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Edelbroek B, Kjellin J, Biryukova I, Liao Z, Lundberg T, Noegel A, Eichinger L, Friedländer M, Söderbom F. Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity. Nucleic Acids Res 2024; 52:3121-3136. [PMID: 38375870 PMCID: PMC11014262 DOI: 10.1093/nar/gkae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Zhen Liao
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Torgny Lundberg
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Angelika A Noegel
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ludwig Eichinger
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Marc R Friedländer
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
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2
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Amaro F, González D, Gutiérrez JC. MicroRNAs in Tetrahymena thermophila: An epigenetic regulatory mechanism in the response to cadmium stress. Microbiol Res 2024; 280:127565. [PMID: 38160574 DOI: 10.1016/j.micres.2023.127565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
Among the epigenetic mechanisms based on non-coding RNA are microRNAs (miRNAs) that are involved in the post-transcriptional regulation of mRNAs. In many organisms, the expression of genes involved in the cellular response to biotic or abiotic stress depends on the regulation, generally inhibitory, performed by miRNAs. For the first time in the eukaryotic microorganism (ciliate-model) Tetrahymena thermophila, miRNAs involved in the post-transcriptional regulation of transcripts linked to the response to cadmium have been isolated and analyzed. Forty de novo miRNAs (we named tte-miRNAs) have been isolated from control and Cd-treated populations (1 or 24 h exposures). An exhaustive comparative analysis of the features of these mature tte-miRNAs and their precursor sequences (pre-tte-miRNAs) confirms that they are true miRNAs. In addition to the three types of miRNA isoforms previously described in other organisms, two new types are also described among the tte-miRNAs studied. A certain percentage of the pre-tte-miRNA sequences are in introns from genes with many introns, and have been defined as 5', 3'-tailed mirtrons. A qRT-PCR analysis of selected tte-miRNAs together with some of their targets has validated them. Cd is one of the most toxic metals for the cell, which must defend itself against its toxicity by various mechanisms, such as expulsion by membrane pumps, chelation by metallothioneins, among others. Like other toxic metals, Cd also causes a well-known series of cellular effects such as intense proteotoxicity. Many of the targets that are regulated by the tte-miRNAs are transcripts encoding proteins that fit into these defense mechanisms and toxic metal effects.
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Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain
| | - David González
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain
| | - Juan-Carlos Gutiérrez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain.
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3
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Hirpara DG, Gajera HP. Intracellular metabolomics and microRNAomics unveil new insight into the regulatory network for potential biocontrol mechanism of stress-tolerant Tricho-fusants interacting with phytopathogen Sclerotium rolfsii Sacc. J Cell Physiol 2023; 238:1288-1307. [PMID: 37021806 DOI: 10.1002/jcp.31009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/07/2023]
Abstract
The present study employed microRNA (miRNA) sequencing and metabolome profiling of Trichoderma parental strains and fusants during normal growth and interaction with the phytopathogen Sclerotium rolfsii Sacc. In-vitro antagonism indicated that abiotic stress-tolerant Tricho-fusant FU21 was examined as a potent biocontroller with mycoparasitic action after 10 days. During interaction with the test pathogen, the most abundant uprising intracellular metabolite was recognized as l-proline, which corresponds to held-down l-alanine, associated with arginine and proline metabolism, biosynthesis of secondary metabolites, and nitrogen metabolism linked to predicted genes controlled by miRNAs viz., cel-miR-8210-3p, hsa-miR-3613-5p, and mml-miR-7174-3p. The miRNAs- mml-miR-320c and mmu-miR-6980-5p were found to be associated with phenylpropanoid biosynthesis, transcription factors, and signal transduction pathways, respectively, and were ascertained downregulated in potent FU21_IB compared with FU21_CB. The amino benzoate degradation and T cell receptor signaling pathways were regulated by miRNAs cel-miR-8210 and tca-miR-3824 as stress tolerance mechanisms of FU21. The intracellular metabolites l-proline, maleic acid, d-fructose, Myo-inositol, arabinitol, d-xylose, mannitol, and butane were significantly elevated as potential biocontrol and stress-tolerant constituents associated with miRNA regulatory pathways in potent FU21_IB. A network analysis between regulatory miRNA-predicted genes and intracellular metabolomics acknowledged possible biocontrol pathways/mechanisms in potent FU21_IB to restrain phytopathogen.
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Affiliation(s)
- Darshna G Hirpara
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Harsukh P Gajera
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, India
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4
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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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Chen L, Yang W, Liu S, Meng Y, Zhu Z, Liang R, Cao K, Xie Y, Li X. Genome-wide analysis and identification of light-harvesting chlorophyll a/b binding (LHC) gene family and BSMV-VIGS silencing TaLHC86 reduced salt tolerance in wheat. Int J Biol Macromol 2023; 242:124930. [PMID: 37236564 DOI: 10.1016/j.ijbiomac.2023.124930] [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: 11/27/2022] [Revised: 04/24/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
The discovery and identification of gene families by using wide-genome and public databases is an effective way to gain initial insight into gene function, which also is one of the current hot spots of research. Chlorophyll ab-binding proteins (LHC) are important for photosynthesis and widely involved in plant adversity stress. However, the study in wheat has not been reported. In this study, we identified 127 TaLHC members from common wheat which were unevenly distributed on all chromosomes except 3B and 3D. All members divided into three subfamilies, LHC a, LHC b and the LHC t which was only discovered in wheat. All of them had maximum expression in leaves and contained multiple light-responsive cis-acting element, which were evidence of the extensive involvement of LHC families in photosynthesis. In addition, we also analyzed their collinear relationship, targeting relationship with miRNA and their responses under different stresses. Based on these analyses, it was found that TaLHC86 was an excellent candidate gene for stress resistance. The full-length ORF of TaLHC86 was 792 bp and was localized on the chloroplasts. The salt tolerance of wheat was reduced when BSMV-VIGS silenced TaLHC86, and the photosynthetic rate and electron transport were also seriously affected. This study made a comprehensive analysis of the TaLHC family and found that TaLHC86 was a good gene for salt tolerance.
