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Echinococcus granulosus Protoscoleces-Derived Exosome-like Vesicles and Egr-miR-277a-3p Promote Dendritic Cell Maturation and Differentiation. Cells 2022; 11:cells11203220. [PMID: 36291088 PMCID: PMC9600664 DOI: 10.3390/cells11203220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022] Open
Abstract
Cystic echinococcosis, a major parasitic disease caused by Echinococcus granulosus, seriously threatens human health. The excretory–secretory (ES) products of E. granulosus can induce immune tolerance in dendritic cells (DCs) to downregulate the host’s immune response; however, the effect of exosomes in the ES products on the DCs has remained unclear. This study showed that E. granulosus protoscoleces-derived exosome-like vesicles (PSC-ELVs) could be internalized by bone marrow-derived dendritic cells (BMDCs), allowing for the delivery of the parasite microRNAs to the BMDCs. Moreover, PSC-ELVs induced BMDCs to produce the proinflammatory cytokinesinterleukin (IL)-6, IL-12, IL-β, tumor necrosis factor-alpha (TNF-α), and interferon-gamma (IFN-γ). PSC-ELVs also upregulated the BMDCs surface marker major histocompatibility complex class II (MHC II), as well as costimulatory molecules CD40, CD80, and CD86. PSC-ELV-derived egr-miR-277a-3p upregulated the IL-6, IL-12, and TNF-α mRNA levels in BMDCs. Moreover, egr-miR-277a-3p directly targeted Nfkb1 (encoding nuclear factor kappa B 1) to significantly suppress the mRNA and protein levels of NF-κB1 in BMDCs, while the expression of NF-κB p65 significantly increased, suggesting that egr-miR-277a-3p induces the production of proinflammatory cytokines by the modification of the NF-kB p65/p50 ratio in BMDCs. These results demonstrated that PSC-ELVs and egr-miR-277a-3p might enhance DCs maturation and differentiation in a cross-species manner, which in turn may modulate the host immune responses and offer a new approach to echinococcosis prevention and treatment.
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2
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Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nat Rev Mol Cell Biol 2022; 23:185-203. [PMID: 34707241 PMCID: PMC9208737 DOI: 10.1038/s41580-021-00425-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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3
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Torri A, Mongelli V, Mondotte JA, Saleh MC. Viral Infection and Stress Affect Protein Levels of Dicer 2 and Argonaute 2 in Drosophila melanogaster. Front Immunol 2020; 11:362. [PMID: 32194567 PMCID: PMC7065269 DOI: 10.3389/fimmu.2020.00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/14/2020] [Indexed: 12/21/2022] Open
Abstract
The small interfering RNA (siRNA) pathway of Drosophila melanogaster, mainly characterized by the activity of the enzymes Dicer 2 (Dcr-2) and Argonaute 2 (Ago-2), has been described as the major antiviral immune response. Several lines of evidence demonstrated its pivotal role in conferring resistance against viral infections at cellular and systemic level. However, only few studies have addressed the regulation and induction of this system upon infection and knowledge on stability and turnover of the siRNA pathway core components transcripts and proteins remains scarce. In the current work, we explore whether the siRNA pathway is regulated following viral infection in D. melanogaster. After infecting different fly strains with two different viruses and modes of infection, we observed changes in Dcr-2 and Ago-2 protein concentrations that were not related with changes in gene expression. This response was observed either upon viral infection or upon stress-related experimental procedure, indicating a bivalent function of the siRNA system operating as a general gene regulation rather than a specific antiviral system.
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Affiliation(s)
- Alessandro Torri
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
| | - Vanesa Mongelli
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
| | - Juan A Mondotte
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
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4
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He X, Wang Y, Fan X, Lei N, Tian Y, Zhang D, Pan W. A schistosome miRNA promotes host hepatic fibrosis by targeting transforming growth factor beta receptor III. J Hepatol 2020; 72:519-527. [PMID: 31738999 DOI: 10.1016/j.jhep.2019.10.029] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 08/06/2019] [Accepted: 10/05/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS MicroRNAs (MiRNAs) derived from parasites, and even from plants, have been detected in body fluids and are known to modulate host genes. In this study, we aimed to investigate if the schistosome miRNAs are involved in the occurrence and progression of hepatic fibrosis during Schistosoma japonicum (S. japonicum) infection. METHODS The presence of miRNAs from S. japonicum (sja-miRNAs) in hepatic stellate cells (HSCs) was detected by RNA sequencing. sja-miRNAs were screened by transfecting HSCs with sja-miRNA mimics. The role of sja-miR-2162 in hepatic fibrosis was evaluated by either elevating its expression in naïve mice or by inhibiting its activity in infected mice, through administration of recombinant adeno-associated virus serotype 8 vectors expressing sja-miR-2162 or miRNA sponges, respectively. RESULTS We identified a miRNA of S. japonicum, sja-miR-2162, that was consistently present in the HSCs of infected mice. Transfection of sja-miR-2162 mimics led to activation of HSC cells in vitro, characterized by elevation of collagens and α-SMA. The rAAV8-mediated delivery of sja-miR-2162 to naïve mice induced hepatic fibrosis, while sustained inhibition of sja-miR-2162 in infected mice attenuated hepatic fibrosis. The transforming growth factor beta receptor III (TGFBR3), a negative regulator of TGF-β signaling, was a direct target of sja-miR-2162 in HSCs. CONCLUSIONS This study demonstrated that pathogen-derived miRNAs directly promote hepatic fibrogenesis in a cross-species manner, and their efficient and sustained inhibition might present a promising therapeutic intervention for infectious diseases. LAY SUMMARY A schistosome-specific microRNA, sja-miR-2162, is consistently present in the hepatic stellate cells of mice infected with S. japonicum, where it promotes hepatic fibrosis in the host through cross-species regulation of host fibrosis-related genes. The efficient and sustained inhibition of pathogen-derived micRNAs may represent a novel therapeutic intervention for infectious diseases.
