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Huang P, Yu H, Asad M, Liao J, Lin S, Pang S, Chu X, Yang G. Functional characteristics of Dicer genes in Plutella xylostella. PEST MANAGEMENT SCIENCE 2024; 80:2109-2119. [PMID: 38133081 DOI: 10.1002/ps.7945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/21/2023] [Accepted: 12/22/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Dicer is an endonuclease that belongs to the RNase III family and can specifically recognize and cleave double-stranded RNA (dsRNA). In most insects, there are two Dicer genes, Dicer-1 (Dcr-1) and Dicer-2 (Dcr-2), which are involved in the micro-RNA and small-interfering RNA pathways in many species, respectively. The function of Dicer in Plutella xylostella remains unknown. RESULTS The full-length open reading frames of P. xylostella Dicer-1 (PxDcr-1) and Dicer-2 (PxDcr-2) were cloned and sequenced. Dcr-1 and Dcr-2 proteins shared similar structural domains with the Dicer-Partner Binding Domain (Dicer-PBD) and the double-strand RNA binding domain (dsRBD) present only in Dcr-1. The phylogenetic trees showed that lepidopteran Dcr-1s or Dcr-2s clustered in one branch, with PxDcr-1 in the basal position and PxDcr-2 closest to Plodia interpunctella Dicer. Two homozygous knockout lines, ΔPxDcr-1 and ΔPxDcr-2, were obtained by using the CRISPR-Cas9 technique. The ΔPxDcr-1 strain exhibited a high mortality rate, a low eclosion rate, a low egg-laying rate, a low hatching rate, and a shriveled ovariole without mature eggs. The ΔPxDcr-2 strain showed no significant difference from the wild-type in terms of survival, development and reproduction, but the RNA interference (RNAi) efficiency caused by dsRNA was significantly reduced. CONCLUSION These findings demonstrate the involvement of PxDcr-1 in the development and reproduction of P. xylostella, specifically in the formation of ovarioles and eggs, and PxDcr-2 is indispensable for RNAi. These findings shed light on the function of Dcr-1 and Dcr-2 in Lepidoptera. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Pengrong Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianying Liao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sujie Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Senbo Pang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuemei Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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Airs PM, Kudrna KE, Lubinski B, Phanse Y, Bartholomay LC. A Comparative Analysis of RNAi Trigger Uptake and Distribution in Mosquito Vectors of Disease. INSECTS 2023; 14:556. [PMID: 37367372 DOI: 10.3390/insects14060556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
Abstract
In mosquitoes, the utilization of RNAi for functional genetics is widespread, usually mediated through introduced double-stranded RNAs (dsRNAs) with sequence identity to a gene of interest. However, RNAi in mosquitoes is often hampered by inconsistencies in target gene knockdown between experimental setups. While the core RNAi pathway is known to function in most mosquito strains, the uptake and biodistribution of dsRNAs across different mosquito species and life stages have yet to be extensively explored as a source of variation in RNAi experiments. To better understand mosquito-RNAi dynamics, the biodistribution of a dsRNA to a heterologous gene, LacZ (iLacZ), was tracked following various routes of exposure in the larval and adult stages of Aedes aegypti, Anopheles gambiae, and Culex pipiens. iLacZ was largely limited to the gut lumen when exposed per os, or to the cuticle when topically applied, but spread through the hemocoel when injected. Uptake of dsRNA was noted in a subset of cells including: hemocytes, pericardial cells of the dorsal vessel, ovarian follicles, and ganglia of the ventral nerve cord. These cell types are all known to undergo phagocytosis, pinocytosis, or both, and as such may actively take up RNAi triggers. In Ae. aegypti, iLacZ was detected for up to one week post exposure by Northern blotting, but uptake and degradation drastically differed across tissues. The results presented here reveal that the uptake of RNAi triggers is distinct and specific to the cell type in vivo.
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Affiliation(s)
- Paul M Airs
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine E Kudrna
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bailey Lubinski
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yashdeep Phanse
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lyric C Bartholomay
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center of Excellence for Vector-Borne Diseases, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Yao Z, Jin H, Li C, Ma W, Zhang W, Lin Y. Knockdown of Dcr1 and Dcr2 limits the lethal effect of C-factor in Chilo suppressalis. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22004. [PMID: 36780173 DOI: 10.1002/arch.22004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Dicer is a highly conserved ribonuclease in evolution. It belongs to the RNase III family and can specifically recognize and cleave double-stranded RNA (dsRNA). In this study, the genome and transcriptome of Chilo suppressalis were analyzed, and it was found that there were two members in the Dicer family, named Dcr1 and Dcr2. The dsRNAs of Dcr1 and Dcr2 genes were synthesized and fed to C. suppressalis larvae. The C-factor of C. suppressalis was selected as the marker gene. The results showed that both Dcr1 and Dcr2 genes were significantly knocked down. The larval mortality was significantly reduced by 43.50% (p < 0.05) after feeding on dsC-factor and dsDcr1. The transcription levels of C-factor genes were significantly increased by 33.95% (p < 0.05) and 32.94% (p < 0.05) when the larvae fed with dsDcr2 + dsC-factor for 72 h and 96 h, respectively. Furthermore, the mortality was significantly decreased by 79% (p < 0.05) after feeding dsC-factor and dsDcr2. These findings imply that Dcr1 can decrease the lethal effect of C-factor gene but cannot affect its RNAi efficiency and Dcr2 can decrease the lethal effect of C-factor gene by inhibiting RNAi efficiency.
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Affiliation(s)
- Zhuotian Yao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Huihui Jin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Changyan Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Weihua Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Yuan L, Jiang X, Gong Q, Gao N. Arsenic resistance protein 2 and microRNA biogenesis: Biological implications in cancer development. Pharmacol Ther 2023; 244:108386. [PMID: 36933704 DOI: 10.1016/j.pharmthera.2023.108386] [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: 01/01/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Arsenic resistance protein 2 (Ars2) is a nuclear protein that plays a critical role in the regulation of microRNA (miRNA) biogenesis. Ars2 is required for cell proliferation and for the early stages of mammalian development through a possible effect on miRNA processing. Increasing evidence reveal that Ars2 is highly expressed in proliferating cancer cells, suggesting that Ars2 may be a potential therapeutic target for cancer. Therefore, development of the novel Ars2 inhibitors could represent the novel therapeutic strategies for treatment of cancer. In this review, we briefly discuss the mechanisms by which Ars2 regulates miRNA biogenesis and its impact on cell proliferation and cancer development. Particularly, we mainly discuss the role of Ars2 in the regulation of cancer development and highlight pharmacological targeting of Ars2 as a promising cancer therapeutic strategy.
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Affiliation(s)
- Liang Yuan
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China
| | - Xiuxing Jiang
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
| | - Ning Gao
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
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5
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Gao L, Wang Y, Abbas M, Zhang T, Ma E, Merzendorfer H, Zhu KY, Zhang J. Both LmDicer-1 and two LmDicer-2s participate in siRNA-mediated RNAi pathway and contribute to high gene silencing efficiency in Locusta migratoria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103865. [PMID: 36336194 DOI: 10.1016/j.ibmb.2022.103865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Dicers belong to a class of large RNase III multidomain ribonucleases and are central components of the RNA interference (RNAi) pathways. In insects, Dicer-2 has been known to cleave long double-stranded RNA (dsRNA) in small interfering RNA (siRNA)-mediated-RNAi pathway. However, Dicer-1 is responsible for cleaving precursor microRNAs (pre28 miRNAs) in miRNA-mediated RNAi pathway. In this study, we identified one LmDicer-1 and two LmDicer-2 (LmDicer-2a and LmDicer-2b) genes in Locusta migratoria. The RNAi of RNAi assay showed that knockdown of each of the Dicer genes reduced RNAi efficiency against a target gene (Lmβ-Tubulin), suggesting that all these genes participated in the siRNA-mediated RNAi pathway. Sequence analyses of the siRNAs generated from dsLmβ-Tubulin after silencing each LmDicer gene showed no significant difference in the pattern of siRNAs mapped to dsLmβ-Tubulin. This result indicated that all the three LmDicers are capable of generating siRNAs from the dsRNA. We then generated recombinant proteins consisting of different domains using Escherichia coli expression system and incubated each recombinant protein with dsLmβ-Tubulin. We found that the recombinant Dicer proteins successfully cleaved dsLmβ-Tubulin. However, LmDicer-2a-R lacking dsRBD domain lost activity, suggesting that dsRBD domain is critical for Dicer function. Furthermore, overexpression of these proteins in Drosophila S2 cells improved RNAi efficiency. Our siRNA affinity chromatography and LC-MS/MS analysis identified LmDicer-2a, LmDicer-2b, LmR2D2, LmAgo2a, LmAgo1, LmStaufen and LmTARBP2 as constituents of RNA-induced silencing complex. Taken together, these data show that both LmDicer-1 and two LmDicer-2s all participate in siRNA-mediated RNAi pathway and likely contribute to high RNAi efficiency in L. migratoria.