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Affiliation(s)
- Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weibing Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shuqing Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhanhua Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiyan Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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6
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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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7
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Hirpara DG, Gajera HP, Savaliya DD, Parakhia MV. Exploring conserved and novel MicroRNA-like small RNAs from stress tolerant Trichoderma fusants and parental strains during interaction with fungal phytopathogen Sclerotium rolfsii Sacc. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105368. [PMID: 36963937 DOI: 10.1016/j.pestbp.2023.105368] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The study investigated potential microRNA-like small RNAs (milRNAs) from multi-stress-tolerant Tricho-fusants and parental strains (P1- Trichoderma virens NBAIITvs12 and P2- Trichoderma koningii MTCC796) for antagonistic activity during interaction with phytopathogen Sclerotium rolfsii. The Trichoderma was cultured in-vitro, with and without antagonism, against the pathogen and total RNA was extracted followed by small RNA library construction and sequencing. The milRNAs were identified by mapping high-quality unique reads against a reference genome. The milRNAs were recognized higher in antagonist Trichoderma during interaction with test pathogen compared to normal growth. The novel milRNAs candidates were found to vary during interaction with the pathogen and normal growth. The gene ontology and functional analysis illustrated that a total of 5828 potential targeted genes were recognized for 93 milRNAs of potent Fu21_IB and 3053 genes for 62 milRNAs of least fusant Fu28_IL. Functional annotation of milRNA-predicted genes integrating KEGG pathways indicates new insights into regulatory mechanisms, by interfering with milRNAs, associated with signal transduction, amino sugar metabolism, benzoate degradation, amino acid metabolism, and steroid and alkaloid metabolism for potential biocontrol of stress-tolerant Tricho-fusant FU21 during interaction with S. rolfsii. The present investigation is the first report of conserved and novel milRNAs from Tricho-fusants and parental strains interacting with S. rolfsii.
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Affiliation(s)
- Darshna G Hirpara
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - H P Gajera
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India.
| | - Disha D Savaliya
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - M V Parakhia
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
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8
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Jing X, Xu L, Huai X, Zhang H, Zhao F, Qiao Y. Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp. Genes (Basel) 2023; 14:genes14010121. [PMID: 36672862 PMCID: PMC9859564 DOI: 10.3390/genes14010121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.
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Affiliation(s)
- Xiaotong Jing
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Linlin Xu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xinjia Huai
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Hong Zhang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Fengli Zhao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- Correspondence:
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9
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Imran M, Liu T, Wang Z, Wang M, Liu S, Gao X, Wang A, Liu S, Tian Z, Zhang M. Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:948751. [PMID: 35958213 PMCID: PMC9361848 DOI: 10.3389/fpls.2022.948751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1-5 and miR159a.1-3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought.
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Affiliation(s)
- Muhammad Imran
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
| | - Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xinyan Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songfeng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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10
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Zhang L, Chen L, Zhang H, Si H, Liu X, Suo X, Hu D. A comparative study of microRNAs in different stages of Eimeria tenella. Front Vet Sci 2022; 9:954725. [PMID: 35937295 PMCID: PMC9353057 DOI: 10.3389/fvets.2022.954725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Apicomplexan parasites have divergent biogenesis machinery for small RNA generation. Analysis has shown that parasites in Plasmodium and Cryptosporidium as well as many species in Leishmania or Trypanosoma do not have a complete machinery in small RNA biogenesis. Recently, the miRNA-generating system of Toxoplasma has been identified as plant/fungal-like and its miRNAome has been elucidated. However, the microRNA (miRNA) expression profiles and their potential regulatory functions in different stages of Eimeria tenella remain largely unknown. In this study, we characterized the RNA silencing machinery of E. tenella and investigated the miRNA population distribution at different life stages by high-throughput sequencing. We characterized the expression of miRNAs in the unsporulated oocyst, sporulated oocyst and schizogony stages, obtaining a total of 392 miRNAs. We identified 58 differentially expressed miRNAs between USO (unsporulated oocysts) and SO (sporulated oocysts) that were significantly enriched for their potential target genes in the regulation of gene expression and chromatin binding, suggesting an epigenetic modulation of sporulating by these miRNAs. In comparing miRNA expression at endogenous and exogenous developmental stages, twenty-four miRNAs were identified differently expressed. Those were mainly associated with the regulation of genes with protein kinase activity, suggesting control of protein phosphorylation. This is the first study about the evolution of miRNA biogenesis system and miRNA control of gene expression in Eimeria species. Our data may lead to functional insights into of the regulation of gene expression during parasite life cycle in apicomplexan parasites.
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Affiliation(s)
- Lei Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Linlin Chen
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hongtao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongbin Si
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xianyong Liu
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xun Suo
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Dandan Hu
- College of Animal Science and Technology, Guangxi University, Nanning, China
- *Correspondence: Dandan Hu
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11
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Zhao JH, Guo HS. RNA silencing: From discovery and elucidation to application and perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:476-498. [PMID: 34964265 DOI: 10.1111/jipb.13213] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
RNA silencing (or RNA interference, RNAi) is a conserved mechanism for regulating gene expression in eukaryotes. The discovery of natural trans-kingdom RNAi indicated that small RNAs act as signaling molecules and enable communication between organisms in different kingdoms. The phenomenon and potential mechanisms of trans-kingdom RNAi are among the most exciting research topics. To better understand trans-kingdom RNAi, we review the history of the discovery and elucidation of RNAi mechanisms. Based on canonical RNAi mechanisms, we summarize the major points of divergence around RNAi pathways in the main eukaryotes' kingdoms, including plants, animals, and fungi. We review the representative incidents associated with the mechanisms and applications of trans-kingdom RNAi in crop protection, and discuss the critical factors that should be considered to develop successful trans-kingdom RNAi-based crop protection strategies.
