1
|
Cvrčková F, Ghosh R, Kočová H. Transmembrane formins as active cargoes of membrane trafficking. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3668-3684. [PMID: 38401146 PMCID: PMC11194305 DOI: 10.1093/jxb/erae078] [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: 12/13/2023] [Accepted: 02/23/2024] [Indexed: 02/26/2024]
Abstract
Formins are a large, evolutionarily old family of cytoskeletal regulators whose roles include actin capping and nucleation, as well as modulation of microtubule dynamics. The plant class I formin clade is characterized by a unique domain organization, as most of its members are transmembrane proteins with possible cell wall-binding motifs exposed to the extracytoplasmic space-a structure that appears to be a synapomorphy of the plant kingdom. While such transmembrane formins are traditionally considered mainly as plasmalemma-localized proteins contributing to the organization of the cell cortex, we review, from a cell biology perspective, the growing evidence that they can also, at least temporarily, reside (and in some cases also function) in endomembranes including secretory and endocytotic pathway compartments, the endoplasmic reticulum, the nuclear envelope, and the tonoplast. Based on this evidence, we propose that class I formins may thus serve as 'active cargoes' of membrane trafficking-membrane-embedded proteins that modulate the fate of endo- or exocytotic compartments while being transported by them.
Collapse
Affiliation(s)
- Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, CZ 128 43 Praha 2, Czechia
| | - Rajdeep Ghosh
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, CZ 128 43 Praha 2, Czechia
| | - Helena Kočová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, CZ 128 43 Praha 2, Czechia
| |
Collapse
|
2
|
Gordillo-Sampedro S, Antounians L, Wei W, Mufteev M, Lendemeijer B, Kushner SA, de Vrij FMS, Zani A, Ellis J. iPSC-derived healthy human astrocytes selectively load miRNAs targeting neuronal genes into extracellular vesicles. Mol Cell Neurosci 2024; 129:103933. [PMID: 38663691 DOI: 10.1016/j.mcn.2024.103933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/31/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
Astrocytes are in constant communication with neurons during the establishment and maturation of functional networks in the developing brain. Astrocytes release extracellular vesicles (EVs) containing microRNA (miRNA) cargo that regulates transcript stability in recipient cells. Astrocyte released factors are thought to be involved in neurodevelopmental disorders. Healthy astrocytes partially rescue Rett Syndrome (RTT) neuron function. EVs isolated from stem cell progeny also correct aspects of RTT. EVs cross the blood-brain barrier (BBB) and their cargo is found in peripheral blood which may allow non-invasive detection of EV cargo as biomarkers produced by healthy astrocytes. Here we characterize miRNA cargo and sequence motifs in healthy human astrocyte derived EVs (ADEVs). First, human induced Pluripotent Stem Cells (iPSC) were differentiated into Neural Progenitor Cells (NPCs) and subsequently into astrocytes using a rapid differentiation protocol. iPSC derived astrocytes expressed specific markers, displayed intracellular calcium transients and secreted ADEVs. miRNAs were identified by RNA-Seq on astrocytes and ADEVs and target gene pathway analysis detected brain and immune related terms. The miRNA profile was consistent with astrocyte identity, and included approximately 80 miRNAs found in astrocytes that were relatively depleted in ADEVs suggestive of passive loading. About 120 miRNAs were relatively enriched in ADEVs and motif analysis discovered binding sites for RNA binding proteins FUS, SRSF7 and CELF5. miR-483-5p was the most significantly enriched in ADEVs. This miRNA regulates MECP2 expression in neurons and has been found differentially expressed in blood samples from RTT patients. Our results identify potential miRNA biomarkers selectively sorted into ADEVs and implicate RNA binding protein sequence dependent mechanisms for miRNA cargo loading.
