1
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Li Y, Kim EJ, Voshall A, Moriyama EN, Cerutti H. Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas. THE PLANT CELL 2023; 35:1868-1887. [PMID: 36945744 DOI: 10.1093/plcell/koad093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 05/30/2023]
Abstract
Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these >26 nt sRNAs are derived from moderately repetitive genomic clusters and their biogenesis is DICER-independent. Interestingly, the sequences generating these >26-nt sRNAs have been conserved and amplified in several Chlamydomonas species. Moreover, expression of these longer sRNAs increases substantially under nitrogen or sulfur deprivation, concurrently with the downregulation of predicted target transcripts. We hypothesize that the transposon-like sequences from which >26-nt sRNAs are produced might have been ancestrally targeted for silencing by the RNAi machinery but, during evolution, certain sRNAs might have fortuitously acquired endogenous target genes and become integrated into gene regulatory networks.
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Affiliation(s)
- Yingshan Li
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
| | - Eun-Jeong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Adam Voshall
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Etsuko N Moriyama
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
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2
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Yamasaki T, Tokutsu R, Sawa H, Razali NN, Hayashi M, Minagawa J. Small RNA-mediated silencing of phototropin suppresses the induction of photoprotection in the green alga Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2023; 120:e2302185120. [PMID: 37098057 PMCID: PMC10160981 DOI: 10.1073/pnas.2302185120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Small RNAs (sRNAs) form complexes with Argonaute proteins and bind to transcripts with complementary sequences to repress gene expression. sRNA-mediated regulation is conserved in a diverse range of eukaryotes and is involved in the control of various physiological functions. sRNAs are present in the unicellular green alga Chlamydomonas reinhardtii, and genetic analyses revealed that the core sRNA biogenesis and action mechanisms are conserved with those of multicellular organisms. However, the roles of sRNAs in this organism remain largely unknown. Here, we report that Chlamydomonas sRNAs contribute to the induction of photoprotection. In this alga, photoprotection is mediated by LIGHT HARVESTING COMPLEX STRESS-RELATED 3 (LHCSR3), whose expression is induced by light signals through the blue-light receptor phototropin (PHOT). We demonstrate here that sRNA-defective mutants showed increased PHOT abundance leading to greater LHCSR3 expression. Disruption of the precursor for two sRNAs predicted to bind to the PHOT transcript also increased PHOT accumulation and LHCSR3 expression. The induction of LHCSR3 in the mutants was enhanced by light containing blue wavelengths, but not by red light, indicating that the sRNAs regulate the degree of photoprotection via regulation of PHOT expression. Our results suggest that sRNAs are involved not only in the regulation of photoprotection but also in biological phenomena regulated by PHOT signaling.
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Affiliation(s)
- Tomohito Yamasaki
- Science and Technology Department, Natural Science Cluster, Kochi University, Kochi780-8520, Japan
| | - Ryutaro Tokutsu
- Division of Environmental Photobiology, National Institute for Basic Biology, Myodaiji, Okazaki444-8585, Japan
| | - Haruhi Sawa
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi780-8520, Japan
| | - Nazifa Naziha Razali
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi780-8520, Japan
| | - Momoka Hayashi
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi780-8520, Japan
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Myodaiji, Okazaki444-8585, Japan
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3
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Zhang E, Gao J, Wei Z, Zeng J, Li J, Li G, Liu J. MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi. THE ISME JOURNAL 2022; 16:2457-2466. [PMID: 35869388 PMCID: PMC9561107 DOI: 10.1038/s41396-022-01291-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The interactions between Emiliania huxleyi and E. huxleyi virus (EhV) regulate marine carbon and sulfur biogeochemical cycles and play a prominent role in global climate change. As a large DNA virus, EhV has developed a novel "virocell metabolism" model to meet its high metabolic needs. Although it has been widely demonstrated that EhV infection can profoundly rewire lipid metabolism, the epigenetic regulatory mechanisms of lipid metabolism are still obscure. MicroRNAs (miRNAs) can regulate biological pathways by targeting hub genes in the metabolic processes. In this study, the transcriptome, lipidome, and miRNAome were applied to investigate the epigenetic regulation of lipid metabolism in E. huxleyi cells during a detailed time course of viral infection. Combined transcriptomic, lipidomic, and physiological experiments revealed reprogrammed lipid metabolism, along with mitochondrial dysfunction and calcium influx through the cell membrane. A total of 69 host miRNAs (including 1 known miRNA) and 7 viral miRNAs were identified, 27 of which were differentially expressed. Bioinformatic prediction revealed that miRNAs involved in the regulation of lipid metabolism and a dual-luciferase reporter assay suggested that phosphatidylinositol 3-kinase (PI3K) gene might be a target of ehx-miR5. Further qPCR and western blot analysis showed a significant negative correlation between the expression of ehx-miR5 and its target gene PI3K, along with the lower activity of its downstream components (p-Akt, p-TOR, SREBP), indicating that lipid metabolism might be regulated by ehx-miR5 through the PI3K-Akt-TOR signaling pathway. Our findings reveal several novel mechanisms of viral strategies to manipulate host lipid metabolism and provide evidence that ehx-miR5 negatively modulates the expression of PI3K and disturbs lipid metabolism in the interactions between E. huxleyi and EhV.