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Affiliation(s)
- Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
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12
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Zhang J, Shi J, Yuan C, Liu X, Du G, Fan R, Zhang B. MicroRNA Expression Profile Analysis of Chlamydomonas reinhardtii during Lipid Accumulation Process under Nitrogen Deprivation Stresses. Bioengineering (Basel) 2021; 9:bioengineering9010006. [PMID: 35049715 PMCID: PMC8773410 DOI: 10.3390/bioengineering9010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production.
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Affiliation(s)
- Jingxian Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chenyang Yuan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiangcen Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guilin Du
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruimei Fan
- Sino-UK Joint Laboratory for Brain Function and Injury and Department of Physiology and Neurobiology, Xinxiang Medical University, Xinxiang 453003, China
- Correspondence: (R.F.); (B.Z.)
| | - Baoguo Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (R.F.); (B.Z.)
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13
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Alvarez-Diaz JC, Richard MMS, Thareau V, Teano G, Paysant-Le-Roux C, Rigaill G, Pflieger S, Gratias A, Geffroy V. Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection. Genes (Basel) 2021; 13:genes13010064. [PMID: 35052407 PMCID: PMC8774654 DOI: 10.3390/genes13010064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB) proteins, RNA-dependent RNA polymerase (RDR), and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant, taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRBs, 5 PvRDRs, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization, and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.
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Affiliation(s)
- Juan C. Alvarez-Diaz
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Manon M. S. Richard
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Gianluca Teano
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Christine Paysant-Le-Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Laboratoire de Mathématiques et Modélisation d’Evry, Université Paris-Saclay, CNRS, Université Evry, INRAE, 91037 Evry, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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15
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Sun D, Ding Z, Shen L, Yang F, Han J, Wu G. miR-410-3P inhibits adipocyte differentiation by targeting IRS-1 in cancer-associated cachexia patients. Lipids Health Dis 2021; 20:115. [PMID: 34563222 PMCID: PMC8465700 DOI: 10.1186/s12944-021-01530-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/24/2021] [Indexed: 11/14/2022] Open
Abstract
Backgrounds Cancer-associated cachexia (CAC) is a metabolic syndrome characterized by progressive depletion of adipose and muscle tissue that cannot be corrected by conventional nutritional therapy. Adipose tissue, an important form of energy storage, exhibits marked loss in the early stages of CAC, which affects quality of life and efficacy of chemotherapy. MicroRNAs (miRNAs) are a class of noncoding RNAs that widely exist in all kinds of eukaryotic cells and play regulatory roles in various biological processes. However, the role of miRNAs in adipose metabolism in CAC has rarely been reported. This study attempted to identify important miRNAs in adipose metabolism in CAC and explore their mechanism to identify a new predictive marker or therapeutic target for CAC-related adipose tissue loss (CAL). Methods In this study, miRNA sequencing was firstly used to identify differentially expressed miRNAs related to CAL and the reliability of the conclusions was verified in large population samples. Furthermore, functional experiments were performed by up and down regulating miR-410-3p in adipocytes. The binding of miR-410-3p to Insulin Receptor Substrate 1 (IRS-1) was verified by Luciferase reporter assay and functional experiments of IRS-1 were performed in adipocytes. Finally, the expression of miR-410-3p in serum exosomes was detected. Results miR-410-3p was selected as differentially expressed miRNA through screening and validation. Adipogenesis was suppressed in miR-410-3p upregulation experiment and increased in downregulation experiment. Luciferase reporter assay showed that miR-410-3p binds to 3′ non-coding region of IRS-1 and represses its expression and ultimately inhibits adipogenesis. miR-410-3p was highly expressed in serum exosomes of CAC patients, which was consistent with results in adipose tissue. Conclusions The expression of miR-410-3p was higher in subcutaneous adipose tissues and serum exosomes of CAC patients, which significantly inhibits adipogenesis and lipid accumulation. The study shows that miR-410-3p could downregulate IRS-1 and downstream adipose differentiation factors including C/EBP-a and PPAR-γ by targeting 3′ noncoding region. Supplementary Information The online version contains supplementary material available at 10.1186/s12944-021-01530-9.
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Affiliation(s)
- Diya Sun
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Zuoyou Ding
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Lei Shen
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Fan Yang
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Jun Han
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China. .,Shanghai Clinical Nutrition Research Centre, Shanghai, China.
| | - Guohao Wu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China. .,Shanghai Clinical Nutrition Research Centre, Shanghai, China.
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16
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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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17
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Santhanagopalan I, Wong R, Mathur T, Griffiths H. Orchestral manoeuvres in the light: crosstalk needed for regulation of the Chlamydomonas carbon concentration mechanism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4604-4624. [PMID: 33893473 PMCID: PMC8320531 DOI: 10.1093/jxb/erab169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 05/19/2023]
Abstract
The inducible carbon concentration mechanism (CCM) in Chlamydomonas reinhardtii has been well defined from a molecular and ultrastructural perspective. Inorganic carbon transport proteins, and strategically located carbonic anhydrases deliver CO2 within the chloroplast pyrenoid matrix where Rubisco is packaged. However, there is little understanding of the fundamental signalling and sensing processes leading to CCM induction. While external CO2 limitation has been believed to be the primary cue, the coupling between energetic supply and inorganic carbon demand through regulatory feedback from light harvesting and photorespiration signals could provide the original CCM trigger. Key questions regarding the integration of these processes are addressed in this review. We consider how the chloroplast functions as a crucible for photosynthesis, importing and integrating nuclear-encoded components from the cytoplasm, and sending retrograde signals to the nucleus to regulate CCM induction. We hypothesize that induction of the CCM is associated with retrograde signals associated with photorespiration and/or light stress. We have also examined the significance of common evolutionary pressures for origins of two co-regulated processes, namely the CCM and photorespiration, in addition to identifying genes of interest involved in transcription, protein folding, and regulatory processes which are needed to fully understand the processes leading to CCM induction.