Collapse
Affiliation(s)
- Sara Gordillo-Sampedro
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lina Antounians
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada; Division of General and Thoracic Surgery, Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Wei
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Bas Lendemeijer
- Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
| | - Steven A Kushner
- Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands; Center of Expertise for Neurodevelopmental Disorders (ENCORE), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Augusto Zani
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada; Division of General and Thoracic Surgery, Hospital for Sick Children, Toronto, ON, Canada; Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
3
|
Blagojevic A, Baldrich P, Schiaffini M, Lechner E, Baumberger N, Hammann P, Elmayan T, Garcia D, Vaucheret H, Meyers BC, Genschik P. Heat stress promotes Arabidopsis AGO1 phase separation and association with stress granule components. iScience 2024; 27:109151. [PMID: 38384836 PMCID: PMC10879784 DOI: 10.1016/j.isci.2024.109151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/17/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. AGO1 associates to the rough endoplasmic reticulum to conduct miRNA-mediated translational repression, mRNA cleavage, and biogenesis of phased siRNAs. Here, we show that a 37°C heat stress (HS) promotes AGO1 protein accumulation in cytosolic condensates where it colocalizes with components of siRNA bodies and of stress granules. AGO1 contains a prion-like domain in its poorly characterized N-terminal Poly-Q domain, which is sufficient to undergo phase separation independently of the presence of SGS3. HS only moderately affects the small RNA repertoire, the loading of AGO1 by miRNAs, and the signatures of target cleavage, suggesting that its localization in condensates protects AGO1 rather than promoting or impairing its activity in reprogramming gene expression during stress. Collectively, our work sheds new light on the impact of high temperature on a main effector of RNA silencing in plants.
Collapse
Affiliation(s)
- Aleksandar Blagojevic
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Marlene Schiaffini
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Esther Lechner
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Nicolas Baumberger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Taline Elmayan
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| |
Collapse
|
4
|
Sharma G, Sultana A, Abdullah KM, Pothuraju R, Nasser MW, Batra SK, Siddiqui JA. Epigenetic regulation of bone remodeling and bone metastasis. Semin Cell Dev Biol 2024; 154:275-285. [PMID: 36379849 PMCID: PMC10175516 DOI: 10.1016/j.semcdb.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Bone remodeling is a continuous and dynamic process of bone formation and resorption to maintain its integrity and homeostasis. Bone marrow is a source of various cell lineages, including osteoblasts and osteoclasts, which are involved in bone formation and resorption, respectively, to maintain bone homeostasis. Epigenetics is one of the elementary regulations governing the physiology of bone remodeling. Epigenetic modifications, mainly DNA methylation, histone modifications, and non-coding RNAs, regulate stable transcriptional programs without causing specific heritable alterations. DNA methylation in CpG-rich promoters of the gene is primarily correlated with gene silencing, and histone modifications are associated with transcriptional activation/inactivation. However, non-coding RNAs regulate the metastatic potential of cancer cells to metastasize at secondary sites. Deregulated or altered epigenetic modifications are often seen in many cancers and interwound with bone-specific tropism and cancer metastasis. Histone acetyltransferases, histone deacetylase, and DNA methyltransferases are promising targets in epigenetically altered cancer. High throughput epigenome mapping and targeting specific epigenetics modifiers will be helpful in the development of personalized epi-drugs for advanced and bone metastasis cancer patients. This review aims to discuss and gather more knowledge about different epigenetic modifications in bone remodeling and metastasis. Further, it provides new approaches for targeting epigenetic changes and therapy research.
Collapse
Affiliation(s)
- Gunjan Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ashrafi Sultana
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - K M Abdullah
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ramesh Pothuraju
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| |
Collapse
|
5
|
Li B, Feng C, Zhang W, Sun S, Yue D, Zhang X, Yang X. Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress. Int J Biol Macromol 2023; 253:126558. [PMID: 37659489 DOI: 10.1016/j.ijbiomac.2023.126558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/29/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
Collapse
Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Cheng Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Wenhao Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| |
Collapse
|
6
|
Ottens F, Efstathiou S, Hoppe T. Cutting through the stress: RNA decay pathways at the endoplasmic reticulum. Trends Cell Biol 2023:S0962-8924(23)00236-2. [PMID: 38008608 DOI: 10.1016/j.tcb.2023.11.003] [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: 09/28/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
Collapse
Affiliation(s)
- Franziska Ottens
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sotirios Efstathiou
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
| |
Collapse
|
7
|
Androutsopoulos G, Styliara I, Zarogianni E, Lazurko N, Valasoulis G, Michail G, Adonakis G. The ErbB Signaling Network and Its Potential Role in Endometrial Cancer. EPIGENOMES 2023; 7:24. [PMID: 37873809 PMCID: PMC10594534 DOI: 10.3390/epigenomes7040024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
Endometrial cancer (EC) is the second most common malignancy of the female reproductive system worldwide. The updated EC classification emphasizes the significant role of various signaling pathways such as PIK3CA-PIK3R1-PTEN and RTK/RAS/β-catenin in EC pathogenesis. Some of these pathways are part of the EGF system signaling network, which becomes hyperactivated by various mechanisms and participates in cancer pathogenesis. In EC, the expression of ErbB receptors is significantly different, compared with the premenopausal and postmenopausal endometrium, mainly because of the increased transcriptional activity of ErbB encoding genes in EC cells. Moreover, there are some differences in ErbB-2 receptor profile among EC subgroups that could be explained by the alterations in pathophysiology and clinical behavior of various EC histologic subtypes. The fact that ErbB-2 receptor expression is more common in aggressive EC histologic subtypes (papillary serous and clear cell) could indicate a future role of ErbB-targeted therapies in well-defined EC subgroups with overexpression of ErbB receptors.