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Affiliation(s)
- Lu Gao
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China; College of Life Science, Shanxi University, Taiyuan, China
| | - Yanli Wang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Mureed Abbas
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Tingting Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Enbo Ma
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | | | - Kun Yan Zhu
- Department of Entomology, 123 Waters Hall, Kansas State University, Manhattan, KS, 66506, USA.
| | - Jianzhen Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China.
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6
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Neural mechanisms to exploit positional geometry for collision avoidance. Curr Biol 2022; 32:2357-2374.e6. [PMID: 35508172 DOI: 10.1016/j.cub.2022.04.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/21/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022]
Abstract
Visual motion provides rich geometrical cues about the three-dimensional configuration of the world. However, how brains decode the spatial information carried by motion signals remains poorly understood. Here, we study a collision-avoidance behavior in Drosophila as a simple model of motion-based spatial vision. With simulations and psychophysics, we demonstrate that walking Drosophila exhibit a pattern of slowing to avoid collisions by exploiting the geometry of positional changes of objects on near-collision courses. This behavior requires the visual neuron LPLC1, whose tuning mirrors the behavior and whose activity drives slowing. LPLC1 pools inputs from object and motion detectors, and spatially biased inhibition tunes it to the geometry of collisions. Connectomic analyses identified circuitry downstream of LPLC1 that faithfully inherits its response properties. Overall, our results reveal how a small neural circuit solves a specific spatial vision task by combining distinct visual features to exploit universal geometrical constraints of the visual world.
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7
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Paturi S, Deshmukh MV. A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective. Front Mol Biosci 2021; 8:643657. [PMID: 34026825 PMCID: PMC8138440 DOI: 10.3389/fmolb.2021.643657] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/07/2021] [Indexed: 01/05/2023] Open
Abstract
The RNA interference pathway (RNAi) is executed by two core enzymes, Dicer and Argonaute, for accomplishing a tailored transcriptional and post-transcriptional gene regulation. Dicer, an RNase III enzyme, initiates the RNAi pathway, plays a pivotal role in fighting infection against pathogens, and acts as a housekeeping enzyme for cellular homeostasis. Here, we review structure-based functional insights of Dicer and its domains present in a diverse group of organisms. Although Dicer and its domains are evolutionarily conserved from microsporidian parasites to humans, recent cryo-electron microscopy structures of Homo sapiens Dicer and Drosophila melanogaster Dicer-2 suggest characteristic variations in the mechanism of the dsRNA substrate recognition. Interestingly, the necessity for more than one functionally distinct Dicer paralogs in insects and plants compared with a single Dicer in other eukaryotic life forms implies Dicer’s role in the interplay of RNAi and other defense mechanisms. Based on the structural and mechanistic information obtained during the last decade, we aim to highlight the significance of key Dicer domains that are crucial to Dicer specific recognition and precise cleavage of dsRNA substrates. Further, the role of Dicer in the formation of Argonaute-based RNA-induced silencing complex (RISC) assembly formation, Dicer’s ability to regulate a complex protein interaction network, and its role in other cellular processes, as well as its therapeutic potentials, are emphasized.
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Affiliation(s)
- Sneha Paturi
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
| | - Mandar V Deshmukh
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
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Regulation of Nucleolar Dominance in Drosophila melanogaster. Genetics 2020; 214:991-1004. [PMID: 32122935 PMCID: PMC7153946 DOI: 10.1534/genetics.119.302471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/26/2020] [Indexed: 12/18/2022] Open
Abstract
In eukaryotic genomes, ribosomal RNA (rRNA) genes exist as tandemly repeated clusters, forming ribosomal DNA (rDNA) loci. Each rDNA locus typically contains hundreds of rRNA genes to meet the high demand of ribosome biogenesis. Nucleolar dominance is a phenomenon whereby individual rDNA loci are entirely silenced or transcribed, and is believed to be a mechanism to control rRNA dosage. Nucleolar dominance was originally noted to occur in interspecies hybrids, and has been shown to occur within a species (i.e., nonhybrid context). However, studying nucleolar dominance within a species has been challenging due to the highly homogenous sequence across rDNA loci. By utilizing single nucleotide polymorphisms between X rDNA and Y rDNA loci in males, as well as sequence variations between two X rDNA loci in females, we conducted a thorough characterization of nucleolar dominance throughout development of Drosophila melanogaster. We demonstrate that nucleolar dominance is a developmentally regulated program that occurs in nonhybrid, wild-type D. melanogaster, where Y rDNA dominance is established during male embryogenesis, whereas females normally do not exhibit dominance between two X rDNA loci. By utilizing various chromosomal complements (e.g., X/Y, X/X, X/X/Y) and a chromosome rearrangement, we show that the short arm of the Y chromosome including the Y rDNA likely contains information that instructs the state of nucleolar dominance. Our study begins to reveal the mechanisms underlying the selection of rDNA loci for activation/silencing in nucleolar dominance in the context of nonhybrid D. melanogaster.
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McMenamin AJ, Daughenbaugh KF, Flenniken ML. The Heat Shock Response in the Western Honey Bee (Apis mellifera) is Antiviral. Viruses 2020; 12:E245. [PMID: 32098425 PMCID: PMC7077298 DOI: 10.3390/v12020245] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022] Open
Abstract
Honey bees (Apismellifera) are an agriculturally important pollinator species that live in easily managed social groups (i.e., colonies). Unfortunately, annual losses of honey bee colonies in many parts of the world have reached unsustainable levels. Multiple abiotic and biotic stressors, including viruses, are associated with individual honey bee and colony mortality. Honey bees have evolved several antiviral defense mechanisms including conserved immune pathways (e.g., Toll, Imd, JAK/STAT) and dsRNA-triggered responses including RNA interference and a non-sequence specific dsRNA-mediated response. In addition, transcriptome analyses of virus-infected honey bees implicate an antiviral role of stress response pathways, including the heat shock response. Herein, we demonstrate that the heat shock response is antiviral in honey bees. Specifically, heat-shocked honey bees (i.e., 42 °C for 4 h) had reduced levels of the model virus, Sindbis-GFP, compared with bees maintained at a constant temperature. Virus-infection and/or heat shock resulted in differential expression of six heat shock protein encoding genes and three immune genes, many of which are positively correlated. The heat shock protein encoding and immune gene transcriptional responses observed in virus-infected bees were not completely recapitulated by administration of double stranded RNA (dsRNA), a virus-associated molecular pattern, indicating that additional virus-host interactions are involved in triggering antiviral stress response pathways.