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Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Rachel Wong
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Tanya Mathur
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
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18
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Lu Y, Gu X, Lin H, Melis A. Engineering microalgae: transition from empirical design to programmable cells. Crit Rev Biotechnol 2021; 41:1233-1256. [PMID: 34130561 DOI: 10.1080/07388551.2021.1917507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Domesticated microalgae hold great promise for the sustainable provision of various bioresources for human domestic and industrial consumption. Efforts to exploit their potential are far from being fully realized due to limitations in the know-how of microalgal engineering. The associated technologies are not as well developed as those for heterotrophic microbes, cyanobacteria, and plants. However, recent studies on microalgal metabolic engineering, genome editing, and synthetic biology have immensely helped to enhance transformation efficiencies and are bringing new insights into this field. Therefore, this article, summarizes recent developments in microalgal biotechnology and examines the prospects for generating specialty and commodity products through the processes of metabolic engineering and synthetic biology. After a brief examination of empirical engineering methods and vector design, this article focuses on quantitative transformation cassette design, elaborates on target editing methods and emerging digital design of algal cellular metabolism to arrive at high yields of valuable products. These advances have enabled a transition of manners in microalgal engineering from single-gene and enzyme-based metabolic engineering to systems-level precision engineering, from cells created with genetically modified (GM) tags to that without GM tags, and ultimately from proof of concept to tangible industrial applications. Finally, future trends are proposed in microalgal engineering, aiming to establish individualized transformation systems in newly identified species for strain-specific specialty and commodity products, while developing sophisticated universal toolkits in model algal species.
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Affiliation(s)
- Yandu Lu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology, Hainan University, Haikou, China.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Xinping Gu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Hanzhi Lin
- Institute of Marine & Environmental Technology, Center for Environmental Science, University of Maryland, College Park, MD, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Rastogi A, Lin X, Lombard B, Loew D, Tirichine L. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms. AIMS GENETICS 2021. [DOI: 10.3934/genet.2015.3.173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractRecent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.
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Affiliation(s)
- Achal Rastogi
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
| | - Xin Lin
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Leïla Tirichine
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
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Abstract
Hundreds of microRNAs (miRNAs) are expressed in distinct spatial and temporal patterns during embryonic and postnatal mouse development. The loss of all miRNAs through the deletion of critical miRNA biogenesis factors results in early lethality. The function of each miRNA stems from their cumulative negative regulation of multiple mRNA targets expressed in a particular cell type. During development, miRNAs often coordinate the timing and direction of cell fate transitions. In adults, miRNAs frequently contribute to organismal fitness through homeostatic roles in physiology. Here, we review how the recent dissection of miRNA-knockout phenotypes in mice as well as advances related to their targets, dosage, and interactions have collectively informed our understanding of the roles of miRNAs in mammalian development and adaptive responses.
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Wang X, Miao X, Chen G, Cui Y, Sun F, Fan J, Gao Z, Meng C. Identification of microRNAs involved in astaxanthin accumulation responding to high light and high sodium acetate (NaAC) stresses in Haematococcus pluvialis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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22
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Meng H, Wang S, Yang W, Ding X, Li N, Chu Z, Li X. Identification of virulence associated milRNAs and their bidirectional targets in Rhizoctonia solani and maize during infection. BMC PLANT BIOLOGY 2021; 21:155. [PMID: 33771101 PMCID: PMC8004440 DOI: 10.1186/s12870-021-02930-w] [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: 12/22/2020] [Accepted: 03/10/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Anastomosis group 1 IA (AG1-IA) of Rhizoctonia solani is the major agent of banded leaf and sheath blight (BLSB) disease that causes severe yield loss in many worldwide crops. MicroRNAs (miRNAs) are ~ 22 nt non-coding RNAs that negatively regulate gene expression levels by mRNA degradation or translation inhibition. A better understanding of miRNA function during AG1-IA infection can expedite to elucidate the molecular mechanisms of fungi-host interactions. RESULTS In this study, we sequenced three small RNA libraries obtained from the mycelium of AG1-IA isolate, non-infected maize sheath and mixed maize sheath 3 days after inoculation. In total, 137 conserved and 34 novel microRNA-like small RNAs (milRNAs) were identified from the pathogen. Among these, one novel and 17 conserved milRNAs were identified as potential virulence-associated (VA) milRNAs. Subsequently, the prediction of target genes for these milRNAs was performed in both AG1-IA and maize, while functional annotation of these targets suggested a link to pathogenesis-related biological processes. Further, expression patterns of these virulence-associated milRNAs demonstrated that theyparticipate in the virulence of AG1-IA. Finally, regulation of one maize targeting gene, GRMZM2G412674 for Rhi-milRNA-9829-5p, was validated by dual-luciferase assay and identified to play a positive role in BLSB resistance in two maize mutants. These results suggest the global differentially expressed milRNAs of R. solani AG1-IA that participate in the regulation of target genes in both AG1-IA and maize to reinforce its pathogenicity. CONCLUSIONS Our data have provided a comprehensive overview of the VA-milRNAs of R. solani and identified that they are probably the virulence factors by directly interfered in host targeting genes. These results offer new insights on the molecular mechanisms of R.solani-maize interactions during the process of infection.