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Affiliation(s)
- Xing He
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China.
| | - Yange Wang
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
| | - Xiaobin Fan
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
| | - Nanhang Lei
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
| | - Yini Tian
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
| | - Dongmei Zhang
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China.
| | - Weiqing Pan
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China.
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5
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Yakovlev AF. The Role of miRNA in Differentiation, Cell Proliferation, and Pathogenesis of Poultry Diseases. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360419030081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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6
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Kashani B, Hasani Bidgoli M, Motahari SA, Sedaghat N, Modarressi MH. You are what you eat: Sequence analysis reveals how plant microRNAs may regulate the human genome. Comput Biol Med 2019; 106:106-113. [PMID: 30708219 DOI: 10.1016/j.compbiomed.2019.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/01/2019] [Accepted: 01/21/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. METHODS miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally alignment with the human CDS (41 results). The identified genes were further analyzed in-silico to find their functions and relations to human diseases. RESULTS Four common plant miRNAs were identified to match perfectly with 22 human transcripts. The identified target genes were involved in a broad range of body functions, from muscle contraction to tumor suppression. We could also indicate some connections between these findings and folk herbology and botanical medicine. CONCLUSIONS The food that we regularly eat has a great potential in affecting our genome and altering body functions. Plant miRNAs can provide means of designing drugs for a vast range of health problems including obesity and cancer, since they target genes involved in cell cycle (CCNC), digestion (GIPR) and muscular contractions (MYLK). They can also target regions of CDS for which we still have no sufficient information, to help boost our knowledge of the human genome.
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Affiliation(s)
- Bahareh Kashani
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | | | - Nafiseh Sedaghat
- Computer Engineering School, Iran University of Science and Technology, Tehran, Iran
| | - Mohammad Hossein Modarressi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
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7
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Oberbauer V, Schaefer MR. tRNA-Derived Small RNAs: Biogenesis, Modification, Function and Potential Impact on Human Disease Development. Genes (Basel) 2018; 9:genes9120607. [PMID: 30563140 PMCID: PMC6315542 DOI: 10.3390/genes9120607] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and the relatively high abundance of tsRNAs has been noted in many high-throughput sequencing data sets, leading to largely correlative assumptions about their potential as biologically active entities. tRNAs are also the most modified RNAs in any cell type. Mutations in tRNA biogenesis factors including tRNA modification enzymes correlate with a variety of human disease syndromes. However, whether it is the lack of tRNAs or the activity of functionally relevant tsRNAs that are causative for human disease development remains to be elucidated. Here, we review the current knowledge in regard to tsRNAs biogenesis, including the impact of RNA modifications on tRNA stability and discuss the existing experimental evidence in support for the seemingly large functional spectrum being proposed for tsRNAs. We also argue that improved methodology allowing exact quantification and specific manipulation of tsRNAs will be necessary before developing these small RNAs into diagnostic biomarkers and when aiming to harness them for therapeutic purposes.
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Affiliation(s)
- Vera Oberbauer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
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8
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Sohrab SS, Suhail M, Ali A, Kamal MA, Husen A, Ahmad F, Azhar EI, Greig NH. Role of viruses, prions and miRNA in neurodegenerative disorders and dementia. Virusdisease 2018; 29:419-433. [PMID: 30539044 DOI: 10.1007/s13337-018-0492-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022] Open
Abstract
Dementia is known as loss of cellular communications in the brain at a region caused by multi-factorial diseases and pathogenic infections. Approximately eighty percent reported cases of Alzheimer's disease are followed by vascular dementia. The common symptoms of dementia include memory loss, concentration problems, thinking, and language solving situations. Dementia is a multifactorial disease but based on latest research; various reports have been published describing the linkage and role of viruses, prions and miRNAs in neurodegeneration and neurodegenerative disorders resulting into dementia and due to this we selected to review and provide latest information related to dementia. MiRNAs are small non-coding RNAs carrying genetic regulatory information contributing to neurological disorders among human and animals. A prion is an infectious agent made of protein material. Recently, it has been reported that prions play a significant role in signaling processes, resulting in amyloidogenesis and neurological disorders. Viruses attack human immune system and central nervous system and affect classical pathways of neurodegenerative diseases. Comprehensive understandings of the expression profiles and activities of these miRNAs, Prions, Viruses will illuminate their roles as potential therapeutic targets in neurodegeneration and may lead to the discovery of breakthrough treatment strategies for neurodegenerative disorders and dementia. The provided information will further be significant not only in neuro-scientific research, but also in designing and development of management strategies for dementia.
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Affiliation(s)
- Sayed Sartaj Sohrab
- 1Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah, 21589 Saudi Arabia
| | - Mohd Suhail
- 2King Fahd Medical Research Center, King Abdulaziz University, P.O. Box No 21589, Jeddah, Saudi Arabia
| | - Ashraf Ali
- 2King Fahd Medical Research Center, King Abdulaziz University, P.O. Box No 21589, Jeddah, Saudi Arabia
| | - Mohammad Amjad Kamal
- 2King Fahd Medical Research Center, King Abdulaziz University, P.O. Box No 21589, Jeddah, Saudi Arabia.,Enzymoics, 7 Peterlee Place, Hebersham, NSW 2770 Australia.,Novel Global Community Educational Foundation, Sydney, Australia
| | - Azamal Husen
- 6Department of Biology, College of Natural and Computational Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia
| | - Fahim Ahmad
- 7Drug Discovery Division, Southern Research Institute, 2000, Ninth Ave, South, Birmingham, AL 35205 USA
| | - Esam Ibraheem Azhar
- 1Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah, 21589 Saudi Arabia.,5Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National, Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224 USA
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9
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Abstract
Darwin's gemmules were supposed to be "thrown off" by cells and were "inconceivably minute and numerous as the stars in heaven." They were capable of self-propagation and diffusion from cell to cell, and circulation through the system. The word "gene" coined by Wilhelm Johannsen, was derived from de Vries's term "pangen," itself a substitute for "gemmule" in Darwin's Pangenesis. Johannsen resisted the "morphological" conception of genes as particles with a certain structure. Morgan's genes were considered to be stable entities arranged in an orderly linear pattern on chromosomes, like beads on a string. In the late 1940s, McClintock challenged the concept of the stability of the gene when she discovered that some genes could move within a chromosome and between chromosomes. In 1948, Mandel and Metais reported the presence of cell-free nucleic acids in human blood for the first time. Over the past several decades, it has been universally accepted that almost all types of cells not only shed molecules such as cell-free DNA (including genomic DNA, tumor DNA and fetal DNA), RNAs (including mRNA and small RNAs) and prions, but also release into the extracellular environment diverse types of membrane vesicles (known as extracellular vesicles) containing DNA, RNA and proteins. Thus Darwin's speculative gemmules of the 19th century have become the experimentally demonstrated circulating cell-free DNA, mobile RNAs, prions and extracellular vesicles.
