |
Collapse
|
61
|
Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
Collapse
Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
| |
Collapse
|
62
|
Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms. FRONTIERS IN PLANT SCIENCE 2015; 6:57. [PMID: 25717333 PMCID: PMC4324062 DOI: 10.3389/fpls.2015.00057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/22/2015] [Indexed: 05/14/2023]
Abstract
Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.
Collapse
Affiliation(s)
- Davide Guerra
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Cristina Crosatti
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Hamid H. Khoshro
- Department of Agronomy and Plant Breeding, Ilam University, Ilam, Iran
| | - Anna M. Mastrangelo
- Cereal Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Foggia, Italy
| | - Erica Mica
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Elisabetta Mazzucotelli
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| |
Collapse
|
63
|
Dolata J, Guo Y, Kołowerzo A, Smoliński D, Brzyżek G, Jarmołowski A, Świeżewski S. NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis. EMBO J 2015; 34:544-58. [PMID: 25568310 DOI: 10.15252/embj.201489478] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The interconnection between transcription and splicing is a subject of intense study. We report that Arabidopsis homologue of spliceosome disassembly factor NTR1 is required for correct expression and splicing of DOG1, a regulator of seed dormancy. Global splicing analysis in atntr1 mutants revealed a bias for downstream 5' and 3' splice site selection and an enhanced rate of exon skipping. A local reduction in PolII occupancy at misspliced exons and introns in atntr1 mutants suggests that directionality in splice site selection is a manifestation of fast PolII elongation kinetics. In agreement with this model, we found AtNTR1 to bind target genes and co-localise with PolII. A minigene analysis further confirmed that strong alternative splice sites constitute an AtNTR1-dependent transcriptional roadblock. Plants deficient in PolII endonucleolytic cleavage showed opposite effects for splice site choice and PolII occupancy compared to atntr1 mutants, and inhibition of PolII elongation or endonucleolytic cleavage in atntr1 mutant resulted in partial reversal of splicing defects. We propose that AtNTR1 is part of a transcription elongation checkpoint at alternative exons in Arabidopsis.
Collapse
Affiliation(s)
- Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznań, Poland
| | - Yanwu Guo
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kołowerzo
- Department of Cell Biology, Faculty of Biology and Environment Protection Toruń, Poland Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Dariusz Smoliński
- Department of Cell Biology, Faculty of Biology and Environment Protection Toruń, Poland Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Grzegorz Brzyżek
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznań, Poland
| | - Szymon Świeżewski
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
64
|
Xie M, Zhang S, Yu B. microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 2015; 72:87-99. [PMID: 25209320 PMCID: PMC11113746 DOI: 10.1007/s00018-014-1728-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/13/2014] [Accepted: 09/04/2014] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) are important regulators of gene expression. After excised from primary miRNA transcript by dicer-like1 (DCL1, an RNAse III enzyme), miRNAs bind and guide their effector protein named argonaute 1 (AGO1) to silence the expression of target RNAs containing their complementary sequences in plants. miRNA levels and activities are tightly controlled to ensure their functions in various biological processes such as development, metabolism and responses to abiotic and biotic stresses. Studies have identified many factors that involve in miRNA accumulation and activities. Characterization of these factors in turn greatly improves our understanding of the processes related to miRNAs. Here, we review recent progress of mechanisms underlying miRNA expression and functions in plants.
Collapse
Affiliation(s)
- Meng Xie
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Shuxin Zhang
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| |
Collapse
|
65
|
Köster T, Meyer K, Weinholdt C, Smith LM, Lummer M, Speth C, Grosse I, Weigel D, Staiger D. Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis. Nucleic Acids Res 2014; 42:9925-36. [PMID: 25104024 PMCID: PMC4150807 DOI: 10.1093/nar/gku716] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a minimum log2 fold change of ± 0.5. Overaccumulation of several pri-miRNAs including pri-miR398b, pri-miR398c, pri-miR172b, pri-miR159a and pri-miR390 at the expense of the mature miRNAs suggested that AtGRP7 affects pri-miRNA processing. Indeed, RNA immunoprecipitation revealed that AtGRP7 interacts with these pri-miRNAs in vivo. Mutation of an arginine in the RNA recognition motif abrogated in vivo binding and the effect on miRNA and pri-miRNA levels, indicating that AtGRP7 inhibits processing of these pri-miRNAs by direct binding. In contrast, pri-miRNAs of selected miRNAs that were elevated or not changed in response to high AtGRP7 levels were not bound in vivo. Reduced accumulation of miR390, an initiator of trans-acting small interfering RNA (ta-siRNA) formation, also led to lower TAS3 ta-siRNA levels and increased mRNA expression of the target AUXIN RESPONSE FACTOR4. Furthermore, AtGRP7 affected splicing of pri-miR172b and pri-miR162a. Thus, AtGRP7 is an hnRNP-like protein with a role in processing of pri-miRNAs in addition to its role in pre-mRNA splicing.
Collapse
Affiliation(s)
- Tino Köster
- Molecular Cell Physiology, Bielefeld University
| | - Katja Meyer
- Molecular Cell Physiology, Bielefeld University
| | - Claus Weinholdt
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany
| | - Lisa M Smith
- Max Planck Institute for Developmental Biology, Tuebingen, Germany Department of Animal & Plant Sciences, University of Sheffield, UK
| | | | - Corinna Speth
- Max Planck Institute for Developmental Biology, Tuebingen, Germany Center for Plant Molecular Biology, University of Tuebingen Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Bielefeld University Institute for Genome Research & Systems Biology, CeBiTec, Bielefeld, Germany
| |
Collapse
|
66
|
Egan ED, Braun CR, Gygi SP, Moazed D. Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex. RNA (NEW YORK, N.Y.) 2014; 20:867-81. [PMID: 24713849 PMCID: PMC4024641 DOI: 10.1261/rna.044479.114] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/03/2014] [Indexed: 05/24/2023]
Abstract
RNA is a central component of gene-silencing pathways that regulate diverse cellular processes. In the fission yeast Schizosaccharomyces pombe, an RNA-based mechanism represses meiotic gene expression during vegetative growth. This pathway depends on the zinc finger protein Red1, which is required to degrade meiotic mRNAs as well as to target histone H3 lysine 9 (H3K9) methylation, a repressive chromatin mark, to a subset of meiotic genes. However, the mechanism of Red1 function is unknown. Here we use affinity purification and mass spectrometry to identify a Red1-containing nuclear RNA silencing (NURS) complex. In addition to Red1, this complex includes the Mtl1, Red5, Ars2, Rmn1, and Iss10 proteins and associates with several other complexes that are involved in either signaling or mediating RNA silencing. By analyzing the effects of gene knockouts and inducible knockdown alleles, we show that NURS subunits regulate RNA degradation and H3K9 methylation at meiotic genes. We also identify roles for individual NURS subunits in interactions with Mmi1, an RNA-binding protein that marks meiotic RNAs for destruction, and the nuclear exosome RNA degradation complex. Finally, we show that the levels of H3K9 methylation at meiotic genes are not sufficient to restrict RNA polymerase II access or repress gene expression during vegetative growth. Our results demonstrate that Red1 partners with other proteins to silence meiotic gene expression at the post-transcriptional level. Conservation of a NURS-like complex in human cells suggests that this pathway plays an ancient and fundamental role in RNA silencing.
Collapse
Affiliation(s)
- Emily D. Egan
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Craig R. Braun
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Danesh Moazed
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|