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Affiliation(s)
- Hongxu Meng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Shaoli Wang
- Yantai Academy of Agricultural Sciences, Yan'tai, 265500, Shandong, People's Republic of China
| | - Wei Yang
- Key Laboratory of Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Xinhua Ding
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Ning Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Xiaoming Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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Middleton H, Yergeau É, Monard C, Combier JP, El Amrani A. Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator. TRENDS IN PLANT SCIENCE 2021; 26:132-141. [PMID: 33036916 DOI: 10.1016/j.tplants.2020.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 05/20/2023]
Abstract
The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels. Here, we propose that miRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, miRNAs as a promising tool for novel holobiont engineering.
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Affiliation(s)
- Harriet Middleton
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France.
| | - Étienne Yergeau
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada
| | - Cécile Monard
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Vegetales, UMR 5546, UPS, CNRS, Auzeville-Tolosane 31320, France
| | - Abdelhak El Amrani
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
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24
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25
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Expression analysis of gamma globin gene switching associated micro RNAs, flowing BCL11A gene inhibition. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Genome-wide identification of Argonautes in Solanaceae with emphasis on potato. Sci Rep 2020; 10:20577. [PMID: 33239724 PMCID: PMC7689493 DOI: 10.1038/s41598-020-77593-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.
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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: 5] [Impact Index Per Article: 1.3] [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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28
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Silva-Martins G, Bolaji A, Moffett P. What does it take to be antiviral? An Argonaute-centered perspective on plant antiviral defense. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6197-6210. [PMID: 32835379 DOI: 10.1093/jxb/eraa377] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
RNA silencing is a major mechanism of constitutive antiviral defense in plants, mediated by a number of proteins, including the Dicer-like (DCL) and Argonaute (AGO) endoribonucleases. Both DCL and AGO protein families comprise multiple members. In particular, the AGO protein family has expanded considerably in different plant lineages, with different family members having specialized functions. Although the general mode of action of AGO proteins is well established, the properties that make different AGO proteins more or less efficient at targeting viruses are less well understood. In this report, we review methodologies used to study AGO antiviral activity and current knowledge about which AGO family members are involved in antiviral defense. In addition, we discuss what is known about the different properties of AGO proteins thought to be associated with this function.
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Affiliation(s)
| | - Ayooluwa Bolaji
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
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29
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Achievements and challenges of genetic engineering of the model green alga Chlamydomonas reinhardtii. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101986] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
The transition of life from single cells to more complex multicellular forms has occurred at least two dozen times among eukaryotes and is one of the major evolutionary transitions, but the early steps that enabled multicellular life to evolve and thrive remain poorly understood. Volvocine green algae are a taxonomic group that is uniquely suited to investigating the step-wise acquisition of multicellular organization. The multicellular volvocine species Volvox carteri exhibits many hallmarks of complex multicellularity including complete germ–soma division of labor, asymmetric cell divisions, coordinated tissue-level morphogenesis, and dimorphic sexes—none of which have obvious analogs in its closest unicellular relative, the model alga Chlamydomonas reinhardtii. Here, I summarize some of the key questions and areas of study that are being addressed with Volvox carteri and how increasing genomic information and methodologies for volvocine algae are opening up the entire group as an integrated experimental system for exploring the evolution of multicellularity and more.
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Affiliation(s)
- James G Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO 63132 USA
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31
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Lou S, Zhu X, Zeng Z, Wang H, Jia B, Li H, Hu Z. Identification of microRNAs response to high light and salinity that involved in beta-carotene accumulation in microalga Dunaliella salina. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101925] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Xue Y, Chen R, Qu L, Cao X. Noncoding RNA: from dark matter to bright star. SCIENCE CHINA-LIFE SCIENCES 2020; 63:463-468. [DOI: 10.1007/s11427-020-1676-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Indexed: 12/16/2022]
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33
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34
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Yang Z, Zhu P, Kang H, Liu L, Cao Q, Sun J, Dong T, Zhu M, Li Z, Xu T. High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.). BMC Genomics 2020; 21:164. [PMID: 32066373 PMCID: PMC7027035 DOI: 10.1186/s12864-020-6567-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/07/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. However, the regulatory mechanism of miRNA-mediated abiotic stress response in sweet potato remains unclear. RESULTS In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed sweet potato cultivars and its untreated control. Twelve small non-coding RNA libraries from NaCl-free (CK) and NaCl-treated (Na150) sweet potato leaves and roots were constructed for salt-responsive miRNA identification in sweet potatoes. A total of 475 known miRNAs (belonging to 66 miRNA families) and 175 novel miRNAs were identified. Among them, 51 (22 known miRNAs and 29 novel miRNAs) were significantly up-regulated and 76 (61 known miRNAs and 15 novel miRNAs) were significantly down-regulated by salinity stress in sweet potato leaves; 13 (12 known miRNAs and 1 novel miRNAs) were significantly up-regulated and 9 (7 known miRNAs and 2 novel miRNAs) were significantly down-regulated in sweet potato roots. Furthermore, 636 target genes of 314 miRNAs were validated by degradome sequencing. Deep sequencing results confirmed by qRT-PCR experiments indicated that the expression of most miRNAs exhibit a negative correlation with the expression of their targets under salt stress. CONCLUSIONS This study provides insights into the regulatory mechanism of miRNA-mediated salt response and molecular breeding of sweet potatoes though miRNA manipulation.