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Affiliation(s)
- Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China; Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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10
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He X, Li F, Bor B, Koyano K, Cen L, Xiao X, Shi W, Wong DTW. Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions. J Dent Res 2018; 97:1236-1243. [PMID: 29702004 DOI: 10.1177/0022034518770605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Coevolution of the human host and its associated microbiota has led to sophisticated interactions to maintain a delicate homeostasis. Emerging evidence suggests that in addition to small molecules, peptides, and proteins, small regulatory noncoding RNAs (sRNAs) might play an important role in cross-domain interactions. In this study, we revealed the presence of diverse host transfer RNA-derived small RNAs (tsRNAs) among human salivary sRNAs. We selected 2 tsRNAs (tsRNA-000794 and tsRNA-020498) for further study based on their high sequence similarity to specific tRNAs from a group of Gram-negative oral bacteria, including Fusobacterium nucleatum, a key oral commensal and opportunistic pathogen. We showed that the presence of F. nucleatum triggers exosome-mediated release of tsRNA-000794 and tsRNA-020498 by human normal oral keratinocyte cells. Furthermore, both tsRNA candidates exerted a growth inhibition effect on F. nucleatum, likely through interference with bacterial protein biosynthesis, but did not affect the growth of Streptococcus mitis, a health-associated oral Gram-positive bacterium whose genome does not carry sequences bearing high similarity to either tsRNA. Our data provide the first line of evidence for the modulatory role of host-derived tsRNAs in the microbial-host interaction.
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Affiliation(s)
- X He
- 1 The Forsyth Institute, Cambridge, MA, USA
| | - F Li
- 2 School of Dentistry, University of California, Los Angeles, Los Angeles, CA, USA.,3 Institute of Diagnostic in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - B Bor
- 1 The Forsyth Institute, Cambridge, MA, USA
| | - K Koyano
- 4 Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.,5 Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - L Cen
- 1 The Forsyth Institute, Cambridge, MA, USA
| | - X Xiao
- 4 Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.,5 Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - W Shi
- 1 The Forsyth Institute, Cambridge, MA, USA
| | - D T W Wong
- 2 School of Dentistry, University of California, Los Angeles, Los Angeles, CA, USA.,4 Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.,5 Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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11
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Shiu PK, Hunter CP. Early Developmental Exposure to dsRNA Is Critical for Initiating Efficient Nuclear RNAi in C. elegans. Cell Rep 2017; 18:2969-2978. [PMID: 28329688 DOI: 10.1016/j.celrep.2017.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 11/17/2022] Open
Abstract
RNAi has enabled researchers to study the function of many genes. However, it is not understood why some RNAi experiments succeed while others do not. Here, we show in C. elegans that pharyngeal muscle is resistant to RNAi when initially exposed to double-stranded RNA (dsRNA) by feeding but sensitive to RNAi in the next generation. Investigating this observation, we find that pharyngeal muscle cells as well as vulval muscle cells require nuclear rather than cytoplasmic RNAi. Further, we find in these cell types that nuclear RNAi silencing is most efficiently triggered during early development, defining a critical period for initiating nuclear RNAi. Finally, using heat-shock-induced dsRNA expression, we show that synMuv B class mutants act in part to extend this critical window. The synMuv-B-dependent early-development-associated critical period for initiating nuclear RNAi suggests that mechanisms that restrict developmental plasticity may also restrict the initiation of nuclear RNAi.
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Affiliation(s)
- Philip K Shiu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Craig P Hunter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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12
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Kumar D, Gong C. Insect RNAi: Integrating a New Tool in the Crop Protection Toolkit. TRENDS IN INSECT MOLECULAR BIOLOGY AND BIOTECHNOLOGY 2017. [PMCID: PMC7121382 DOI: 10.1007/978-3-319-61343-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protecting crops against insect pests is a major focus area in crop protection. Over the past two decades, biotechnological interventions, especially Bt proteins, have been successfully implemented across the world and have had major impacts on reducing chemical pesticide applications. As insects continue to adapt to insecticides, both chemical and protein-based, new methods, molecules, and modes of action are necessary to provide sustainable solutions. RNA interference (RNAi) has emerged as a significant tool to knock down or alter gene expression profiles in a species-specific manner. In the past decade, there has been intense research on RNAi applications in crop protection. This chapter looks at the current state of knowledge in the field and outlines the methodology, delivery methods, and precautions required in designing targets. Assessing the targeting of specific gene expression is also an important part of a successful RNAi strategy. The current literature on the use of RNAi in major orders of insect pests is reviewed, along with a perspective on the regulatory aspects of the approach. Risk assessment of RNAi would focus on molecular characterization, food/feed risk assessment, and environmental risk assessment. As more RNAi-based products come through regulatory systems, either via direct application or plant expression based, the impact of this approach on crop protection will become clearer.