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Affiliation(s)
- Enquan Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jingjing Gao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zehua Wei
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jun Zeng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jian Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Guiling Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
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4
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Sunny JS, Saleena LM. In-Silico Analysis of rSNPsin miRNA:mRNA Duplex Involved in Insulin Signaling Genes Shows a Possible Pathogenesis of Insulin Resistance. Microrna 2021; 10:200-205. [PMID: 34503438 DOI: 10.2174/2211536610666210909164348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Insulin resistance is a condition in which the body produces insulin but is unable to use it effectively. Aberrations in insulin signaling are known to play a crucial role in pathogenesis of this disease state. Eventually patients will have glucose build up in their blood instead of being absorbed by the cells, leading to type 2 diabetes. OBJECTIVE In the current study we focus on understanding the role of rSNP mediated miRNA:mRNA dysregulation and its impact on the above metabolic condition. METHODS More than 30 genes involved in insulin signaling pathway were found using KEGG database. The 3'UTR end of genes was studied by using RegRNA and Ensembl, whereas TargetScan along with miRbase were used to identify their target miRNAs.Binding free energy was used as a parameter to analyze the affect of polymorphism on the miRNA:mRNA duplex formation.Further, UNA fold was used to determine the heat capacity changes. RESULTS The following genes INSR, INS, GLUT4, FOXO1, IL6, TRIB3 and SREBF1 were selected for analysis. Multiple miRNAs, hsa-miR-16-5p, hsa-miR-15a-15p were identified in the SNP occurring region for INSR. INS too showed similar results.INSR, INS and TRIB3 were found to have the maximum change in their binding free energy due to rSNP variation. A destabilisation in the heat capacity values was observed too, contributed due to rSNP induction. CONCLUSION A direct relationship between miRNA target polymorphism and the stability of the miRNA:mRNA duplex was observed. The current methodology used to study insulin resistance pathogenesis could elaborate on our existing knowledge of miRNA mediated disease states.
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Affiliation(s)
- Jithin S Sunny
- Department of Biotechnology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai TN. India
| | - Lilly M Saleena
- Department of Biotechnology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai TN. India
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Paul S, Bravo Vázquez LA, Márquez Nafarrate M, Gutiérrez Reséndiz AI, Srivastava A, Sharma A. The regulatory activities of microRNAs in non-vascular plants: a mini review. PLANTA 2021; 254:57. [PMID: 34424349 DOI: 10.1007/s00425-021-03707-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Marilyn Márquez Nafarrate
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Av. Eugenio Garza Sada, No. 2501 Tecnologico, CP 64849, Monterrey, Mexico
| | - Ana Isabel Gutiérrez Reséndiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
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6
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Müller SY, Matthews NE, Valli AA, Baulcombe DC. The small RNA locus map for Chlamydomonas reinhardtii. PLoS One 2020; 15:e0242516. [PMID: 33211749 PMCID: PMC7676726 DOI: 10.1371/journal.pone.0242516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/04/2020] [Indexed: 11/19/2022] Open
Abstract
Small (s)RNAs play crucial roles in the regulation of gene expression and genome stability across eukaryotes where they direct epigenetic modifications, post-transcriptional gene silencing, and defense against both endogenous and exogenous viruses. It is known that Chlamydomonas reinhardtii, a well-studied unicellular green algae species, possesses sRNA-based mechanisms that are distinct from those of land plants. However, definition of sRNA loci and further systematic classification is not yet available for this or any other algae. Here, using data-driven machine learning approaches including Multiple Correspondence Analysis (MCA) and clustering, we have generated a comprehensively annotated and classified sRNA locus map for C. reinhardtii. This map shows some common characteristics with higher plants and animals, but it also reveals distinct features. These results are consistent with the idea that there was diversification in sRNA mechanisms after the evolutionary divergence of algae from higher plant lineages.
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Affiliation(s)
- Sebastian Y. Müller
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas E. Matthews
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Adrian A. Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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7
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Azaman SNA, Satharasinghe DA, Tan SW, Nagao N, Yusoff FM, Yeap SK. Identification and Analysis of microRNAs in Chlorella sorokiniana Using High-Throughput Sequencing. Genes (Basel) 2020; 11:genes11101131. [PMID: 32992970 PMCID: PMC7599482 DOI: 10.3390/genes11101131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/29/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
Chlorella is a popular microalga with robust physiological and biochemical characteristics, which can be cultured under various conditions. The exploration of the small RNA content of Chlorella could improve strategies for the enhancement of metabolite production from this microalga. In this study, stress was introduced to the Chlorella sorokiniana culture to produce high-value metabolites such as carotenoids and phenolic content. The small RNA transcriptome of C. sorokiniana was sequenced, focusing on microRNA (miRNA) content. From the analysis, 98 miRNAs were identified in cultures subjected to normal and stress conditions. The functional analysis result showed that the miRNA targets found were most often involved in the biosynthesis of secondary metabolites, followed by protein metabolism, cell cycle, and porphyrin and chlorophyll metabolism. Furthermore, the biosynthesis of secondary metabolites such as carotenoids, terpenoids, and lipids was found mostly in stress conditions. These results may help to improve our understanding of regulatory mechanisms of miRNA in the biological and metabolic process of Chlorella species. It is important and timely to determine the true potential of this microalga species and to support the potential for genetic engineering of microalgae as they receive increasing focus for their development as an alternative source of biofuel, food, and health supplements.