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Affiliation(s)
- Zhengmei Yang
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Panpan Zhu
- 0000 0001 0356 9399grid.14005.30Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 South Korea
| | - Hunseung Kang
- 0000 0001 0356 9399grid.14005.30Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 South Korea
| | - Lin Liu
- 0000 0001 0472 9649grid.263488.3Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Qinghe Cao
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121 Jiangsu China
| | - Jian Sun
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Tingting Dong
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Mingku Zhu
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Zongyun Li
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Tao Xu
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
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35
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Sampathi S, Acharya P, Zhao Y, Wang J, Stengel KR, Liu Q, Savona MR, Hiebert SW. The CDK7 inhibitor THZ1 alters RNA polymerase dynamics at the 5' and 3' ends of genes. Nucleic Acids Res 2019; 47:3921-3936. [PMID: 30805632 PMCID: PMC6486546 DOI: 10.1093/nar/gkz127] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/22/2019] [Indexed: 01/01/2023] Open
Abstract
The t(8;21) is one of the most frequent chromosomal translocations associated with acute myeloid leukemia (AML). We found that t(8;21) AML were extremely sensitive to THZ1, which triggered apoptosis after only 4 h. We used precision nuclear run-on transcription sequencing (PROseq) to define the global effects of THZ1 and other CDK inhibitors on RNA polymerase II dynamics. Inhibition of CDK7 using THZ1 caused wide-spread loss of promoter-proximal paused RNA polymerase. This loss of 5′ pausing was associated with accumulation of polymerases in the body of a large number of genes. However, there were modest effects on genes regulated by ‘super-enhancers’. At the 3′ ends of genes, treatment with THZ1 suppressed RNA polymerase ‘read through’ at the end of the last exon, which resembled a phenotype associated with a mutant RNA polymerase with slower elongation rates. Consistent with this hypothesis, polyA site-sequencing (PolyA-seq) did not detect differences in poly A sites after THZ1 treatment. PROseq analysis after short treatments with THZ1 suggested that these 3′ effects were due to altered CDK7 activity at the 5′ end of long genes, and were likely to be due to slower rates of elongation.
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Affiliation(s)
- Shilpa Sampathi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R Savona
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37027.,Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37027
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36
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Sun D, Han L, Cao R, Wang H, Jiang J, Deng Y, Yu X. Prediction of a miRNA-mRNA functional synergistic network for cervical squamous cell carcinoma. FEBS Open Bio 2019; 9:2080-2092. [PMID: 31642613 PMCID: PMC6886301 DOI: 10.1002/2211-5463.12747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 01/16/2023] Open
Abstract
Cervical squamous cell carcinoma (CSCC) accounts for a significant proportion of cervical cancer; thus, there is a need for novel and noninvasive diagnostic biomarkers for this malignancy. In this study, we performed integrated analysis of a dataset from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) between CSCC, cervical intraepithelial neoplasia (CIN) and healthy control subjects. We further established protein-protein interaction and DEmiRNA-target gene interaction networks, and performed functional annotation of the target genes of DEmiRNAs. In total, we identified 1375 DEGs and 19 DEmiRNAs in CIN versus normal control, and 2235 DEGs and 33 DEmiRNAs in CSCC versus CIN by integrated analysis. Our protein-protein interaction network indicates that the common DEGs, Cyclin B/cyclin-dependent kinase 1 (CDK1), CCND1, ESR1 and Aurora kinase A (AURKA), are the top four hub genes. P53 and prostate cancer were identified as significantly enriched signaling pathways of common DEGs and DEmiRNA targets, respectively. We validated that expression levels of three DEGs (TYMS, SASH1 and CDK1) and one DEmiRNA of hsa-miR-99a were altered in blood samples of patients with CSCC. In conclusion, a total of four DEGs (TYMS, SASH1, CDK1 and AURKA) and two DEmiRNAs (hsa-miR-21 and hsa-miR-99a) may be involved in the pathogenesis of CIN and the progression of CIN into CSCC. Of these, TYMS is predicted to be regulated by hsa-miR-99a and SASH1 to be regulated by hsa-miR-21.
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Affiliation(s)
- Dan Sun
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Lu Han
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Rui Cao
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Huali Wang
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Jiyong Jiang
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Yanjie Deng
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Xiaohui Yu
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
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Posner R, Laubenbacher R. Connecting the molecular function of microRNAs to cell differentiation dynamics. J R Soc Interface 2019; 16:20190437. [PMID: 31551049 PMCID: PMC6769318 DOI: 10.1098/rsif.2019.0437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs form a class of short, non-coding RNA molecules which are essential for proper development in tissue-based plants and animals. To help explain their role in gene regulation, a number of mathematical and computational studies have demonstrated the potential canalizing effects of microRNAs. However, such studies have typically focused on the effects of microRNAs on only one or a few target genes. Consequently, it remains unclear how these small-scale effects add up to the experimentally observed developmental outcomes resulting from microRNA perturbation at the whole-genome level. To answer this question, we built a general computational model of cell differentiation to study the effect of microRNAs in genome-scale gene regulatory networks. Our experiments show that in large gene regulatory networks, microRNAs can control differentiation time without significantly changing steady-state gene expression profiles. This temporal regulatory role cannot be naturally replicated using protein-based transcription factors alone. While several microRNAs have been shown to regulate differentiation time in vivo, our findings provide a new explanation of how the cumulative molecular actions of individual microRNAs influence genome-scale cellular dynamics. Taken together, these results may help explain why tissue-based organisms exclusively depend on miRNA-mediated regulation, while their more primitive counterparts do not.
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Affiliation(s)
- Russell Posner
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA
| | - Reinhard Laubenbacher
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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Salomé PA, Merchant SS. A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism. THE PLANT CELL 2019; 31:1682-1707. [PMID: 31189738 PMCID: PMC6713297 DOI: 10.1105/tpc.18.00952] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/20/2019] [Accepted: 06/08/2019] [Indexed: 05/13/2023]
Abstract
The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.