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Affiliation(s)
- Dhiraj Kumar
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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13
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Quintana JF, Babayan SA, Buck AH. Small RNAs and extracellular vesicles in filarial nematodes: From nematode development to diagnostics. Parasite Immunol 2017; 39. [PMID: 27748953 DOI: 10.1111/pim.12395] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 02/06/2023]
Abstract
Parasitic nematodes have evolved sophisticated mechanisms to communicate with their hosts in order to survive and successfully establish an infection. The transfer of RNA within extracellular vesicles (EVs) has recently been described as a mechanism that could contribute to this communication in filarial nematodes. It has been shown that these EVs are loaded with several types of RNAs, including microRNAs, leading to the hypothesis that parasites could actively use these molecules to manipulate host gene expression and to the exciting prospect that these pathways could result in new diagnostic and therapeutic strategies. Here, we review the literature on the diverse RNAi pathways that operate in nematodes and more specifically our current knowledge of extracellular RNA (exRNA) and EVs derived from filarial nematodes in vitro and within their hosts. We further detail some of the issues and questions related to the capacity of RNA-mediated communication to function in parasite-host interactions and the ability of exRNA to enable us to distinguish and detect different nematode parasites in their hosts.
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Affiliation(s)
- J F Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S A Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - A H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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14
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Chan SY, Snow JW. Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals. GENES AND NUTRITION 2017; 12:13. [PMID: 29308096 PMCID: PMC5753850 DOI: 10.1186/s12263-017-0561-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/19/2017] [Indexed: 02/07/2023]
Abstract
The notion of uptake of active diet-derived small RNAs (sRNAs) in recipient organisms could have significant implications for our understanding of oral therapeutics and nutrition, for the safe use of RNA interference (RNAi) in agricultural biotechnology, and for ecological relationships. Yet, the transfer and subsequent regulation of gene activity by diet-derived sRNAs in ingesting mammals are still heavily debated. Here, we synthesize current information based on multiple independent studies of mammals, invertebrates, and plants. Rigorous assessment of these data emphasize that uptake of active dietary sRNAs is neither a robust nor a prevalent mechanism to maintain steady-state levels in higher organisms. While disagreement still continues regarding whether such transfer may occur in specialized contexts, concerns about technical difficulties and a lack of consensus on appropriate methods have led to questions regarding the reproducibility and biologic significance of some seemingly positive results. For any continuing investigations, concerted efforts should be made to establish a strong mechanistic basis for potential effects of dietary sRNAs and to agree on methodological guidelines for realizing such proof. Such processes would ensure proper interpretation of studies aiming to prove dietary sRNA activity in mammals and inform potential for application in therapeutics and agriculture.
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Affiliation(s)
- Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, BST 1704.2, 200 Lothrop Street, Pittsburgh, PA 15261 USA
| | - Jonathan W Snow
- Department of Biology, Barnard College, New York, NY 10027 USA
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15
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Luo Y, Wang P, Wang X, Wang Y, Mu Z, Li Q, Fu Y, Xiao J, Li G, Ma Y, Gu Y, Jin L, Ma J, Tang Q, Jiang A, Li X, Li M. Detection of dietetically absorbed maize-derived microRNAs in pigs. Sci Rep 2017; 7:645. [PMID: 28381865 PMCID: PMC5428504 DOI: 10.1038/s41598-017-00488-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/27/2017] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs are a class of small RNAs that are important in post-transcriptional gene regulation in animals and plants. These single-stranded molecules are widely distributed in organisms and influence fundamental biological processes. Interestingly, recent studies have reported that diet-derived plant miRNAs could regulate mammalian gene expression, and these studies have broadened our view of cross-kingdom communication. In the present study, we evaluated miRNA levels in cooked maize-containing chow diets, and found that plant miRNAs were resistant to the harsh cooking conditions to a certain extent. After feeding fresh maize to pigs (7 days), maize-derived miRNAs could be detected in porcine tissues and serum, and the authenticity of these plant miRNAs was confirmed by using oxidization reactions. Furthermore, in vivo and in vitro experiments demonstrated that dietary maize miRNAs could cross the gastrointestinal tract and enter the porcine bloodstream. In the porcine cells, we found that plant miRNAs are very likely to specifically target their endogenous porcine mRNAs and influence gene expression in a fashion similar to that of mammalian miRNAs. Our results indicate that maize-derived miRNAs can cross the gastrointestinal tract and present in pigs, and these exogenous miRNAs have the potential to regulate mammalian gene expression.
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Affiliation(s)
- Yi Luo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengjun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiping Mu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Chongqing Three Gorges University, Chongqing, 404000, China
| | - Qingzhi Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- The Fishery Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 611731, China
| | - Yuhua Fu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juan Xiao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guojun Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Anan Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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16
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Chan SY, Snow JW. Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture. RNA Biol 2017; 14:402-414. [PMID: 27763816 PMCID: PMC5411125 DOI: 10.1080/15476286.2016.1248329] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 02/08/2023] Open
Abstract
The putative transfer and gene regulatory activities of diet-derived small RNAs (sRNAs) in ingesting animals are still debated. The existence of natural uptake of diet-derived sRNA by invertebrate species could have significant implication for our understanding of ecological relationships and could synergize with efforts to use RNA interference (RNAi) technology in agriculture. Here, we synthesize information gathered from studies in invertebrates using natural or artificial dietary delivery of sRNA and from studies of sRNA in vertebrate animals and plants to review our current understanding of uptake and impact of natural diet-derived sRNA on invertebrates. Our understanding has been influenced and sometimes confounded by the diversity of invertebrates and ingested plants studied, our limited insights into how gene expression may be modulated by dietary sRNAs at the mechanistic level, and the paucity of studies focusing directly on natural uptake of sRNA. As such, we suggest 2 strategies to investigate this phenomenon more comprehensively and thus facilitate the realization of its potentially broad impact on ecology and agriculture in the future.
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Affiliation(s)
- Stephen Y. Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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17
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Braukmann F, Jordan D, Miska E. Artificial and natural RNA interactions between bacteria and C. elegans. RNA Biol 2017; 14:415-420. [PMID: 28332918 DOI: 10.1080/15476286.2017.1297912] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nineteen years after Lisa Timmons and Andy Fire first described RNA transfer from bacteria to C. elegans in an experimental setting 48 the biologic role of this trans-kingdom RNA-based communication remains unknown. Here we summarize our current understanding on the mechanism and potential role of such social RNA.