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Affiliation(s)
- Siti Nor Ani Azaman
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Dilan Amila Satharasinghe
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science University of Peradeniya, Peradeniya 20400, Sri Lanka;
| | - Sheau Wei Tan
- Laboratory of Vaccine and Biomolecules (VacBio), Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Norio Nagao
- 102 Naname-go, Shinkamigoto-cho, Minami Matsuura-gun, Nagasaki 857-4214, Japan;
| | - Fatimah M. Yusoff
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia;
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900 Selangor, Malaysia
- Correspondence:
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8
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Sun T, Wang Y, Anwar M, Lou S, Zeng Y, Li H, Hu Z. Short tandem target mimics inhibit Chlamydomonas reinhardtii microRNAs. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Fridrich A, Hazan Y, Moran Y. Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms. Bioessays 2019; 41:e1800169. [PMID: 30919506 DOI: 10.1002/bies.201800169] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 01/28/2019] [Indexed: 12/20/2022]
Abstract
Short ("seed") or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post-transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA-regulated processes are reported. However, in non-models, these reports mostly rely on computational prediction alone. Many times, further bioinformatic analyses such as Gene Ontology (GO) enrichment are based on these in silico projections. Here such approaches are reviewed, their caveats are highlighted and the ease of picking false targets from predicted lists is demonstrated. Discoveries that shed new light on how miRNAs evolved to regulate targets in various phyletic groups are discussed, in addition to the pitfalls of target identification in non-model organisms. The goal is to prevent the misuse of bioinformatic tools, as they cannot bypass the biological understanding of miRNA-target regulation.
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Affiliation(s)
- Arie Fridrich
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Yael Hazan
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
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10
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Chung BYW, Valli A, Deery MJ, Navarro FJ, Brown K, Hnatova S, Howard J, Molnar A, Baulcombe DC. Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression. Sci Rep 2019; 9:11091. [PMID: 31366981 PMCID: PMC6668577 DOI: 10.1038/s41598-019-47415-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3′UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identified as the predominant miRNA with effects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom. .,Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom.
| | - Adrian Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.,Department of Plant Molecular Genetics, Spanish National Centre for Biotechnology, Madrid, 28049, Spain
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Francisco J Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
| | - Silvia Hnatova
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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11
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Li Z, An X, Zhu T, Yan T, Wu S, Tian Y, Li J, Wan X. Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize. Int J Mol Sci 2019; 20:ijms20143480. [PMID: 31311189 PMCID: PMC6678786 DOI: 10.3390/ijms20143480] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 02/07/2023] Open
Abstract
The “competing endogenous RNA (ceRNA) hypothesis” has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory network (GRN) has been gradually revealed during the past two decades. However, it is still unknown whether ceRNAs contribute to anther development and sexual reproduction in plants. We performed RNA and small RNA sequencing of anther tissues sampled at three developmental stages in two maize lines. A total of 28,233 stably transcribed loci, 61 known and 51 potentially novel microRNAs (miRNAs) were identified from the transcriptomes. Predicted ceRNAs and target genes were found to conserve in sequences of recognition sites where their corresponding miRNAs bound. We then reconstructed 79 ceRNA-miRNA-target gene regulatory networks consisting of 51 known miRNAs, 28 potentially novel miRNAs, 619 ceRNA-miRNA pairs, and 869 miRNA-target gene pairs. More than half of the regulation pairs showed significant negative correlations at transcriptional levels. Several well-studied miRNA-target gene pairs associated with plant flower development were located in some networks, including miR156-SPL, miR159-MYB, miR160-ARF, miR164-NAC, miR172-AP2, and miR319-TCP pairs. Six target genes in the networks were found to be orthologs of functionally confirmed genes participating in anther development in plants. Our results provide an insight that the ceRNA-miRNA-target gene regulatory networks likely contribute to anther development in maize. Further functional studies on a number of ceRNAs, miRNAs, and target genes will facilitate our deep understanding on mechanisms of anther development and sexual plants reproduction.
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Affiliation(s)
- Ziwen Li
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Xueli An
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Taotao Zhu
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
| | - Tingwei Yan
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
| | - Suowei Wu
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Youhui Tian
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
| | - Jinping Li
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China.
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China.