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Affiliation(s)
- Patrice A Salomé
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
| | - Sabeeha S Merchant
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
- University of California, Berkeley, Departments of Plant and Microbial Biology and Molecular and Cell Biology, Berkeley, CA 94720
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Lineage-Specific Evolved MicroRNAs Regulating NB-LRR Defense Genes in Triticeae. Int J Mol Sci 2019; 20:ijms20133128. [PMID: 31248042 PMCID: PMC6651130 DOI: 10.3390/ijms20133128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023] Open
Abstract
Disease resistance genes encoding proteins with nucleotide binding sites and Leucine-Rich Repeat (NB-LRR) domains include many members involved in the effector-triggered immunity pathway in plants. The transcript levels of these defense genes are negatively regulated by diverse microRNAs (miRNAs) in angiosperms and gymnosperms. In wheat, using small RNA expression datasets and degradome datasets, we identified five miRNA families targeting NB-LRR defense genes in monocots, some of which arose in the Triticeae species era. These miRNAs regulate different types of NB-LRR genes, most of them with coil-coiled domains, and trigger the generation of secondary small interfering RNAs (siRNA) as a phased pattern in the target site regions. In addition to acting in response to biotic stresses, they are also responsive to abiotic stresses such as heat, drought, salt, and light stress. Their copy number and expression variation in Triticeae suggest a rapid birth and death frequency. Altogether, non-conserved miRNAs as conserved transcriptional regulators in gymnosperms and angiosperms regulating the disease resistance genes displayed quick plasticity including the variations of sequences, gene copy number, functions, and expression level, which accompanied with NB-LRR genes may be tune-regulated to plants in natural environments with various biotic and abiotic stresses.
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MicroRNA-29b Enhances Osteoclast Survival by Targeting BCL-2-Modifying Factor after Lipopolysaccharide Stimulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:6018180. [PMID: 31093317 PMCID: PMC6481009 DOI: 10.1155/2019/6018180] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/11/2019] [Accepted: 02/12/2019] [Indexed: 12/31/2022]
Abstract
Recent findings suggest that microRNAs (miRs) play a critical role in osteoclastogenesis, which regulates bone loss. We hypothesized that inflammation induces miR-29b, which increases the survival rate in osteoclasts (OCs), leading to bone loss. The expression level of miR-29b increased in OC stimulated by lipopolysaccharide (LPS) in an in vitro system which correlated with its increase in tibiae from mice that received LPS injections compared with those that received vehicle treatment. An miR-29b mimic increased OC survival rate without any change in OC differentiation, and furthermore, the inhibition of endogenous miR-29b induced by LPS decreased OC survival rate. Increased OC survival rate after overexpression of miR-29b was associated with antiapoptotic activity, as shown by staining annexin V-positive cells. We found that a target gene of miR-29b is BCL-2-modifying factor (Bmf), which acts as a proapoptotic factor, and that miR-29b binds to the 3′-UTR of Bmf. Our data demonstrate that LPS-induced miR-29b increases the number of OC by enhancing OC survival through decreased BMF.
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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 PMCID: PMC6701991 DOI: 10.1002/bies.201800169] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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42
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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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Curcio JSD, Batista MP, Paccez JD, Novaes E, Soares CMDA. In silico characterization of microRNAs-like sequences in the genome of Paracoccidioides brasiliensis. Genet Mol Biol 2019; 42:95-107. [PMID: 30776047 PMCID: PMC6428129 DOI: 10.1590/1678-4685-gmb-2018-0014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/22/2018] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells have different mechanisms of post-transcriptional regulation.
Among these mechanisms, microRNAs promote regulation of targets by cleavage or
degradation of the mRNA. Fungi of the Paracoccidioides complex
are the etiological agents of the main systemic mycosis of Latin America. These
fungi present a plasticity to adapt and survive in different conditions, and the
presence of microRNAs-like molecules could be part of the mechanisms that
provide such plasticity. MicroRNAs produced by the host influence the
progression of this mycosis in the lungs besides regulating targets involved in
apoptosis in macrophage, activation of T and B cells and the production of
cytokines. Therefore, this work analyzed the presence of regions in the genome
of this fungus with a potential to encode microRNAs-like molecules. Here we show
by analysis of sequence similarity the presence of 18 regions, putatively coding
for microRNAs-like molecules in the Paracoccidioides
brasiliensis genome. We also described the conservation of dicer
and argonaut proteins and the cognate transcripts induced in the yeast parasitic
phase. This work represents a starting point for the analysis of the presence of
those molecules in the morphological stages of the fungus and their role in
fungal development.
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Affiliation(s)
- Juliana S de Curcio
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brazil
| | - Mariana P Batista
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil
| | - Juliano D Paccez
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Minas Gerais, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, Goiânia, GO, Brazil
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44
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Bt Md Nasir NAN, Islam AKMA, Anuar N, Yaakob Z. Genetic Improvement and Challenges for Cultivation of Microalgae for Biodiesel: A Review. MINI-REV ORG CHEM 2019. [DOI: 10.2174/1570193x15666180627115502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microalgae are a viable alternative for biofuel production to replace the world dependency on
fossil fuel. It has a wide range of application for the sustainable production of biomaterials. Microalgae
can convert solar energy into important natural components by utilizing marginal nutrients, wastewater
and exhaust CO2 without sharing expensive crop field. Microalgae also have the potentiality to generate
several promising components such as Polyunsaturated Fatty Acids (PUFAs), organic pigments and
pharmaceutically important hydrocarbons. Cultivation and production of microalgae biomass have multifaceted
challenges due to the requirement of large volume of water for the algae growth, high processing
cost and contamination by pathogens. Genetic improvement and modifications are essential to
construct superior microalgae for manufacturing industries using various methods such as selection of
novel strain, stress tolerance, resistance to pathogens, product development and metabolic pathways and
cellular contents. In addition, technologies related to cultivation, harvesting, extraction and processing
are essential to develop for the growth of novel microalgae strains.