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Affiliation(s)
- Alexander J. McMenamin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Katie F. Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Michelle L. Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
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Pasquier C, Agnel S, Robichon A. Transcriptome-wide-scale-predicted dsRNAs potentially involved in RNA homoeostasis are remarkably excluded from genes with no/very low expression in all developmental stages. RNA Biol 2020; 17:554-570. [PMID: 31971862 DOI: 10.1080/15476286.2020.1717154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA interference (RNAi) refers to a conserved posttranscriptional mechanism for the degradation of RNA by short dsRNAs. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length that are transcribed from the full transcriptome and susceptible to being loaded onto Argonaute type 2 was performed through computational searches in the Drosophila model. We report the segments of RNAs that are complementary to mRNAs originating from introns, the exons of mRNAs and lncRNAs as a potential source of siRNAs. A full catalogue of the mRNAs that fulfill these criteria is presented, along with the quantification of multiple annealing. The catalogue was assessed for biological validation using three published lists: two for Ago2-associated RNAs and one for dsRNAs isolated from a crude extract. A broad spectrum of mRNAs were found to theoretically form intermolecular segmental dsRNAs, which should qualify them as Dicer/Ago2 substrates if they exist in vivo. These results suggest a genome-wide scale of mRNA homoeostasis via RNAi metabolism and could extend the known roles of canonical miRNAs and hairpin RNAs. The distribution of the genes for which transcripts are engaged in intermolecular segmental pairing is largely lacking in the gene collections defined as showing no expression in each individual developmental stage from early embryos to adulthood. This trend was also observed for the genes showing very low expression from the 8-12-hour embryonic to larval stage 2. This situation was also suggested by the 3 lists generated with minimal 20-, 25- and 30-base pairing lengths.
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Affiliation(s)
- Claude Pasquier
- Laboratoire d'informatique, signaux et système (I3S) CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Sandra Agnel
- Agrobiotech Institute (ISA)INRA, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Alain Robichon
- Agrobiotech Institute (ISA)INRA, CNRS, Université Côte d'Azur, Sophia Antipolis, France
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Sala L, Chandrasekhar S, Vidigal JA. AGO unchained: Canonical and non-canonical roles of Argonaute proteins in mammals. Front Biosci (Landmark Ed) 2020; 25:1-42. [PMID: 31585876 DOI: 10.2741/4793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Argonaute (AGO) proteins play key roles in animal physiology by binding to small RNAs and regulating the expression of their targets. In mammals, they do so through two distinct pathways: the miRNA pathway represses genes through a multiprotein complex that promotes both decay and translational repression; the siRNA pathway represses transcripts through direct Ago2-mediated cleavage. Here, we review our current knowledge of mechanistic details and physiological requirements of both these pathways and briefly discuss their implications to human disease.
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Affiliation(s)
- Laura Sala
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Srividya Chandrasekhar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA,
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La Marca JE, Diepstraten ST, Hodge AL, Wang H, Hart AH, Richardson HE, Somers WG. Strip and Cka negatively regulate JNK signalling during Drosophila spermatogenesis. Development 2019; 146:dev.174292. [PMID: 31164352 DOI: 10.1242/dev.174292] [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] [Received: 11/28/2018] [Accepted: 05/24/2019] [Indexed: 12/16/2022]
Abstract
One fundamental property of a stem cell niche is the exchange of molecular signals between its component cells. Niche models, such as the Drosophila melanogaster testis, have been instrumental in identifying and studying the conserved genetic factors that contribute to niche molecular signalling. Here, we identify jam packed (jam), an allele of Striatin interacting protein (Strip), which is a core member of the highly conserved Striatin-interacting phosphatase and kinase (STRIPAK) complex. In the developing Drosophila testis, Strip cell-autonomously regulates the differentiation and morphology of the somatic lineage, and non-cell-autonomously regulates the proliferation and differentiation of the germline lineage. Mechanistically, Strip acts in the somatic lineage with its STRIPAK partner, Connector of kinase to AP-1 (Cka), where they negatively regulate the Jun N-terminal kinase (JNK) signalling pathway. Our study reveals a novel role for Strip/Cka in JNK pathway regulation during spermatogenesis within the developing Drosophila testis.
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Affiliation(s)
- John E La Marca
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia 3086
| | - Sarah T Diepstraten
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia 3086
| | - Amy L Hodge
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia 3086
| | - Hongyan Wang
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857.,National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Adam H Hart
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia 3086
| | - Helena E Richardson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia 3086
| | - W Gregory Somers
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia 3086
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Abou Elela S, Ji X. Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1521. [PMID: 30548404 DOI: 10.1002/wrna.1521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022]
Abstract
The double-stranded RNA-binding protein (dsRBP) family controls RNA editing, stability, and function in all eukaryotes. The central feature of this family is the recognition of a generic RNA duplex using highly conserved double-stranded RNA-binding domain (dsRBD) that recognizes the characteristic distance between the minor grooves created by the RNA helix. Variations on this theme that confer species and functional specificities have been reported but most dsRBPs retain their capacity to bind generic dsRNA. The ribonuclease III (RNase III) family members fall into four classes, represented by bacterial RNase III, yeast Rnt1p, human Drosha, and human Dicer, respectively. Like all dsRBPs and most members of the RNase III family, Rnt1p has a dsRBD, but unlike most of its kin, it poorly binds to generic RNA helices. Instead, Rnt1p, the only known RNase III expressed in Saccharomyces cerevisiae that lacks the RNAi (RNA interference) machinery, recognizes a specific class of stem-loop structures. To recognize the specific substrates, the dsRBD of Rnt1p is specialized, featuring a αβββααα topology and a sequence-specific RNA-binding motif at the C-terminus. Since the discovery of Rnt1p in 1996, significant progress has been made in studies of its genetics, function, structure, and mechanism of action, explaining the reasons and mechanisms for the increased specificity of this enzyme and its impact on the mechanism of RNA degradation. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sherif Abou Elela
- Microbiology and Infectiology Department, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland
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14
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Gotesman M, Menanteau-Ledouble S, Saleh M, Bergmann SM, El-Matbouli M. A new age in AquaMedicine: unconventional approach in studying aquatic diseases. BMC Vet Res 2018; 14:178. [PMID: 29879957 PMCID: PMC5992843 DOI: 10.1186/s12917-018-1501-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/24/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Marine and aquaculture industries are important sectors of the food production and global trade. Unfortunately, the fish food industry is challenged with a plethora of infectious pathogens. The freshwater and marine fish communities are rapidly incorporating novel and most up to date techniques for detection, characterization and treatment strategies. Rapid detection of infectious diseases is important in preventing large disease outbreaks. MAIN TEXT One hundred forty-six articles including reviews papers were analyzed and their conclusions evaluated in the present paper. This allowed us to describe the most recent development research regarding the control of diseases in the aquatic environment as well as promising avenues that may result in beneficial developments. For the characterization of diseases, traditional sequencing and histological based methods have been augmented with transcriptional and proteomic studies. Recent studies have demonstrated that transcriptional based approaches using qPCR are often synergistic to expression based studies that rely on proteomic-based techniques to better understand pathogen-host interactions. Preventative therapies that rely on prophylactics such as vaccination with protein antigens or attenuated viruses are not always feasible and therefore, the development of therapies based on small nucleotide based medicine is on the horizon. Of those, RNAi or CRISPR/Cas- based therapies show great promise in combating various types of diseases caused by viral and parasitic agents that effect aquatic and fish medicine. CONCLUSIONS In our modern times, when the marine industry has become so vital for feed and economic stability, even the most extreme alternative treatment strategies such as the use of small molecules or even the use of disease to control invasive species populations should be considered.