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12
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Satish D, Mukherjee SK, Gupta D. PAmiRDB: A web resource for plant miRNAs targeting viruses. Sci Rep 2019; 9:4627. [PMID: 30874591 PMCID: PMC6420685 DOI: 10.1038/s41598-019-41027-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/19/2019] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged to be essential constituents of host antiviral-defense mechanisms. The miRNA mediated antiviral mechanism was first experimentally established in animals, which proved that host miRNAs regulate viral gene expression by targeting the animal virus mRNAs. There are comparatively fewer reports about such interactions in plants, however, artificial miRNA studies prove that miRNAs play similar antiviral role in plants too. To explore the extent of this phenomenon in plant genomes, and in the absence of any publicly available resource for prediction of plant miRNAs targeting viruses, we were motivated to predict such interactions of plant miRNAs and viral genes. The intriguing results of the predictions are compiled as a database, which we have named as PAmiRDB. The current version of PAmiRDB includes more than 2600 plant miRNAs and their specific interactions with corresponding targets in approximately 500 viral species (predominantly from the major plant-infecting virus families of geminiviruses and potyviruses). PAmiRDB is a database of known plant miRNAs and their predicted targets in virus genomes. The innovative database query-interface enables global and comprehensive investigation of such predicted interactions between host miRNAs and viral genes. The database integrated-tools also helps researchers to design experiments to confirm such interactions. PAmiRDB is available at http://bioinfo.icgeb.res.in/pamirdb
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Affiliation(s)
- Deepshikha Satish
- Translational Bioinformatics Group, International Centre For Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Sunil Kumar Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre For Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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Navarro FJ, Baulcombe DC. miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii. ACS Synth Biol 2019; 8:358-370. [PMID: 30624905 DOI: 10.1021/acssynbio.8b00393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.
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Affiliation(s)
- Francisco J. Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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14
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Lou S, Sun T, Li H, Hu Z. Mechanisms of microRNA-mediated gene regulation in unicellular model alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:244. [PMID: 30202439 PMCID: PMC6129010 DOI: 10.1186/s13068-018-1249-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/31/2018] [Indexed: 05/30/2023]
Abstract
MicroRNAs are a class of endogenous non-coding RNAs that play a vital role in post-transcriptional gene regulation in eukaryotic cells. In plants and animals, miRNAs are implicated in diverse roles ranging from immunity against viral infections, developmental pathways, molecular pathology of cancer and regulation of protein expression. However, the role of miRNAs in the unicellular model green alga Chlamydomonas reinhardtii remains unclear. The mode of action of miRNA-induced gene silencing in C. reinhardtii is very similar to that of higher eukaryotes, in terms of the activation of the RNA-induced silencing complex and mRNA targeting. Certain studies indicate that destabilization of mRNAs and mRNA turnover could be the major possible functions of miRNAs in eukaryotic algae. Here, we summarize recent findings that have advanced our understanding of miRNA regulatory mechanisms in C. reinhardtii.
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Affiliation(s)
- Sulin Lou
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Ting Sun
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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15
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Wang Y, Zhuang X, Chen M, Zeng Z, Cai X, Li H, Hu Z. An endogenous microRNA (miRNA1166.1) can regulate photobio-H 2 production in eukaryotic green alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:126. [PMID: 29743954 PMCID: PMC5930490 DOI: 10.1186/s13068-018-1126-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/20/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Hydrogen photoproduction from green microalgae is regarded as a promising alternative solution for energy problems. However, the simultaneous oxygen evolution from microalgae can prevent continuous hydrogen production due to the hypersensitivity of hydrogenases to oxygen. Sulfur deprivation can extend the duration of algal hydrogen production, but it is uneconomical to alternately culture algal cells in sulfur-sufficient and sulfur-deprived media. RESULTS In this study, we developed a novel way to simulate sulfur-deprivation treatment while constantly maintaining microalgal cells in sulfur-sufficient culture medium by overexpressing an endogenous microRNA (miR1166.1). Based on our previous RNA-seq analysis in the model green alga Chlamydomonas reinhardtii, three endogenous miRNAs responsive to sulfur deprivation (cre-miR1166.1, cre-miR1150.3, and cre-miR1158) were selected. Heat-inducible expression vectors containing the selected miRNAs were constructed and transformed into C. reinhardtii. Comparison of H2 production following heat induction in the three transgenic strains and untransformed control group identified miR1166.1 as the best candidate for H2 production regulation. Moreover, enhanced photobio-H2 production was observed with repeated induction of miR1166.1 expression. CONCLUSIONS This study is the first to identify a physiological function of endogenous miR1166.1 and to show that a natural miRNA can regulate hydrogen photoproduction in the unicellular model organism C. reinhardtii.