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Affiliation(s)
- Nor-Anis N. Bt Md Nasir
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia, Kuantan Kampus, 25710, Kuantan, Pahang Darul Makmur, Malaysia
| | - A. K. M. Aminul Islam
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nurina Anuar
- Department of Chemical and Process Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, 43600, Malaysia
| | - Zahira Yaakob
- Department of Chemical and Process Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, 43600, Malaysia
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45
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Wang B, Zhang F, Hu J, Gao X, Bian P, Liu Y, Wang G. Cre-miR914-regulated RPL18 is involved with UV-B adaptation in Chlamydomonas reinhardtii. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:151-159. [PMID: 30537602 DOI: 10.1016/j.jplph.2018.11.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
UV radiation is a serious threat to life, and algae have developed highly efficient adaptations to UV radiation through the course of evolution. To date, studies investigating the mechanisms of UV adaptation in algae have focused on physiological regulation and associated protein coding genes, with only a few reports on associated protein non-coding genes. In a previous study, we found that Cre-miR914 was significantly down-regulated in Chlamydomonas reinhardtii in response to heat shock. In the present study, we aimed to determine whether Cre-miR914 plays a role in response to UV-B radiation. Our bioinformatics analysis indicated that the potential target gene of Cre-miR914 is ribosomal protein L18 (RPL18). We also measured the expression of Cre-miR914 and RPL18 in response to UV-B radiation through qPCR analysis. Then, we constructed cell lines overexpressing Cre-miR914 or RPL18, and performed survival experiments under UV-B stress. The results showed that Cre-miR914 overexpression decreased resistance while RPL18 overexpression enhanced tolerance to UV-B radiation. These results indicate that Cre-miR914 and its potential target gene RPL18 are involved in the adaptation to UV-B in C. reinhardtii.
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Affiliation(s)
- Bo Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengge Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jinlu Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiang Gao
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Po Bian
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui, 230031, China
| | - Yongding Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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46
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Kwon YM, Kim KW, Choi TY, Kim SY, Kim JYH. Manipulation of the microalgal chloroplast by genetic engineering for biotechnological utilization as a green biofactory. World J Microbiol Biotechnol 2018; 34:183. [PMID: 30478596 DOI: 10.1007/s11274-018-2567-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022]
Abstract
The chloroplast is an essential organelle in microalgae for conducting photosynthesis, thus enabling the photoautotrophic growth of microalgae. In addition to photosynthesis, the chloroplast is capable of various biochemical processes for the synthesis of proteins, lipids, carbohydrates, and terpenoids. Due to these attractive characteristics, there has been increasing interest in the biotechnological utilization of microalgal chloroplast as a sustainable alternative to the conventional production platforms used in industrial biotechnology. Since the first demonstration of microalgal chloroplast transformation, significant development has occurred over recent decades in the manipulation of microalgal chloroplasts through genetic engineering. In the present review, we describe the advantages of the microalgal chloroplast as a production platform for various bioproducts, including recombinant proteins and high-value metabolites, features of chloroplast genetic systems, and the development of transformation methods, which represent important factors for gene expression in the chloroplast. Furthermore, we address the expression of various recombinant proteins in the microalgal chloroplast through genetic engineering, including reporters, biopharmaceutical proteins, and industrial enzymes. Finally, we present many efforts and achievements in the production of high-value metabolites in the microalgal chloroplast through metabolic engineering. Based on these efforts and advances, the microalgal chloroplast represents an economically viable and sustainable platform for biotechnological applications in the near future.
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Affiliation(s)
- Yong Min Kwon
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Kyung Woo Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Tae-Young Choi
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Sun Young Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Jaoon Young Hwan Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea.
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47
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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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48
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Njaci I, Williams B, Castillo-González C, Dickman MB, Zhang X, Mundree S. Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis. PLANTS (BASEL, SWITZERLAND) 2018; 7:E68. [PMID: 30200279 PMCID: PMC6161015 DOI: 10.3390/plants7030068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022]
Abstract
Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.
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Affiliation(s)
- Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Martin B Dickman
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
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49
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Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F. Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum. RNA Biol 2018; 15:937-954. [PMID: 29966484 PMCID: PMC6161686 DOI: 10.1080/15476286.2018.1481697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.
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Affiliation(s)
- Zhen Liao
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Jonas Kjellin
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Marc P Hoeppner
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden.,c Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology , Kiel , Germany
| | - Manfred Grabherr
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden
| | - Fredrik Söderbom
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
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50
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Olina AV, Kulbachinskiy AV, Aravin AA, Esyunina DM. Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes. BIOCHEMISTRY (MOSCOW) 2018; 83:483-497. [PMID: 29738683 DOI: 10.1134/s0006297918050024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Noncoding RNAs play essential roles in genetic regulation in all organisms. In eukaryotic cells, many small noncoding RNAs act in complex with Argonaute proteins and regulate gene expression by recognizing complementary RNA targets. The complexes of Argonaute proteins with small RNAs also play a key role in silencing of mobile genetic elements and, in some cases, viruses. These processes are collectively called RNA interference. RNA interference is a powerful tool for specific gene silencing in both basic research and therapeutic applications. Argonaute proteins are also found in prokaryotic organisms. Recent studies have shown that prokaryotic Argonautes can also cleave their target nucleic acids, in particular DNA. This activity of prokaryotic Argonautes might potentially be used to edit eukaryotic genomes. However, the molecular mechanisms of small nucleic acid biogenesis and the functions of Argonaute proteins, in particular in bacteria and archaea, remain largely unknown. Here we briefly review available data on the RNA interference processes and Argonaute proteins in eukaryotes and prokaryotes.
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Affiliation(s)
- A V Olina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| | - A V Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - A A Aravin
- California Institute of Technology, Division of Biology, Pasadena, CA 91125, USA
| | - D M Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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