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Affiliation(s)
- Michael Gotesman
- Department of Biology, New York City College of Technology of the City University of New York, Brooklyn, New York, USA
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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15
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Guan RB, Li HC, Miao XX. Prediction of effective RNA interference targets and pathway-related genes in lepidopteran insects by RNA sequencing analysis. INSECT SCIENCE 2018; 25:356-367. [PMID: 28058810 DOI: 10.1111/1744-7917.12437] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/29/2016] [Accepted: 12/15/2016] [Indexed: 06/06/2023]
Abstract
When using RNA interference (RNAi) to study gene functions in Lepidoptera insects, we discovered that some genes could not be suppressed; instead, their expression levels could be up-regulated by double-stranded RNA (dsRNA). To predict which genes could be easily silenced, we treated the Asian corn borer (Ostrinia furnacalis) with dsGFP (green fluorescent protein) and dsMLP (muscle lim protein). A transcriptome sequence analysis was conducted using the cDNAs 6 h after treatment with dsRNA. The results indicated that 160 genes were up-regulated and 44 genes were down-regulated by the two dsRNAs. Then, 50 co-up-regulated, 25 co-down-regulated and 43 unaffected genes were selected to determine their RNAi responses. All the 25 down-regulated genes were knocked down by their corresponding dsRNA. However, several of the up-regulated and unaffected genes were up-regulated when treated with their corresponding dsRNAs instead of being knocked down. The genes up-regulated by the dsGFP treatment may be involved in insect immune responses or the RNAi pathway. When the immune-related genes were excluded, only seven genes were induced by dsGFP, including ago-2 and dicer-2. These results not only provide a reference for efficient RNAi target predications, but also provide some potential RNAi pathway-related genes for further study.
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Affiliation(s)
- Ruo-Bing Guan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hai-Chao Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xue-Xia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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16
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Camargo C, Wu K, Fishilevich E, Narva KE, Siegfried BD. Knockdown of RNA interference pathway genes in western corn rootworm, Diabrotica virgifera virgifera, identifies no fitness costs associated with Argonaute 2 or Dicer-2. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 148:103-110. [PMID: 29891360 DOI: 10.1016/j.pestbp.2018.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/07/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
The use of transgenic crops that induce silencing of essential genes using double-stranded RNA (dsRNA) through RNA interference (RNAi) in western corn rootworm, Diabrotica virgifera virgifera, is likely to be an important component of new technologies for the control of this important corn pest. Previous studies have demonstrated that the dsRNA response in D. v. virgifera depends on the presence of RNAi pathway genes including Dicer-2 and Argonaute 2, and that downregulation of these genes limits the lethality of environmental dsRNA. A potential resistance mechanism to lethal dsRNA may involve loss of function of RNAi pathway genes. Howver, the potential for resistance to evolve may depend on whether these pathway genes have essential functions such that the loss of function of core proteins in the RNAi pathway will have fitness costs in D. v. virgifera. Fitness costs associated with potential resistance mechanisms have a central role in determining how resistance can evolve to RNAi technologies in western corn rootworm. We evaluated the effect of dsRNA and microRNA pathway gene knockdown on the development of D. v. virgifera larvae through short-term and long-term exposures to dsRNA for Dicer and Argonaute genes. Downregulation of Argonaute 2, Dicer-2, Dicer-1 did not significantly affect larval survivorship or development through short and long-term exposure to dsRNA. However, downregulation of Argonaute 1 reduced larval survivorship and delayed development. The implications of these results as they relate to D. v. virgifera resistance to lethal dsRNA are discussed.
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Affiliation(s)
- Carolina Camargo
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States
| | - Ke Wu
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States
| | - Elane Fishilevich
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Kenneth E Narva
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Blair D Siegfried
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States.
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17
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Down‐regulation of intracellular anti‐apoptotic proteins, particularly c‐FLIP by therapeutic agents; the novel view to overcome resistance to TRAIL. J Cell Physiol 2018; 233:6470-6485. [DOI: 10.1002/jcp.26585] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/08/2018] [Indexed: 12/24/2022]
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18
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Meng F, Yang M, Li Y, Li T, Liu X, Wang G, Wang Z, Jin X, Li W. Functional Analysis of RNA Interference-Related Soybean Pod Borer ( Lepidoptera) Genes Based on Transcriptome Sequences. Front Physiol 2018; 9:383. [PMID: 29773992 PMCID: PMC5943558 DOI: 10.3389/fphys.2018.00383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/28/2018] [Indexed: 11/30/2022] Open
Abstract
RNA interference (RNAi) is useful for controlling pests of agriculturally important crops. The soybean pod borer (SPB) is the most important soybean pest in Northeastern Asia. In an earlier study, we confirmed that the SPB could be controlled via transgenic plant-mediated RNAi. Here, the SPB transcriptome was sequenced to identify RNAi-related genes, and also to establish an RNAi-of-RNAi assay system for evaluating genes involved in the SPB systemic RNAi response. The core RNAi genes, as well as genes potentially involved in double-stranded RNA (dsRNA) uptake were identified based on SPB transcriptome sequences. A phylogenetic analysis and the characterization of these core components as well as dsRNA uptake related genes revealed that they contain conserved domains essential for the RNAi pathway. The results of the RNAi-of-RNAi assay involving Laccase 2 (a critical cuticle pigmentation gene) as a marker showed that genes encoding the sid-like (Sil1), scavenger receptor class C (Src), and scavenger receptor class B (Srb3 and Srb4) proteins of the endocytic pathway were required for SPB cellular uptake of dsRNA. The SPB response was inferred to contain three functional small RNA pathways (i.e., miRNA, siRNA, and piRNA pathways). Additionally, the SPB systemic RNA response may rely on systemic RNA interference deficient transmembrane channel-mediated and receptor-mediated endocytic pathways. The results presented herein may be useful for developing RNAi-mediated methods to control SPB infestations in soybean.
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Affiliation(s)
- Fanli Meng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Mingyu Yang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianyu Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xinxin Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Guoyue Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Zhanchun Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xianhao Jin
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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20
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Xie YF, Niu JZ, Jiang XZ, Yang WJ, Shen GM, Wei D, Smagghe G, Wang JJ. Influence of various stressors on the expression of core genes of the small interfering RNA pathway in the oriental fruit fly, Bactrocera dorsalis. INSECT SCIENCE 2017; 24:418-430. [PMID: 28547890 DOI: 10.1111/1744-7917.12311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/02/2015] [Indexed: 06/07/2023]
Abstract
RNA interference (RNAi)-based technology has emerged as a potential tool for controlling insect pests, however, previous studies found that the efficiency of RNAi in Bactrocera dorsalis was variable. In nature, insects often meet various challenges, such as pathogen infections, extreme temperatures, lack of nutrition and heavy metals. To better understand the association of the stressors with efficiency of RNAi, in the current study we tested the expression of three core genes, dicer2 (Bddcr2), r2d2 (Bdr2d2) and argonaute2 (Bdago2), of the small interfering RNA (siRNA) pathway of B. dorsalis upon various stressors. Our results showed that all three genes were upregulated by the infection of invertebrate iridescent virus 6, which suggested a function of the siRNA pathway against viral infection. The loading of FeCl3 could also increase the expression of Bddcr2. The treatments of Escherichia coli, extremely high (40°C) and low (0°C) temperatures, as well as starvation, could negatively influence the expression of Bddcr2 and/or Bdago2. In total, our results showed that various stressors could influence the expression of core components of B. dorsalis siRNA pathway. This highlights further speculation on the RNAi efficiency upon these stressors. Considering the complexity and variation of RNAi efficiency in different conditions, these results provide initial aspects in possible environmental stressors to influence the activity of the siRNA pathway, but the real impact of RNAi efficiency posed by these stressors requires further studies.
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Affiliation(s)
- Yi-Fei Xie
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Hunan Academy of Forestry, Changsha, China
| | - Jin-Zhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Xuan-Zhao Jiang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Wen-Jia Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Guang-Mao Shen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Dong Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Guy Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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21
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Rojas-Benítez D, Eggers C, Glavic A. Modulation of the Proteostasis Machinery to Overcome Stress Caused by Diminished Levels of t6A-Modified tRNAs in Drosophila. Biomolecules 2017; 7:biom7010025. [PMID: 28272317 PMCID: PMC5372737 DOI: 10.3390/biom7010025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/28/2017] [Indexed: 12/17/2022] Open
Abstract
Transfer RNAs (tRNAs) harbor a subset of post-transcriptional modifications required for structural stability or decoding function. N6-threonylcarbamoyladenosine (t6A) is a universally conserved modification found at position 37 in tRNA that pair A-starting codons (ANN) and is required for proper translation initiation and to prevent frame shift during elongation. In its absence, the synthesis of aberrant proteins is likely, evidenced by the formation of protein aggregates. In this work, our aim was to study the relationship between t6A-modified tRNAs and protein synthesis homeostasis machinery using Drosophila melanogaster. We used the Gal4/UAS system to knockdown genes required for t6A synthesis in a tissue and time specific manner and in vivo reporters of unfolded protein response (UPR) activation. Our results suggest that t6A-modified tRNAs, synthetized by the threonyl-carbamoyl transferase complex (TCTC), are required for organismal growth and imaginal cell survival, and is most likely to support proper protein synthesis.