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Affiliation(s)
- Yuting Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Xiaoshan Zhuang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Meirong Chen
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhiyong Zeng
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Xiaoqi Cai
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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Affiliation(s)
- Hiro-Oki Iwakawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
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17
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Chung BYW, Deery MJ, Groen AJ, Howard J, Baulcombe DC. Endogenous miRNA in the green alga Chlamydomonas regulates gene expression through CDS-targeting. NATURE PLANTS 2017; 3:787-794. [PMID: 28970560 PMCID: PMC5662147 DOI: 10.1038/s41477-017-0024-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/31/2017] [Indexed: 05/29/2023]
Abstract
MicroRNAs (miRNAs) are 21-24-nucleotide RNAs present in many eukaryotes that regulate gene expression as part of the RNA-induced silencing complex. The sequence identity of the miRNA provides the specificity to guide the silencing effector Argonaute (AGO) protein to target mRNAs via a base-pairing process 1 . The AGO complex promotes translation repression and/or accelerated decay of this target mRNA 2 . There is overwhelming evidence both in vivo and in vitro that translation repression plays a major role 3-7 . However, there has been controversy about which of these three mechanisms is more significant in vivo, especially when effects of miRNA on endogenous genes cannot be faithfully represented by reporter systems in which, at least in metazoans, the observed repression vastly exceeds that typically observed for endogenous mRNAs 8,9 . Here, we provide a comprehensive global analysis of the evolutionarily distant unicellular green alga Chlamydomonas reinhardtii to quantify the effects of miRNA on protein synthesis and RNA abundance. We show that, similar to metazoan steady-state systems, endogenous miRNAs in Chlamydomonas can regulate gene expression both by destabilization of the mRNA and by translational repression. However, unlike metazoan miRNA where target site utilization localizes mainly to 3' UTRs, in Chlamydomonas utilized target sites lie predominantly within coding regions. These results demonstrate the evolutionarily conserved mode of action for miRNAs, but details of the mechanism diverge between the plant and metazoan kingdoms.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Arnoud J Groen
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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18
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You C, Cui J, Wang H, Qi X, Kuo LY, Ma H, Gao L, Mo B, Chen X. Conservation and divergence of small RNA pathways and microRNAs in land plants. Genome Biol 2017; 18:158. [PMID: 28835265 PMCID: PMC5569507 DOI: 10.1186/s13059-017-1291-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants. Results Using 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms. Conclusions Our phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1291-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chenjiang You
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China
| | - Hui Wang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, People's Republic of China
| | - Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China. .,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA. .,Howard Hughes Medical Institute, University of California, Riverside, 92521, CA, USA.
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Voshall A, Kim EJ, Ma X, Yamasaki T, Moriyama EN, Cerutti H. miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation. Sci Rep 2017; 7:5462. [PMID: 28710366 PMCID: PMC5511227 DOI: 10.1038/s41598-017-05561-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/30/2017] [Indexed: 12/17/2022] Open
Abstract
The unicellular alga Chlamydomonas reinhardtii contains many types of small RNAs (sRNAs) but the biological role(s) of bona fide microRNAs (miRNAs) remains unclear. To address their possible function(s) in responses to nutrient availability, we examined miRNA expression in cells cultured under different trophic conditions (mixotrophic in the presence of acetate or photoautotrophic in the presence or absence of nitrogen). We also reanalyzed miRNA expression data in Chlamydomonas subject to sulfur or phosphate deprivation. Several miRNAs were differentially expressed under the various trophic conditions. However, in transcriptome analyses, the majority of their predicted targets did not show expected changes in transcript abundance, suggesting that they are not subject to miRNA-mediated RNA degradation. Mutant strains, defective in sRNAs or in ARGONAUTE3 (a key component of sRNA-mediated gene silencing), did not display major phenotypic defects when grown under multiple nutritional regimes. Additionally, Chlamydomonas miRNAs were not conserved, even in algae of the closely related Volvocaceae family, and many showed features resembling those of recently evolved, species-specific miRNAs in the genus Arabidopsis. Our results suggest that, in C. reinhardtii, miRNAs might be subject to relatively fast evolution and have only a minor, largely modulatory role in gene regulation under diverse trophic states.
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Affiliation(s)
- Adam Voshall
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Eun-Jeong Kim
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xinrong Ma
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tomohito Yamasaki
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi Prefecture, Japan
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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20
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Munusamy P, Zolotarov Y, Meteignier LV, Moffett P, Strömvik MV. De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome. Sci Rep 2017; 7:43861. [PMID: 28276452 PMCID: PMC5343461 DOI: 10.1038/srep43861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/31/2017] [Indexed: 01/24/2023] Open
Abstract
Gene regulation at the transcriptional and translational level leads to diversity in phenotypes and function in organisms. Regulatory DNA or RNA sequence motifs adjacent to the gene coding sequence act as binding sites for proteins that in turn enable or disable expression of the gene. Whereas the known DNA and RNA binding proteins range in the thousands, only a few motifs have been examined. In this study, we have predicted putative regulatory motifs in groups of untranslated regions from genes regulated at the translational level in Arabidopsis thaliana under normal and stressed conditions. The test group of sequences was divided into random subgroups and subjected to three de novo motif finding algorithms (Seeder, Weeder and MEME). In addition to identifying sequence motifs, using an in silico tool we have predicted microRNA target sites in the 3′ UTRs of the translationally regulated genes, as well as identified upstream open reading frames located in the 5′ UTRs. Our bioinformatics strategy and the knowledge generated contribute to understanding gene regulation during stress, and can be applied to disease and stress resistant plant development.