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Affiliation(s)
- Fabian Braukmann
- a Gurdon Institute, University of Cambridge , Cambridge , UK.,b Department of Genetics , University of Cambridge , Cambridge , UK
| | - David Jordan
- a Gurdon Institute, University of Cambridge , Cambridge , UK.,b Department of Genetics , University of Cambridge , Cambridge , UK
| | - Eric Miska
- a Gurdon Institute, University of Cambridge , Cambridge , UK.,b Department of Genetics , University of Cambridge , Cambridge , UK.,c Wellcome Trust Sanger Institute , Wellcome Trust Genome Campus, Cambridge , UK
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18
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LeBoeuf AC, Waridel P, Brent CS, Gonçalves AN, Menin L, Ortiz D, Riba-Grognuz O, Koto A, Soares ZG, Privman E, Miska EA, Benton R, Keller L. Oral transfer of chemical cues, growth proteins and hormones in social insects. eLife 2016; 5:e20375. [PMID: 27894417 PMCID: PMC5153251 DOI: 10.7554/elife.20375] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/14/2016] [Indexed: 01/02/2023] Open
Abstract
Social insects frequently engage in oral fluid exchange - trophallaxis - between adults, and between adults and larvae. Although trophallaxis is widely considered a food-sharing mechanism, we hypothesized that endogenous components of this fluid might underlie a novel means of chemical communication between colony members. Through protein and small-molecule mass spectrometry and RNA sequencing, we found that trophallactic fluid in the ant Camponotus floridanus contains a set of specific digestion- and non-digestion related proteins, as well as hydrocarbons, microRNAs, and a key developmental regulator, juvenile hormone. When C. floridanus workers' food was supplemented with this hormone, the larvae they reared via trophallaxis were twice as likely to complete metamorphosis and became larger workers. Comparison of trophallactic fluid proteins across social insect species revealed that many are regulators of growth, development and behavioral maturation. These results suggest that trophallaxis plays previously unsuspected roles in communication and enables communal control of colony phenotypes.
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Affiliation(s)
- Adria C LeBoeuf
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Patrice Waridel
- Protein Analysis FacilityUniversity of LausanneLausanneSwitzerland
| | - Colin S Brent
- Arid Land Agricultural Research Center, USDA-ARSMaricopaUnited States
| | - Andre N Gonçalves
- Department of Biochemistry and ImmunologyInstituto de Ciências Biológicas, Universidade Federal de Minas GeraisMinas GeraisBrazil
- Gurdon InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Laure Menin
- Institute of Chemical Sciences and EngineeringEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Daniel Ortiz
- Institute of Chemical Sciences and EngineeringEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Oksana Riba-Grognuz
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Akiko Koto
- The Department of Genetics, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Zamira G Soares
- Department of Biochemistry and ImmunologyInstituto de Ciências Biológicas, Universidade Federal de Minas GeraisMinas GeraisBrazil
- Gurdon InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Eric A Miska
- Gurdon InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Richard Benton
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Laurent Keller
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
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19
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Masood M, Everett CP, Chan SY, Snow JW. Negligible uptake and transfer of diet-derived pollen microRNAs in adult honey bees. RNA Biol 2016; 13:109-18. [PMID: 26680555 DOI: 10.1080/15476286.2015.1128063] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The putative transfer and gene regulatory activities of diet-derived miRNAs in ingesting animals are still debated. Importantly, no study to date has fully examined the role of dietary uptake of miRNA in the honey bee, a critical pollinator in both agricultural and natural ecosystems. After controlled pollen feeding experiments in adult honey bees, we observed that midguts demonstrated robust increases in plant miRNAs after pollen ingestion. However, we found no evidence of biologically relevant delivery of these molecules to proximal or distal tissues of recipient honey bees. Our results, therefore, support the premise that pollen miRNAs ingested as part of a typical diet are not robustly transferred across barrier epithelia of adult honey bees under normal conditions. Key future questions include whether other small RNA species in honey bee diets behave similarly and whether more specialized and specific delivery mechanisms exist for more efficient transport, particularly in the context of stressed barrier epithelia.
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Affiliation(s)
- Maryam Masood
- a Department of Biology , Barnard College , New York , NY , 10027 , USA
| | - Claire P Everett
- a Department of Biology , Barnard College , New York , NY , 10027 , USA
| | - Stephen Y Chan
- b Vascular Medicine Institute, University of Pittsburgh Medical Center , Pittsburgh , PA , 15261 , USA
| | - Jonathan W Snow
- a Department of Biology , Barnard College , New York , NY , 10027 , USA
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20
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Houri-Ze'evi L, Rechavi O. Plastic germline reprogramming of heritable small RNAs enables maintenance or erasure of epigenetic memories. RNA Biol 2016; 13:1212-1217. [PMID: 27592591 PMCID: PMC5207387 DOI: 10.1080/15476286.2016.1229732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In Caenorhabditis elegans small RNAs can regulate genes across generations. The mysterious tendency of heritable RNA interference (RNAi) responses to terminate after 3–5 generations has been referred to as “the bottleneck to RNAi inheritance.” We have recently shown that the re-setting of epigenetic inheritance after 3–5 generations is not due to passive dilution of the original RNA trigger, but instead results from an active, multigenerational, and small RNA-mediated regulatory pathway. In this “Point of View” manuscript we suggest that the process that leads to the erasure of the ancestral small RNA-encoded memory is a specialized type of germline reprogramming mechanism, analogous to the processes that robustly remove parental DNA methylation and histone modifications early in development in different organisms. Traditionally, germline reprogramming mechanisms that re-set chromatin are thought to stand in the way of inheritance of memories of parental experiences. We found that reprogramming of heritable small RNAs takes multiple generations to complete, enabling long-term inheritance of small RNA responses. Moreover, the duration of this reprogramming process can be prolonged significantly if new heritable RNAi responses are provoked. A dedicated signaling pathway that is responsive to environmental cues can tune the epigenetic state of the RNAi inheritance system, so that inheritance of particular small RNA species can be extended.