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Affiliation(s)
- Diego Rojas-Benítez
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800024, Chile..
| | - Cristián Eggers
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800024, Chile..
| | - Alvaro Glavic
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800024, Chile..
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22
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Ahlers LRH, Bastos RG, Hiroyasu A, Goodman AG. Invertebrate Iridescent Virus 6, a DNA Virus, Stimulates a Mammalian Innate Immune Response through RIG-I-Like Receptors. PLoS One 2016; 11:e0166088. [PMID: 27824940 PMCID: PMC5100955 DOI: 10.1371/journal.pone.0166088] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/22/2016] [Indexed: 12/21/2022] Open
Abstract
Insects are not only major vectors of mammalian viruses, but are also host to insect-restricted viruses that can potentially be transmitted to mammals. While mammalian innate immune responses to arboviruses are well studied, less is known about how mammalian cells respond to viruses that are restricted to infect only invertebrates. Here we demonstrate that IIV-6, a DNA virus of the family Iridoviridae, is able to induce a type I interferon-dependent antiviral immune response in mammalian cells. Although IIV-6 is a DNA virus, we demonstrate that the immune response activated during IIV-6 infection is mediated by the RIG-I-like receptor (RLR) pathway, and not the canonical DNA sensing pathway via cGAS/STING. We further show that RNA polymerase III is required for maximal IFN-β secretion, suggesting that viral DNA is transcribed by this enzyme into an RNA species capable of activating the RLR pathway. Finally, we demonstrate that the RLR-driven mammalian innate immune response to IIV-6 is functionally capable of protecting cells from subsequent infection with the arboviruses Vesicular Stomatitis virus and Kunjin virus. These results represent a novel example of an invertebrate DNA virus activating a canonically RNA sensing pathway in the mammalian innate immune response, which reduces viral load of ensuing arboviral infection.
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Affiliation(s)
- Laura R. H. Ahlers
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- NIH Protein Biotechnology Graduate Training Program, Washington State University, Pullman, Washington, United States of America
| | - Reginaldo G. Bastos
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Aoi Hiroyasu
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Alan G. Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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23
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Azlan A, Dzaki N, Azzam G. Argonaute: The executor of small RNA function. J Genet Genomics 2016; 43:481-94. [PMID: 27569398 DOI: 10.1016/j.jgg.2016.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/08/2016] [Accepted: 06/17/2016] [Indexed: 01/06/2023]
Abstract
The discovery of small non-coding RNAs - microRNA (miRNA), short interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) - represents one of the most exciting frontiers in biology specifically on the mechanism of gene regulation. In order to execute their functions, these small RNAs require physical interactions with their protein partners, the Argonaute (AGO) family proteins. Over the years, numerous studies have made tremendous progress on understanding the roles of AGO in gene silencing in various organisms. In this review, we summarize recent progress of AGO-mediated gene silencing and other cellular processes in which AGO proteins have been implicated with a particular focus on progress made in flies, humans and other model organisms as compliment.
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Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia; Advance Medical and Dental Institute, Universiti Sains Malaysia, Penang 11800, Malaysia.
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24
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Gotesman M, Soliman H, Besch R, El-Matbouli M. Inhibition of spring viraemia of carp virus replication in an Epithelioma papulosum cyprini cell line by RNAi. JOURNAL OF FISH DISEASES 2015; 38:197-207. [PMID: 24460815 PMCID: PMC4303980 DOI: 10.1111/jfd.12227] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 05/08/2023]
Abstract
Spring viraemia of carp virus (SVCV) is an aetiological agent of a serious disease affecting carp farms in Europe and is a member of the Rhabdoviridae family of viruses. The genome of SVCV codes for five proteins: nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). RNA-mediated interference (RNAi) by small interfering RNAs (siRNAs) is a powerful tool to inhibit gene transcription and is used to study genes important for viral replication. In previous studies regarding another member of Rhabdoviridae, siRNA inhibition of the rabies virus nucleoprotein gene provided in vitro and in vivo protection against rabies. In this study, synthetic siRNA molecules were designed to target SVCV-N and SVCV-P transcripts to inhibit SVCV replication and were tested in an epithelioma papulosum cyprini (EPC) cell line. Inhibition of gene transcription was measured by real-time quantitative reverse-transcription PCR (RT-qPCR). The efficacy of using siRNA for inhibition of viral replication was analysed by RT-qPCR measurement of a reporter gene (glycoprotein) expression and by virus endpoint titration. Inhibition of nucleoprotein and phosphoprotein gene expression by siRNA reduced SVCV replication. However, use of tandem siRNAs that target phosphoprotein and nucleoprotein worked best at reducing SVCV replication.
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Affiliation(s)
- M Gotesman
- Clinical Division of Fish Medicine, University of Veterinary MedicineVienna, Austria
| | - H Soliman
- Clinical Division of Fish Medicine, University of Veterinary MedicineVienna, Austria
- Fish Medicine and Management, Faculty of Veterinary Medicine, University of AssiutAssiut, Egypt
| | - R Besch
- Clinic and Policlinic for Dermatology and Allergology, Department of Dermatology, Ludwig-Maximilian UniversityMunich, Germany
| | - M El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary MedicineVienna, Austria
- CorrespondenceM El-Matbouli, Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria (e-mail: )
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Morel V, Lepicard S, Rey AN, Parmentier ML, Schaeffer L. Drosophila Nesprin-1 controls glutamate receptor density at neuromuscular junctions. Cell Mol Life Sci 2014; 71:3363-79. [PMID: 24492984 PMCID: PMC11113563 DOI: 10.1007/s00018-014-1566-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/20/2013] [Accepted: 01/16/2014] [Indexed: 01/06/2023]
Abstract
Nesprin-1 is a core component of a protein complex connecting nuclei to cytoskeleton termed LINC (linker of nucleoskeleton and cytoskeleton). Nesprin-1 is anchored to the nuclear envelope by its C-terminal KASH domain, the disruption of which has been associated with neuronal and neuromuscular pathologies, including autosomal recessive cerebellar ataxia and Emery-Dreifuss muscular dystrophy. Here, we describe a new and unexpected role of Drosophila Nesprin-1, Msp-300, in neuromuscular junction. We show that larvae carrying a deletion of Msp-300 KASH domain (Msp-300 (∆KASH) ) present a locomotion defect suggestive of a myasthenia, and demonstrate the importance of muscle Msp-300 for this phenotype, using tissue-specific RNAi knock-down. We show that Msp-300 (∆KASH) mutants display abnormal neurotransmission at the larval neuromuscular junction, as well as an imbalance in postsynaptic glutamate receptor composition with a decreased percentage of GluRIIA-containing receptors. We could rescue Msp-300 (∆KASH) locomotion phenotypes by GluRIIA overexpression, suggesting that the locomotion impairment associated with the KASH domain deletion is due to a reduction in junctional GluRIIA. In summary, we found that Msp-300 controls GluRIIA density at the neuromuscular junction. Our results suggest that Drosophila is a valuable model for further deciphering how Nesprin-1 and LINC disruption may lead to neuronal and neuromuscular pathologies.