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Affiliation(s)
- Prabhakaran Munusamy
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| | - Yevgen Zolotarov
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| | | | - Peter Moffett
- Department of Biology, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Martina V Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
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21
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Yamasaki T, Cerutti H. Cooperative processing of primary miRNAs by DUS16 and DCL3 in the unicellular green alga Chlamydomonas reinhardtii. Commun Integr Biol 2017; 10:e1280208. [PMID: 28289490 PMCID: PMC5333524 DOI: 10.1080/19420889.2017.1280208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 11/05/2022] Open
Abstract
We have previously reported that the RNA-binding protein Dull slicer 16 (DUS16) plays a key role in the processing of primary miRNAs (pri-miRNAs) in the unicellular green alga Chlamydomonas reinhardtii. In the present report, we elaborate on the interaction of DUS16 with Dicer-like 3 (DCL3) during pri-miRNA processing. Comprehensive analyses of small RNA libraries derived from mutant and wild-type algal strains allowed the de novo prediction of 35 pri-miRNA genes, including 9 previously unknown ones. The pri-miRNAs dependent on DUS16 for processing largely overlapped with those dependent on DCL3. Our findings suggest that DUS16 and DCL3 work cooperatively, presumably as components of a microprocessor complex, in the processing of the majority of pri-miRNAs in C. reinhardtii.
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Affiliation(s)
- Tomohito Yamasaki
- Division of Environmental Photobiology, National Institute for Basic Biology , Okazaki, Aichi, Japan
| | - Heriberto Cerutti
- School of Biological Science and Center for Plant Science Innovation, University of Nebraska-Lincoln , Lincoln, NE, USA
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22
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Cui J, You C, Chen X. The evolution of microRNAs in plants. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:61-67. [PMID: 27886593 PMCID: PMC5342909 DOI: 10.1016/j.pbi.2016.11.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are a central player in post-transcriptional regulation of gene expression and are involved in numerous biological processes in eukaryotes. Knowledge of the origins and divergence of miRNAs paves the way for a better understanding of the complexity of the regulatory networks that they participate in. The biogenesis, degradation, and regulatory activities of miRNAs are relatively better understood, but the evolutionary history of miRNAs still needs more exploration. Inverted duplication of target genes, random hairpin sequences and small transposable elements constitute three main models that explain the origination of miRNA genes (MIR). Both inter-species and intra-species divergence of miRNAs exhibits functional adaptation and adaptation to changing environments in evolution. Here we summarize recent progress in studies on the evolution of MIR and related genes.
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Affiliation(s)
- Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Chenjiang You
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, PR China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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23
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RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2016; 113:10720-5. [PMID: 27582463 DOI: 10.1073/pnas.1523230113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Canonical microRNAs (miRNAs) are embedded in duplexed stem-loops in long precursor transcripts and are excised by sequential cleavage by DICER nuclease(s). In this miRNA biogenesis pathway, dsRNA-binding proteins play important roles in animals and plants by assisting DICER. However, these RNA-binding proteins are poorly characterized in unicellular organisms. Here we report that a unique RNA-binding protein, Dull slicer-16 (DUS16), plays an essential role in processing of primary-miRNA (pri-miRNA) transcripts in the unicellular green alga Chlamydomonas reinhardtii In animals and plants, dsRNA-binding proteins involved in miRNA biogenesis harbor two or three dsRNA-binding domains (dsRBDs), whereas DUS16 contains one dsRBD and also an ssRNA-binding domain (RRM). The null mutant of DUS16 showed a drastic reduction in most miRNA species. Production of these miRNAs was complemented by expression of full-length DUS16, but the expression of RRM- or dsRBD-truncated DUS16 did not restore miRNA production. Furthermore, DUS16 is predominantly localized to the nucleus and associated with nascent (unspliced form) pri-miRNAs and the DICER-LIKE 3 protein. These results suggest that DUS16 recognizes pri-miRNA transcripts cotranscriptionally and promotes their processing into mature miRNAs as a component of a microprocessor complex. We propose that DUS16 is an essential factor for miRNA production in Chlamydomonas and, because DUS16 is functionally similar to the dsRNA-binding proteins involved in miRNA biogenesis in animals and land plants, our report provides insight into this mechanism in unicellular eukaryotes.
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24
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Valli AA, Santos BACM, Hnatova S, Bassett AR, Molnar A, Chung BY, Baulcombe DC. Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs. Genome Res 2016; 26:519-29. [PMID: 26968199 PMCID: PMC4817775 DOI: 10.1101/gr.199703.115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/10/2016] [Indexed: 01/20/2023]
Abstract
We describe here a forward genetic screen to investigate the biogenesis, mode of action, and biological function of miRNA-mediated RNA silencing in the model algal species, Chlamydomonas reinhardtii. Among the mutants from this screen, there were three at Dicer-like 3 that failed to produce both miRNAs and siRNAs and others affecting diverse post-biogenesis stages of miRNA-mediated silencing. The DCL3-dependent siRNAs fell into several classes including transposon- and repeat-derived siRNAs as in higher plants. The DCL3-dependent miRNAs differ from those of higher plants, however, in that many of them are derived from mRNAs or from the introns of pre-mRNAs. Transcriptome analysis of the wild-type and dcl3 mutant strains revealed a further difference from higher plants in that the sRNAs are rarely negative switches of mRNA accumulation. The few transcripts that were more abundant in dcl3 mutant strains than in wild-type cells were not due to sRNA-targeted RNA degradation but to direct DCL3 cleavage of miRNA and siRNA precursor structures embedded in the untranslated (and translated) regions of the mRNAs. Our analysis reveals that the miRNA-mediated RNA silencing in C. reinhardtii differs from that of higher plants and informs about the evolution and function of this pathway in eukaryotes.