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Affiliation(s)
- Leah Houri-Ze'evi
- a Department of Neurobiology , Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University , Tel Aviv , Israel
| | - Oded Rechavi
- a Department of Neurobiology , Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University , Tel Aviv , Israel
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21
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Wang J, Barr MM. Ciliary Extracellular Vesicles: Txt Msg Organelles. Cell Mol Neurobiol 2016; 36:449-57. [PMID: 26983828 PMCID: PMC4886304 DOI: 10.1007/s10571-016-0345-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/08/2016] [Indexed: 01/12/2023]
Abstract
Cilia are sensory organelles that protrude from cell surfaces to monitor the surrounding environment. In addition to its role as sensory receiver, the cilium also releases extracellular vesicles (EVs). The release of sub-micron sized EVs is a conserved form of intercellular communication used by all three kingdoms of life. These extracellular organelles play important roles in both short and long range signaling between donor and target cells and may coordinate systemic responses within an organism in normal and diseased states. EV shedding from ciliated cells and EV-cilia interactions are evolutionarily conserved phenomena, yet remarkably little is known about the relationship between the cilia and EVs and the fundamental biology of EVs. Studies in the model organisms Chlamydomonas and Caenorhabditis elegans have begun to shed light on ciliary EVs. Chlamydomonas EVs are shed from tips of flagella and are bioactive. Caenorhabditis elegans EVs are shed and released by ciliated sensory neurons in an intraflagellar transport-dependent manner. Caenorhabditis elegans EVs play a role in modulating animal-to-animal communication, and this EV bioactivity is dependent on EV cargo content. Some ciliary pathologies, or ciliopathies, are associated with abnormal EV shedding or with abnormal cilia-EV interactions. Until the 21st century, both cilia and EVs were ignored as vestigial or cellular junk. As research interest in these two organelles continues to gain momentum, we envision a new field of cell biology emerging. Here, we propose that the cilium is a dedicated organelle for EV biogenesis and EV reception. We will also discuss possible mechanisms by which EVs exert bioactivity and explain how what is learned in model organisms regarding EV biogenesis and function may provide insight to human ciliopathies.
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Affiliation(s)
- Juan Wang
- Department of Genetics and The Human Genetics Institute of New Jersey, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Maureen M Barr
- Department of Genetics and The Human Genetics Institute of New Jersey, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA.
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22
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E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans. Sci Rep 2015; 5:9597. [PMID: 25873159 PMCID: PMC4397834 DOI: 10.1038/srep09597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/09/2015] [Indexed: 02/01/2023] Open
Abstract
The discovery of RNA interference (RNAi) in C. elegans has had a major impact on scientific research, led to the rapid development of RNAi tools and has inspired RNA-based therapeutics. Astonishingly, nematodes, planaria and many insects take up double-stranded RNA (dsRNA) from their environment to elicit RNAi; the biological function of this mechanism is unclear. Recently, the E. coli OxyS non-coding RNA was shown to regulate gene expression in C. elegans when E. coli is offered as food. This was surprising given that C. elegans is unlikely to encounter E. coli in nature. To directly test the hypothesis that the E. coli OxyS non-coding RNA triggers the C. elegans RNAi pathway, we sequenced small RNAs from C. elegans after feeding with bacteria. We clearly demonstrate that the OxyS non-coding RNA does not trigger an RNAi response in C. elegans. We conclude that the biology of environmental RNAi remains to be discovered.
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23
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Weiberg A, Bellinger M, Jin H. Conversations between kingdoms: small RNAs. Curr Opin Biotechnol 2015; 32:207-215. [PMID: 25622136 DOI: 10.1016/j.copbio.2014.12.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 12/30/2022]
Abstract
Humans, animals, and plants are constantly under attack from pathogens and pests, resulting in severe consequences on global human health and crop production. Small RNA (sRNA)-mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of sRNAs and RNAi to the communication between hosts and some eukaryotic pathogens, pests, parasites, or symbiotic microorganisms. Mobile silencing signals—most likely sRNAs—are capable of translocating from the host to its interacting organism, and vice versa. In this review, we will provide an overview of sRNA communications between different kingdoms, with a primary focus on the advances in plant-pathogen interaction systems.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Marschal Bellinger
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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24
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Okoye IS, Coomes SM, Pelly VS, Czieso S, Papayannopoulos V, Tolmachova T, Seabra MC, Wilson MS. MicroRNA-containing T-regulatory-cell-derived exosomes suppress pathogenic T helper 1 cells. Immunity 2014; 41:89-103. [PMID: 25035954 PMCID: PMC4104030 DOI: 10.1016/j.immuni.2014.05.019] [Citation(s) in RCA: 426] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/15/2014] [Indexed: 01/21/2023]
Abstract
Foxp3(+) T regulatory (Treg) cells prevent inflammatory disease but the mechanistic basis of suppression is not understood completely. Gene silencing by RNA interference can act in a cell-autonomous and non-cell-autonomous manner, providing mechanisms of intercellular regulation. Here, we demonstrate that non-cell-autonomous gene silencing, mediated by miRNA-containing exosomes, is a mechanism employed by Treg cells to suppress T-cell-mediated disease. Treg cells transferred microRNAs (miRNA) to various immune cells, including T helper 1 (Th1) cells, suppressing Th1 cell proliferation and cytokine secretion. Use of Dicer-deficient or Rab27a and Rab27b double-deficient Treg cells to disrupt miRNA biogenesis or the exosomal pathway, respectively, established a requirement for miRNAs and exosomes for Treg-cell-mediated suppression. Transcriptional analysis and miRNA inhibitor studies showed that exosome-mediated transfer of Let-7d from Treg cell to Th1 cells contributed to suppression and prevention of systemic disease. These studies reveal a mechanism of Treg-cell-mediated suppression mediated by miRNA-containing exosomes.