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Affiliation(s)
- Véronique Morel
- Equipe Différenciation Neuromusculaire, CNRS, UMR5239, Ecole Normale Supérieure-Lyon, 46 allée d'Italie, 69364, Lyon Cedex 07, France,
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Gantier MP. Processing of Double-Stranded RNA in Mammalian Cells: A Direct Antiviral Role? J Interferon Cytokine Res 2014; 34:469-77. [DOI: 10.1089/jir.2014.0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Michael P. Gantier
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
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Lu DH, Wu M, Pu J, Feng A, Zhang Q, Han ZJ. A functional study of two dsRNA binding protein genes in Laodelphax striatellus. PEST MANAGEMENT SCIENCE 2013; 69:1034-1039. [PMID: 23828787 DOI: 10.1002/ps.3553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/05/2013] [Accepted: 04/05/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND One of the key limiting factors for using RNA interference technology to develop new pest control practices is the toxicological effectiveness. In order to explore potential methods to improve the efficiency of RNAi in insects, we cloned two dsRNA binding proteins from Laodelphax striatellus and investigated their functions. RESULTS In this study, the genes homologous to the dsRNA binding proteins TRBP and STAU in L. striatellus were first cloned and designated as LsTRBP and LsSTAU. Using the chitinase gene Chi, which has been confirmed to have lethal effects when knocked down by RNAi, as a reporter, the functions of these two dsRNA binding proteins were then investigated by using dsRNA feeding. The results showed that feeding with dsChi alone caused significant lethal effects, with a mortality four-fold higher than that of the control, whereas feeding with dsTRBP or dsSTAU alone did not yield any significant lethal effects. When dsChi was fed in the mixture 1:1 with dsSTAU, it also resulted in high mortality, which was a little lower than feeding with dsChi alone, but not statistically significant. However, when fed in the 1:1 mixture with dsTRBP, the lethal effect of dsChi was completely eliminated. Further analysis of gene expression found that single dsRNA depressed only its own target gene. When treated in 1:1 mixture, dsSTAU or dsChi did not change significantly the depression of the other dsRNA, but dsTRAB counteracted almost all the effect of dsChi. CONCLUSION These results indicate that the loss of LsTRBP can significantly inhibit dsChi-mediated genetic interference. These findings not only suggest that the LsTRBP gene in L. striatellus plays an important role in regulating RNAi but also imply that the metabolic regulation of dsRNAs with respect to genetic interference in L. striatellus is similar to that in higher animal species.
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Affiliation(s)
- Ding-Hao Lu
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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Zhu L, Masaki Y, Tatsuke T, Li Z, Mon H, Xu J, Lee JM, Kusakabe T. A MC motif in silkworm Argonaute 1 is indispensible for translation repression. INSECT MOLECULAR BIOLOGY 2013; 22:320-330. [PMID: 23521747 DOI: 10.1111/imb.12023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Small RNA-mediated gene silencing is a fundamental gene regulatory mechanism, which is conserved in many organisms. Argonaute (Ago) family proteins in the RNA-induced silencing complex (RISC) play crucial roles in RNA interference (RNAi) pathways. In the silkworm Bombyx mori, four Ago proteins have been identified, named as Ago1, Ago2, Ago3 and Siwi. Ago2 participates in double-stranded RNA (dsRNA)-induced RNAi, whereas Ago3 and Siwi are involved in the Piwi-interacting RNA (piRNA) pathway. However, there is no experimental evidence concerning silkworm Ago1 (BmAgo1) in the RNAi mechanism. In the present study, we analysed the function of BmAgo1 in the microRNA (miRNA)-mediated RNAi pathway using tethering and miRNA sensor reporter assays. These results clearly demonstrate that BmAgo1 plays an indispensable role in translation repression in silkworm. Moreover, coimmunoprecipitation data indicated that BmAgo1 interacts with BmDcp2, an orthologue of mRNA-decapping enzyme 2 (Dcp2) protein in the Drosophila processing-bodies (P-bodies). Substitutions of two conserved phenylalanines (F522 and F557) by valines in the MC motif strongly impaired the function of BmAgo1 in translation repression and its localization in P-bodies, suggesting that these two amino acid residues in the MC motif of BmAgo1 are prerequisites for mRNA translation repression in B. mori.
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Affiliation(s)
- L Zhu
- Laboratory of Silkworm Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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Sabin LR, Zheng Q, Thekkat P, Yang J, Hannon GJ, Gregory BD, Tudor M, Cherry S. Dicer-2 processes diverse viral RNA species. PLoS One 2013; 8:e55458. [PMID: 23424633 PMCID: PMC3570552 DOI: 10.1371/journal.pone.0055458] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/28/2012] [Indexed: 12/24/2022] Open
Abstract
RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double-stranded (ds)RNA precursors by Dicer and guide the RNA-induced silencing complex (RISC) to targets. Although principles governing small RNA sorting into RISC have been uncovered, the spectrum of RNA species that can be targeted by Dicer proteins, particularly the viral RNAs present during an infection, are poorly understood. Dicer-2 potently restricts viral infection in insects by generating virus-derived siRNAs from viral RNA. To better characterize the substrates of Dicer-2, we examined the virus-derived siRNAs produced during the Drosophila antiviral RNAi response to four different viruses using high-throughput sequencing. We found that each virus was uniquely targeted by the RNAi pathway; dicing substrates included dsRNA replication intermediates and intramolecular RNA stem loops. For instance, a putative intergenic RNA hairpin encoded by Rift Valley Fever virus generates abundant small RNAs in both Drosophila and mosquito cells, while repetitive sequences within the genomic termini of Vaccinia virus, which give rise to abundant small RNAs in Drosophila, were found to be transcribed in both insect and mammalian cells. Moreover, we provide evidence that the RNA species targeted by Dicer-2 can be modulated by the presence of a viral suppressor of RNAi. This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi.
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MESH Headings
- Animals
- Drosophila Proteins/metabolism
- Drosophila melanogaster/enzymology
- Drosophila melanogaster/virology
- Genome, Viral/genetics
- Genomics
- Inverted Repeat Sequences
- RNA Helicases/metabolism
- RNA Interference
- RNA Processing, Post-Transcriptional
- RNA Viruses/genetics
- RNA, Double-Stranded/biosynthesis
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/biosynthesis
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribonuclease III/metabolism
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Affiliation(s)
- Leah R. Sabin
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Qi Zheng
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pramod Thekkat
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jamie Yang
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Brian D. Gregory
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (MT); (BDG); (SC)
| | - Matthew Tudor
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (MT); (BDG); (SC)
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (MT); (BDG); (SC)
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Wynant N, Verlinden H, Breugelmans B, Simonet G, Vanden Broeck J. Tissue-dependence and sensitivity of the systemic RNA interference response in the desert locust, Schistocerca gregaria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:911-917. [PMID: 23022143 DOI: 10.1016/j.ibmb.2012.09.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/10/2012] [Accepted: 09/13/2012] [Indexed: 05/28/2023]
Abstract
We report on a comprehensive study of the systemic RNAi-response in the desert locust, Schistocerca gregaria. Upon intra-abdominal injection of dsRNA for two housekeeping genes (alpha-tubulin 1a and gapdh) in the range of pg amounts of dsRNA per mg tissue, a potent reduction of their corresponding mRNA was obtained. Moreover, the observed transcript knockdown significantly increased in at least a 10 days period and eventually resulted in high mortality upon silencing of the alpha-tubulin 1a gene. A more moderate RNAi-response was however observed in the reproductive systems. Analysis of the tissue-dependent transcript level profile of several putative RNAi-genes indicated reduced levels of two genes, namely sg-dicer-2 and sg-argonaute-2, in the reproductive systems. By silencing these components, we confirmed their importance in the RNAi-process and suggest that their expression levels are determinant for tissue-dependent differences in the potency of RNAi in the desert locust.
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Affiliation(s)
- Niels Wynant
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium.