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Affiliation(s)
- Adrian A Valli
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Bruno A C M Santos
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Silvia Hnatova
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Andrew R Bassett
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Attila Molnar
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Betty Y Chung
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
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25
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Yamasaki T, Kim EJ, Cerutti H, Ohama T. Argonaute3 is a key player in miRNA-mediated target cleavage and translational repression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:258-268. [PMID: 26686836 DOI: 10.1111/tpj.13107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) play important roles in diverse biological processes in eukaryotes, generally through degradation and/or inhibition of the translation of target mRNAs. MicroRNAs are loaded into Argonaute (AGO) proteins to form the RNA-induced silencing complex (RISC) and used as guides to identify complementary transcripts. The distinct functions and features, such as associated small RNA classes and modes of silencing, of individual AGO paralogs have been well documented in multicellular eukaryotes. However, this aspect of miRNA function remains poorly understood in the unicellular green alga Chlamydomonas reinhardtii, which contains three AGO paralogs. In this study, we isolated AGO2 and AGO3 insertional mutants and confirmed that AGO3 is more abundantly expressed than AGO2. MicroRNA-directed target transcript cleavage and translational repression were impaired in the AGO3 mutant background, indicating that AGO3 can mediate both modes of silencing. In contrast, although the AGO2 mutant is not a null, the involvement of AGO2 in miRNA-directed silencing appears to be more limited. Our results strongly suggest that miRNA-mediated post-transcriptional gene silencing relies primarily on AGO3 in Chlamydomonas.
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Affiliation(s)
- Tomohito Yamasaki
- Department of Environmental Systems Engineering, Kochi University of Technology (KUT), 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
| | - Eun-Jeong Kim
- School of Biological Science and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Heriberto Cerutti
- School of Biological Science and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Takeshi Ohama
- Department of Environmental Systems Engineering, Kochi University of Technology (KUT), 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
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26
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Wang F, Polydore S, Axtell MJ. More than meets the eye? Factors that affect target selection by plant miRNAs and heterochromatic siRNAs. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:118-24. [PMID: 26246393 PMCID: PMC4732885 DOI: 10.1016/j.pbi.2015.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/12/2015] [Accepted: 06/19/2015] [Indexed: 05/19/2023]
Abstract
MicroRNAs, which target mRNAs for post-transcriptional regulation, and heterochromatic siRNAs, which target chromatin causing DNA methylation, make up the majority of the endogenous regulatory small RNA pool in most plant specimens. They both function to guide Argonaute proteins to targeted nucleic acids on the basis of complementarity. Recent work on plant miRNA-target interactions has clarified the general ''rules' of complementarity, while also providing several intriguing exceptions to these rules. In addition, emerging evidence suggests that several factors besides miRNA-target complementarity affect plant miRNA function. For heterochromatic siRNAs, recent work has made progress towards comprehensively identifying potential target regions, but numerous fundamental questions remain to be answered.
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Affiliation(s)
- Feng Wang
- Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
| | - Seth Polydore
- Genetics Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Genetics Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Department of Biology, Penn State University, University Park, PA 16802, USA.
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27
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Kong F, Yamasaki T, Kurniasih SD, Hou L, Li X, Ivanova N, Okada S, Ohama T. Robust expression of heterologous genes by selection marker fusion system in improved Chlamydomonas strains. J Biosci Bioeng 2015; 120:239-45. [DOI: 10.1016/j.jbiosc.2015.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/30/2014] [Accepted: 01/06/2015] [Indexed: 01/07/2023]
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28
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Kim EJ, Ma X, Cerutti H. Gene silencing in microalgae: mechanisms and biological roles. BIORESOURCE TECHNOLOGY 2015; 184:23-32. [PMID: 25466994 DOI: 10.1016/j.biortech.2014.10.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 05/18/2023]
Abstract
Microalgae exhibit enormous diversity and can potentially contribute to the production of biofuels and high value compounds. However, for most species, our knowledge of their physiology, metabolism, and gene regulation is fairly limited. In eukaryotes, gene silencing mechanisms play important roles in both the reversible repression of genes that are required only in certain contexts and the suppression of genome invaders such at transposons. The recent sequencing of several algal genomes is providing insights into the complexity of these mechanisms in microalgae. Collectively, glaucophyte, red, and green microalgae contain the machineries involved in repressive histone H3 lysine methylation, DNA cytosine methylation, and RNA interference. However, individual species often only have subsets of these gene silencing mechanisms. Moreover, current evidence suggests that algal silencing systems function in transposon and transgene repression but their role(s) in gene regulation or other cellular processes remains virtually unexplored, hindering rational genetic engineering efforts.