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Affiliation(s)
- Isobel S Okoye
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London NW7 1AA, UK
| | - Stephanie M Coomes
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London NW7 1AA, UK
| | - Victoria S Pelly
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London NW7 1AA, UK
| | - Stephanie Czieso
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London NW7 1AA, UK
| | | | - Tanya Tolmachova
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Miguel C Seabra
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Mark S Wilson
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London NW7 1AA, UK.
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25
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Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH. Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science 2014; 345:808-11. [PMID: 25124438 DOI: 10.1126/science.1253122] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.
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Affiliation(s)
- Gunjune Kim
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Megan L LeBlanc
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eric K Wafula
- Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Claude W dePamphilis
- Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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26
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Abstract
This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals. In this case, we need to take this into account fully to understand how a given biological equilibrium is obtained. Despite many observations of trans-kingdom RNA signal transfer, several mechanistic aspects of these signals remain unknown. Such RNA signal transfer is already being exploited for practical purposes, though. Pathogen genes can be silenced by plant-produced sRNAs designed to affect these genes. This is also known as Host-Induced Genes Silencing (HIGS), and it has the potential to become an important disease-control method in the future.
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Affiliation(s)
- Marijn Knip
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria E. Constantin
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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27
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Sagy O, Shamir R, Rechavi O. Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria. Front Genet 2014; 5:275. [PMID: 25221566 PMCID: PMC4148067 DOI: 10.3389/fgene.2014.00275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/26/2014] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing requires insertion of random fragments of the sequenced organism’s DNA into a unicellular host, most often Escherichia coli bacteria. This manipulation was found in the past to be analogous to naturally occurring horizontal gene transfer, and moreover has proved valuable to understanding toxicity of foreign genetic elements to E. coli. Sequencing of the Caenorhabditis elegans genome was similarly achieved via DNA transformation into E. coli. However, numerous attempts have proven a significant percentage of the genome unclonable using bacteria, although clonable via yeast. We examined the genomic segments that were not clonable in bacteria but were clonable in yeast, and observed that, in line with previous hypotheses, such sequences are more repetitive on average compared with the entire C. elegans genome. In addition, we found that these gap-sequences encode significantly more for DNA transposons. Surprisingly, we discovered that although the vast majority of the C. elegans genome is clonable in bacteria (77.5%), almost all the thousands of sequences that encode for PIWI-interacting small RNAs, or 21U-RNAs (91.6%) were only clonable in yeast. These results might help understanding why most piRNAs in C. elegans are physically clustered on particular loci on chromosome IV. In worms and in a large number of other organisms, piRNAs serve to distinguish “Self” from “Non-Self” sequences, and thus to protect the integrity of the genome against foreign genetic elements, such as transposons. We discuss the possible implications of these discoveries.
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Affiliation(s)
- Or Sagy
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
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28
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Sarkies P, Miska EA. Small RNAs break out: the molecular cell biology of mobile small RNAs. Nat Rev Mol Cell Biol 2014; 15:525-35. [DOI: 10.1038/nrm3840] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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Jung H, Gkogkas CG, Sonenberg N, Holt CE. Remote control of gene function by local translation. Cell 2014; 157:26-40. [PMID: 24679524 PMCID: PMC3988848 DOI: 10.1016/j.cell.2014.03.005] [Citation(s) in RCA: 243] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/04/2014] [Accepted: 03/04/2014] [Indexed: 12/12/2022]
Abstract
The subcellular position of a protein is a key determinant of its function. Mounting evidence indicates that RNA localization, where specific mRNAs are transported subcellularly and subsequently translated in response to localized signals, is an evolutionarily conserved mechanism to control protein localization. On-site synthesis confers novel signaling properties to a protein and helps to maintain local proteome homeostasis. Local translation plays particularly important roles in distal neuronal compartments, and dysregulated RNA localization and translation cause defects in neuronal wiring and survival. Here, we discuss key findings in this area and possible implications of this adaptable and swift mechanism for spatial control of gene function.
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Affiliation(s)
- Hosung Jung
- Department of Anatomy, Brain Research Institute, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, South Korea
| | - Christos G Gkogkas
- Patrick Wild Centre, Centre for Integrative Physiology, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada.
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, Anatomy Building, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK.
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30
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Li X, Wang Q, Liu Y. Inherited small RNAs: new insights into Darwin's cell theory. Trends Cell Biol 2014; 24:387-8. [PMID: 24815682 DOI: 10.1016/j.tcb.2014.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 04/15/2014] [Accepted: 04/16/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Xiuju Li
- Henan Institute of Science and Technology, Xinxiang, 453003, China; Department of Biochemistry, Faculty of Medicine, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Qinglian Wang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yongsheng Liu
- Henan Institute of Science and Technology, Xinxiang, 453003, China; Department of Biochemistry, Faculty of Medicine, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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Abstract
Discoveries over the past decade portend a paradigm shift in molecular biology. Evidence suggests that RNA is not only functional as a messenger between DNA and protein but also involved in the regulation of genome organization and gene expression, which is increasingly elaborate in complex organisms. Regulatory RNA seems to operate at many levels; in particular, it plays an important part in the epigenetic processes that control differentiation and development. These discoveries suggest a central role for RNA in human evolution and ontogeny. Here, we review the emergence of the previously unsuspected world of regulatory RNA from a historical perspective.
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Affiliation(s)
- Kevin V Morris
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John S Mattick
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; the School of Biotechnology and Biomedical Sciences, and St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
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32
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Pogue AI, Hill JM, Lukiw WJ. MicroRNA (miRNA): sequence and stability, viroid-like properties, and disease association in the CNS. Brain Res 2014; 1584:73-9. [PMID: 24709119 DOI: 10.1016/j.brainres.2014.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/06/2014] [Accepted: 03/28/2014] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) constitute a relatively recently-discovered class of small non-coding RNAs (sncRNAs) that are gaining considerable attention in the molecular-genetic regulatory mechanisms that contribute to human health and disease. As highly soluble and mobile entities, emerging evidence indicates that miRNAs posess a highly selected ribonucleotide sequence structure, are part of an evolutionary ancient genetic signaling system, resemble the plant pathogens known as viroids in their structure, mode of generation and function, and are very abundant in the physiological fluids that surround cells and tissues. Persistence and altered abundance of miRNAs in the extracellular fluid (ECF) or cerebrospinal fluid (CSF) may play a role in the intercellular spreading of disease systemically, and throughout functionally-linked cellular and tissue systems such as the central nervous system (CNS). This short communication will review some of the more fascinating features of these highly structured single stranded RNAs (ssRNAs) with emphasis on their presence and function in the human CNS, with particular reference to Alzheimer׳s disease (AD) wherever possible.