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von Brandenstein M, Richter C, Fries JWU. MicroRNAs: Small but amazing, and their association with endothelin. Life Sci 2012; 91:475-89. [PMID: 22771694 DOI: 10.1016/j.lfs.2012.06.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the expressional regulation of genes by inhibiting gene translation. MicroRNAs are recruited and incorporated into the miRISC, ribonucleoprotein complex, targeting specific mRNAs through mechanisms specific for a miRNA sequence. Here we review the biogenesis, regulation, and monitoring of miRNAs, as well as the current evidence for potential roles of miRNAs in human diseases associated with activation of the endothelin system. These diseases include cancer, kidney disease, cardiovascular diseases, inflammatory diseases, infectious diseases, and blood diseases, that may all be aggravated by aberrant miRNA expression. In this review we will also discuss regulatory mechanisms determining production of miRNA as well as measuring or targeting miRNAs as potential novel approaches for diagnosis and treatment. Targeting miRNAs possibly will allow one to detect diseases or to interfere with the progression of diseases associated with activation of the endothelin system.
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Azzam G, Smibert P, Lai EC, Liu JL. Drosophila Argonaute 1 and its miRNA biogenesis partners are required for oocyte formation and germline cell division. Dev Biol 2012; 365:384-94. [PMID: 22445511 DOI: 10.1016/j.ydbio.2012.03.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 03/05/2012] [Accepted: 03/07/2012] [Indexed: 11/16/2022]
Abstract
Argonaute 1 (Ago1) is a member of the Argonaute/PIWI protein family involved in small RNA-mediated gene regulation. In Drosophila, Ago1 plays a specific role in microRNA (miRNA) biogenesis and function. Previous studies have demonstrated that Ago1 regulates the fate of germline stem cells. However, the function of Ago1 in other aspects of oogenesis is still elusive. Here we report the function of Ago1 in developing egg chambers. We find that Ago1 protein is enriched in the oocytes and is also highly expressed in the cytoplasm of follicle cells. Clonal analysis of multiple ago1 mutant alleles shows that many mutant egg chambers contain only 8 nurse cells without an oocyte which is phenocopied in dicer-1, pasha and drosha mutants. Our results suggest that Ago1 and its miRNA biogenesis partners play a role in oocyte determination and germline cell division in Drosophila.
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Affiliation(s)
- Ghows Azzam
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, South Parks Road, University of Oxford, Oxford, UK
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33
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Molecular characterization of Drosophila cells persistently infected with Flock House virus. Virology 2011; 419:43-53. [PMID: 21872290 DOI: 10.1016/j.virol.2011.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 06/06/2011] [Accepted: 08/04/2011] [Indexed: 11/24/2022]
Abstract
Little is known about the molecular determinants causing and sustaining viral persistent infections at the cellular level. We found that Drosophila cells persistently infected (PI) with Flock House virus (FHV) invariably harbor defective viral RNAs, which are replicated by the FHV RNA-dependent RNA polymerase. Some defective RNAs encoded a functional B2 protein, the FHV suppressor of RNA interference, which might contribute to maintenance of virus persistence. Viral small interfering RNAs (vsiRNAs) of both polarities were detected in PI cells and primarily mapped to regions of the viral genome that were preserved in the isolated defective RNAs. This indicated that defective RNAs could represent major sources of vsiRNAs. Immunofluorescence analysis revealed that mitochondria and viral proteins are differentially distributed in PI cells and lytically infected cells, which may partly explain the reduction in infectious viral progeny. Our results provide a basis for further investigations of the molecular mechanisms underlying persistent infections.
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34
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White KE, Humphrey DM, Hirth F. The dopaminergic system in the aging brain of Drosophila. Front Neurosci 2010; 4:205. [PMID: 21165178 PMCID: PMC3002484 DOI: 10.3389/fnins.2010.00205] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 10/30/2010] [Indexed: 11/29/2022] Open
Abstract
Drosophila models of Parkinson's disease are characterized by two principal phenotypes: the specific loss of dopaminergic (DA) neurons in the aging brain and defects in motor behavior. However, an age-related analysis of these baseline parameters in wildtype Drosophila is lacking. Here we analyzed the DA system and motor behavior in aging Drosophila. DA neurons in the adult brain can be grouped into bilateral symmetric clusters, each comprising a stereotypical number of cells. Analysis of TH > mCD8::GFP and cell type-specific MARCM clones revealed that DA neurons show cluster-specific, stereotypical projection patterns with terminal arborization in target regions that represent distinct functional areas of the adult brain. Target areas include the mushroom bodies, involved in memory formation and motivation, and the central complex, involved in the control of motor behavior, indicating that similar to the mammalian brain, DA neurons in the fly brain are involved in the regulation of specific behaviors. Behavioral analysis revealed that Drosophila show an age-related decline in startle-induced locomotion and negative geotaxis. Motion tracking however, revealed that walking activity, and exploration behavior, but not centrophobism increase at late stages of life. Analysis of TH > Dcr2, mCD8::GFP revealed a specific effect of Dcr2 expression on walking activity but not on exploratory or centrophobic behavior, indicating that the siRNA pathway may modulate distinct DA behaviors in Drosophila. Moreover, DA neurons were maintained between early- and late life, as quantified by TH > mCD8::GFP and anti-TH labeling, indicating that adult onset, age-related degeneration of DA neurons does not occur in the aging brain of Drosophila. Taken together, our data establish baseline parameters in Drosophila for the study of Parkinson's disease as well as other disorders affecting DA neurons and movement control.
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Affiliation(s)
- Katherine E White
- Department of Neuroscience, Institute of Psychiatry, Medical Research Council Centre for Neurodegeneration Research, King's College London London, UK
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35
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Abstract
The goal of personalized medicine is to treat each patient with the best drug: optimal therapeutic benefit with minimal side effects. The genomic revolution is rapidly identifying the genetic contribution to the diseased state as well as its contribution to drug efficacy and toxicity. The ability to perform genome-wide studies has led to an overwhelming number of candidate genes and/or their associated variants; however, understanding which are of therapeutic importance is becoming the greatest unmet need in the personalized medicine field. A related issue is the need to improve our methods of identifying and characterizing therapeutic drugs in the context of the complex genomic landscape of the intact body. Drosophila have proven to be a powerful tool for understanding the basic biological mechanisms of human development. This article will review Drosophila as a whole animal tool for gene and drug discovery. We will examine how Drosophila can be used to both sort through the myriad of hits coming from human genome-wide scans and to dramatically improve the early steps in pharmaceutical drug development.
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Affiliation(s)
- Yumi Kasai
- Department of Genetics & Genomic Sciences, Mount Sinai School of Medicine, One Gustave L Levy Place, NY 10029-6574, USA
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36
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Khoo CCH, Piper J, Sanchez-Vargas I, Olson KE, Franz AWE. The RNA interference pathway affects midgut infection- and escape barriers for Sindbis virus in Aedes aegypti. BMC Microbiol 2010; 10:130. [PMID: 20426860 PMCID: PMC2877022 DOI: 10.1186/1471-2180-10-130] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/28/2010] [Indexed: 11/23/2022] Open
Abstract
Background The RNA interference (RNAi) pathway acts as an innate antiviral immune response in Aedes aegypti, modulating arbovirus infection of mosquitoes. Sindbis virus (SINV; family: Togaviridae, genus: Alphavirus) is an arbovirus that infects Ae. aegypti in the laboratory. SINV strain TR339 encounters a midgut escape barrier (MEB) during infection of Ae. aegypti. The nature of this barrier is not well understood. To investigate the role of the midgut as the central organ determining vector competence for arboviruses, we generated transgenic mosquitoes in which the RNAi pathway was impaired in midgut tissue of bloodfed females. We used these mosquitoes to reveal effects of RNAi impairment in the midgut on SINV replication, midgut infection and dissemination efficiencies, and mosquito longevity. Results As a novel tool for studying arbovirus-mosquito interactions, we engineered a transgenic mosquito line with an impaired RNAi pathway in the midgut of bloodfed females by silencing expression of the Aa-dcr2 gene. In midgut tissue of the transgenic Carb/dcr16 line, Aa-dcr2 expression was reduced ~50% between 1-7 days post-bloodmeal (pbm) when compared to the recipient mosquito strain. After infection with SINV-TR339EGFP, Aa-dcr2 expression levels were enhanced in both mosquito strains. In the RNAi pathway impaired mosquito strain SINV titers and midgut infection rates were significantly higher at 7 days pbm. There was also a strong tendency for increased virus dissemination rates among the transgenic mosquitoes. Between 7-14 days pbm, SINV was diminished in midgut tissue of the transgenic mosquitoes. Transgenic impairment of the RNAi pathway and/or SINV infection did not affect longevity of the mosquitoes. Conclusions We showed that RNAi impaired transgenic mosquitoes are a useful tool for studying arbovirus-mosquito interactions at the molecular level. Following ingestion by Ae. aegypti, the recombinant SINV-TR339EGFP was confronted with both MEB and a midgut infection barrier (MIB). Impairment of the RNAi pathway in the midgut strongly reduced both midgut barriers for the virus. This confirms that the endogenous RNAi pathway of Ae. aegypti modulates vector competence for SINV in the midgut. The RNAi pathway acts as a gatekeeper to the incoming virus by affecting infection rate of the midgut, intensity of infection, and dissemination from the midgut to secondary tissues.