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Affiliation(s)
- Eun-Jeong Kim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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29
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Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. Genetics 2015; 200:105-21. [PMID: 25769981 DOI: 10.1534/genetics.115.174797] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/11/2015] [Indexed: 11/18/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii harbors many types of small RNAs (sRNAs) but little is known about their role(s) in the regulation of endogenous genes and cellular processes. To define functional microRNAs (miRNAs) in Chlamydomonas, we characterized sRNAs associated with an argonaute protein, AGO3, by affinity purification and deep sequencing. Using a stringent set of criteria for canonical miRNA annotation, we identified 39 precursor miRNAs, which produce 45 unique, AGO3-associated miRNA sequences including 13 previously reported miRNAs and 32 novel ones. Potential miRNA targets were identified based on the complementarity of miRNAs with candidate binding sites on transcripts and classified, depending on the extent of complementarity, as being likely to be regulated through cleavage or translational repression. The search for cleavage targets identified 74 transcripts. However, only 6 of them showed an increase in messenger RNA (mRNA) levels in a mutant strain almost devoid of sRNAs. The search for translational repression targets, which used complementarity criteria more stringent than those empirically required for a reduction in target protein levels, identified 488 transcripts. However, unlike observations in metazoans, most predicted translation repression targets did not show appreciable changes in transcript abundance in the absence of sRNAs. Additionally, of three candidate targets examined at the protein level, only one showed a moderate variation in polypeptide amount in the mutant strain. Our results emphasize the difficulty in identifying genuine miRNA targets in Chlamydomonas and suggest that miRNAs, under standard laboratory conditions, might have mainly a modulatory role in endogenous gene regulation in this alga.
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Hu J, Deng X, Shao N, Wang G, Huang K. Rapid construction and screening of artificial microRNA systems in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:1052-64. [PMID: 24974733 DOI: 10.1111/tpj.12606] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 06/17/2014] [Accepted: 06/24/2014] [Indexed: 05/09/2023]
Abstract
The unicellular green algae Chlamydomonas reinhardtii is a classic model for the study of flagella/cilia and photosynthesis, and it has recently been exploited for producing biopharmaceuticals and biofuel. Due to the low frequency of homologous recombination, reverse genetic manipulation in Chlamydomonas relies mainly on miRNA- and siRNA-based knockdown methods. However, the difficulty in constructing artificial miRNA vectors, laborious screening of knockdown transformants, and undesired epigenetic silencing of exogenous miRNA constructs limit their application. We have established a one-step procedure to construct an artificial miRNA precursor by annealing eight oligonucleotides of approximately 40 nucleotides. In the final construct, the Gaussia princeps luciferase gene (G-Luc) is positioned between the promoter and the artificial miRNA precursor so that knockdown strains may quickly be screened by visualizing luciferase luminescence using a photon-counting camera. Furthermore, the luciferase activity of transformants correlates with the knockdown level of two test target proteins: the chloroplast protein VIPP1 (vesicle inducing protein in plastids 1) and the flagellar protein CDPK3 (calcium-dependent protein kinase 3). Adding an intron from RBCS2 (ribulose bisphosphate carboxylase/oxygenase small subunit 2) to the miRNA construct enhanced both the luciferase activity and the miRNA knockdown efficiency. A second miRNA vector incorporated the promoter of the nitrate reductase gene to allow inducible expression of the artificial miRNA. These vectors will facilitate application of the artificial miRNA and provide tools for studying the mechanism of epigenetics in Chlamydomonas, and may also be adapted for use in other model organisms.
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Affiliation(s)
- Jinlu Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China; University of the Chinese Academy of Sciences, Beijing, 100039, China
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31
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Liu Q, Wang F, Axtell MJ. Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. THE PLANT CELL 2014; 26:741-53. [PMID: 24510721 PMCID: PMC3967037 DOI: 10.1105/tpc.113.120972] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 05/17/2023]
Abstract
MicroRNAs (miRNAs) guide RNA-induced silencing complexes to target RNAs based on miRNA-target complementarity. Using a dual-luciferase based sensor system in Nicotiana benthamiana, we quantitatively assessed the relationship between miRNA-target complementarity and silencing efficacy measured at both the RNA and protein levels, using several conserved miRNAs and their known target sites from Arabidopsis thaliana. We found that naturally occurring sites have variable efficacies attributable to their complementarity patterns. We also observed that sites with a few mismatches to the miRNA 3' regions, which are common in plants, are often equally effective and sometimes more effective than perfectly matched sites. By contrast, mismatches to the miRNA 5' regions strongly reduce or eliminate repression efficacy but are nonetheless present in several natural sites, suggesting that in some cases, suboptimal miRNA efficacies are either tolerated or perhaps selected for. Central mismatches fully abolished repression efficacy in our system, but such sites then became effective miRNA target mimics. Complementarity patterns that are functional in animals (seed sites, 3'-supplementary sites, and centered sites) did not reliably confer repression, regardless of context (3'-untranslated region or open reading frame) or measurement type (RNA or protein levels). Overall, these data provide a robust and empirical foundation for understanding, predicting, and designing functional miRNA target sites in plants.
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Affiliation(s)
- Qikun Liu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Feng Wang
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael J. Axtell
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Plant Biology PhD Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
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