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Affiliation(s)
| | - James M Hill
- Departments of Neurology, Neuroscience and Ophthalmology, LSU Neuroscience Center, School of Medicine, Louisiana State University Health Sciences Center, 2020 Gravier Street, Suite 904, New Orleans, LA 70112, USA
| | - Walter J Lukiw
- Alchem Biotek, Toronto, ON, Canada, M5S 1A8; Departments of Neurology, Neuroscience and Ophthalmology, LSU Neuroscience Center, School of Medicine, Louisiana State University Health Sciences Center, 2020 Gravier Street, Suite 904, New Orleans, LA 70112, USA.
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33
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Novel transcriptome data analysis implicates circulating microRNAs in epigenetic inheritance in mammals. Gene 2014; 538:366-72. [DOI: 10.1016/j.gene.2014.01.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/23/2013] [Accepted: 01/20/2014] [Indexed: 12/30/2022]
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34
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Hill JM, Lukiw WJ. Comparing miRNAs and viroids; highly conserved molecular mechanisms for the transmission of genetic information. Front Cell Neurosci 2014; 8:45. [PMID: 24600348 PMCID: PMC3929837 DOI: 10.3389/fncel.2014.00045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/01/2014] [Indexed: 12/29/2022] Open
Affiliation(s)
- James M Hill
- LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Microbiology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Pharmacology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Microbiology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Neurology, Louisiana State University Health Sciences Center New Orleans, LA, USA
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35
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Hill JM, Zhao Y, Bhattacharjee S, Lukiw WJ. miRNAs and viroids utilize common strategies in genetic signal transfer. Front Mol Neurosci 2014; 7:10. [PMID: 24574963 PMCID: PMC3918644 DOI: 10.3389/fnmol.2014.00010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/22/2014] [Indexed: 12/29/2022] Open
Affiliation(s)
- James M Hill
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Microbiology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
| | - Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
| | - Surjyadipta Bhattacharjee
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
| | - Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Neurology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
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36
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Witwer KW, Hirschi KD. Transfer and functional consequences of dietary microRNAs in vertebrates: concepts in search of corroboration: negative results challenge the hypothesis that dietary xenomiRs cross the gut and regulate genes in ingesting vertebrates, but important questions persist. Bioessays 2014; 36:394-406. [PMID: 24436255 PMCID: PMC4109825 DOI: 10.1002/bies.201300150] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
If validated, diet-derived foreign microRNA absorption and function in consuming vertebrates would drastically alter our understanding of nutrition and ecology. RNA interference (RNAi) mechanisms of Caenorhabditis elegans are enhanced by uptake of environmental RNA and amplification and systemic distribution of RNAi effectors. Therapeutic exploitation of RNAi in treating human disease is difficult because these accessory processes are absent or diminished in most animals. A recent report challenged multiple paradigms, suggesting that ingested microRNAs (miRNAs) are transferred to blood, accumulate in tissues, and exert canonical regulation of endogenous transcripts. Independent replication of these findings has been elusive, and multiple disconfirmatory findings have been published. In the face of mounting negative results, any additional positive reports must provide the proverbial “extraordinary proof” to support such claims. In this article, we review the evidence for and against a significant role for dietary miRNAs in influencing gene expression, and make recommendations for future studies.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, Baltimore, MD, USA
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37
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Pogue AI, Clement C, Hill JM, Lukiw WJ. Evolution of microRNA (miRNA) Structure and Function in Plants and Animals: Relevance to Aging and Disease. ACTA ACUST UNITED AC 2014; 2. [PMID: 26146648 PMCID: PMC4489142 DOI: 10.4172/2329-8847.1000119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - James M Hill
- Departments of Ophthalmology, LSU Neuroscience Center, USA ; Departments of Microbiology, LSU Neuroscience Center, USA ; Departments of Pharmacology, LSU Neuroscience Center, USA ; Departments of Neurology, LSU Neuroscience Center, USA
| | - Walter J Lukiw
- Alchem Biotek, Toronto ON, M5S 1A8, Canada ; Departments of Ophthalmology, LSU Neuroscience Center, USA ; Departments of Neurology, LSU Neuroscience Center, USA
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38
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Abstract
The elaborate morphology of neurons together with the information processing that occurs in remote dendritic and axonal compartments makes the use of decentralized cell biological machines necessary. Recent years have witnessed a revolution in our understanding of signaling in neuronal compartments and the manifold functions of a variety of RNA molecules that regulate protein translation and other cellular functions. Here we discuss the view that mRNA localization and RNA-regulated and localized translation underlie many fundamental neuronal processes and highlight key issues for future experiments.
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39
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Burroughs AM, Ando Y, Aravind L. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:141-81. [PMID: 24311560 DOI: 10.1002/wrna.1210] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022]
Abstract
Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense-antisense transcriptional products, (2) genome-encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNAi. They were recruited alongside RNaseIII domains and RNA-dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs.
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Affiliation(s)
- Alexander Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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40
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Affiliation(s)
- David Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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41
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Bhattacharjee S, Lukiw WJ. Alzheimer's disease and the microbiome. Front Cell Neurosci 2013; 7:153. [PMID: 24062644 PMCID: PMC3775450 DOI: 10.3389/fncel.2013.00153] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/26/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Surjyadipta Bhattacharjee
- Departments of Neurology, Neuroscience and Ophthalmology, LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA
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