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Affiliation(s)
- Cynthia C H Khoo
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Evans JD, Spivak M. Socialized medicine: individual and communal disease barriers in honey bees. J Invertebr Pathol 2009; 103 Suppl 1:S62-72. [PMID: 19909975 DOI: 10.1016/j.jip.2009.06.019] [Citation(s) in RCA: 220] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 06/30/2009] [Indexed: 11/16/2022]
Abstract
Honey bees are attacked by numerous parasites and pathogens toward which they present a variety of individual and group-level defenses. In this review, we briefly introduce the many pathogens and parasites afflicting honey bees, highlighting the biology of specific taxonomic groups mainly as they relate to virulence and possible defenses. Second, we describe physiological, immunological, and behavioral responses of individual bees toward pathogens and parasites. Third, bees also show behavioral mechanisms for reducing the disease risk of their nestmates. Accordingly, we discuss the dynamics of hygienic behavior and other group-level behaviors that can limit disease. Finally, we conclude with several avenues of research that seem especially promising for understanding host-parasite relationships in bees and for developing breeding or management strategies for enhancing honey bee health. We discuss how human efforts to maintain healthy colonies intersect with similar efforts by the bees, and how bee management and breeding protocols can affect disease traits in the short and long term.
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Affiliation(s)
- Jay D Evans
- USDA-ARS Bee Research Lab, BARC-East Bldg. 476, Beltsville, MD 20705, USA.
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38
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Sabin LR, Zhou R, Gruber JJ, Lukinova N, Bambina S, Berman A, Lau CK, Thompson CB, Cherry S. Ars2 regulates both miRNA- and siRNA- dependent silencing and suppresses RNA virus infection in Drosophila. Cell 2009; 138:340-51. [PMID: 19632183 DOI: 10.1016/j.cell.2009.04.045] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 03/02/2009] [Accepted: 04/20/2009] [Indexed: 11/25/2022]
Abstract
Intrinsic immune responses autonomously inhibit viral replication and spread. One pathway that restricts viral infection in plants and insects is RNA interference (RNAi), which targets and degrades viral RNA to limit infection. To identify additional genes involved in intrinsic antiviral immunity, we screened Drosophila cells for modulators of viral infection using an RNAi library. We identified Ars2 as a key component of Drosophila antiviral immunity. Loss of Ars2 in cells, or in flies, increases susceptibility to RNA viruses. Consistent with its antiviral properties, we found that Ars2 physically interacts with Dcr-2, modulates its activity in vitro, and is required for siRNA-mediated silencing. Furthermore, we show that Ars2 plays an essential role in miRNA-mediated silencing, interacting with the Microprocessor and stabilizing pri-miRNAs. The identification of Ars2 as a player in these small RNA pathways provides new insight into the biogenesis of small RNAs that may be extended to other systems.
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Affiliation(s)
- Leah R Sabin
- Department of Microbiology, Penn Genome Frontiers Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Wu T, Zhao Y, Hao Z, Zhao H, Wang W. Involvement of PU.1 in mouse adar-1 gene transcription induced by high-dose esiRNA. Int J Biol Macromol 2009; 45:157-62. [PMID: 19422845 DOI: 10.1016/j.ijbiomac.2009.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 04/24/2009] [Accepted: 04/24/2009] [Indexed: 11/16/2022]
Abstract
Adar-1 gene plays an important role in the negative regulation of RNA interference. We previously showed that increased adar-1 mRNA level was associated with the rebound of gene expression after RNAi suppression. In this study, we identified a PU.1 binding site upstream from transcription start point of adar-1 gene and is essential for the promoter activity. Knockdown and over-expression of the PU.1 gene resulted in decreased and increased activity of adar-1 promoter, respectively. Our results suggest that transcription factor PU.1, could bind to the adar-1 promoter and play a key role in activating transcription of gene induced by high-dose esiRNAs.
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Affiliation(s)
- Tongde Wu
- Department of Biochemistry, School of Life Sciences, Fudan University, No. 220 Handan Road, Liren Building 106, Shanghai 200433, PR China
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40
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PENG JJ. Progress of studies on Dicer structure and function. YI CHUAN = HEREDITAS 2009; 30:1550-6. [DOI: 10.3724/sp.j.1005.2008.01550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Mortimer NT, Moberg KH. Regulation of Drosophila embryonic tracheogenesis by dVHL and hypoxia. Dev Biol 2009; 329:294-305. [PMID: 19285057 DOI: 10.1016/j.ydbio.2009.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 01/27/2009] [Accepted: 03/03/2009] [Indexed: 01/01/2023]
Abstract
The tracheal system of Drosophila melanogaster is an interconnected network of gas-filled epithelial tubes that develops during embryogenesis and functions as the main gas-exchange organ in the larva. Larval tracheal cells respond to hypoxia by activating a program of branching and growth driven by HIF-1alpha/sima-dependent expression of the breathless (btl) FGF receptor. By contrast, the ability of the developing embryonic tracheal system to respond to hypoxia and integrate hard-wired branching programs with sima-driven tracheal remodeling is not well understood. Here we show that embryonic tracheal cells utilize the conserved ubiquitin ligase dVHL to control the HIF-1 alpha/sima hypoxia response pathway, and identify two distinct phases of tracheal development with differing hypoxia sensitivities and outcomes: a relatively hypoxia-resistant 'early' phase during which sima activity conflicts with normal branching and stunts migration, and a relatively hypoxia-sensitive 'late' phase during which the tracheal system uses the dVHL/sima/btl pathway to drive increased branching and growth. Mutations in the archipelago (ago) gene, which antagonizes btl transcription, re-sensitize early embryos to hypoxia, indicating that their relative resistance can be reversed by elevating activity of the btl promoter. These findings reveal a second type of tracheal hypoxic response in which Sima activation conflicts with developmental tracheogenesis, and identify the dVHL and ago ubiquitin ligases as key determinants of hypoxia sensitivity in tracheal cells. The identification of an early stage of tracheal development that is vulnerable to hypoxia is an important addition to models of the invertebrate hypoxic response.
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Affiliation(s)
- Nathan T Mortimer
- Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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Chen Y, Huang L. Tumor-targeted delivery of siRNA by non-viral vector: safe and effective cancer therapy. Expert Opin Drug Deliv 2009; 5:1301-11. [PMID: 19040393 DOI: 10.1517/17425240802568505] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RNA interference technology has been developed as a potential therapeutic agent for many indications, including cancer. Silencing a specific oncogene in tumor cells brings about cell death both in vitro and in vivo. However, there is a great need for powerful delivery strategies to enhance the therapeutic effect of small interfering RNA (siRNA). This review summarizes different signaling pathways inhibited by siRNA and the advantages of targeted siRNA as a delivery system.
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Affiliation(s)
- Yunching Chen
- University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Division of Molecular Pharmaceutics, Campus Box 7360 Kerr Hall, Chapel Hill, NC 27599, USA
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