Collapse
Affiliation(s)
- Georgios Androutsopoulos
- Gynaecological Oncology Unit, Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece
- Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece; (I.S.); (E.Z.); (N.L.); (G.M.); (G.A.)
| | - Ioanna Styliara
- Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece; (I.S.); (E.Z.); (N.L.); (G.M.); (G.A.)
| | - Evgenia Zarogianni
- Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece; (I.S.); (E.Z.); (N.L.); (G.M.); (G.A.)
| | - Nadia Lazurko
- Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece; (I.S.); (E.Z.); (N.L.); (G.M.); (G.A.)
| | - George Valasoulis
- Department of Obstetrics and Gynaecology, Medical School, University of Thessaly, 41334 Larisa, Greece;
- Hellenic National Public Health Organization—ECDC, 15123 Athens, Greece
| | - Georgios Michail
- Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece; (I.S.); (E.Z.); (N.L.); (G.M.); (G.A.)
| | - Georgios Adonakis
- Department of Obstetrics and Gynaecology, School of Medicine, University of Patras, 26504 Rion, Greece; (I.S.); (E.Z.); (N.L.); (G.M.); (G.A.)
| |
Collapse
|
8
|
Singh S, Hu X, Dixelius C. Dynamics of nucleic acid mobility. Genetics 2023; 225:iyad132. [PMID: 37491977 PMCID: PMC10471207 DOI: 10.1093/genetics/iyad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species.
Collapse
Affiliation(s)
- Shailja Singh
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| | - Xinyi Hu
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| |
Collapse
|
9
|
Dejima K, Imae R, Suehiro Y, Yoshida K, Mitani S. An endomembrane zinc transporter negatively regulates systemic RNAi in Caenorhabditis elegans. iScience 2023; 26:106930. [PMID: 37305693 PMCID: PMC10250833 DOI: 10.1016/j.isci.2023.106930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/18/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Double-stranded RNA (dsRNA) regulates gene expression in a sequence-dependent manner. In Caenorhabditis elegans, dsRNA spreads through the body and leads to systemic RNA silencing. Although several genes involved in systemic RNAi have been genetically identified, molecules that mediate systemic RNAi remain largely unknown. Here, we identified ZIPT-9, a C. elegans homolog of ZIP9/SLC39A9, as a broad-spectrum negative regulator of systemic RNAi. We showed that RSD-3, SID-3, and SID-5 genetically act in parallel for efficient RNAi, and that zipt-9 mutants suppress the RNAi defects of all the mutants. Analysis of a complete set of deletion mutants for SLC30 and SLC39 family genes revealed that only zipt-9 mutants showed altered RNAi activity. Based on these results and our analysis using transgenic Zn2+ reporters, we propose that ZIPT-9-dependent Zn2+ homeostasis, rather than overall cytosolic Zn2+, modulates systemic RNAi activity. Our findings reveal a previously unknown function of zinc transporters in negative RNAi regulation.
Collapse
Affiliation(s)
- Katsufumi Dejima
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Rieko Imae
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Yuji Suehiro
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Keita Yoshida
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| |
Collapse
|
10
|
Kim YJ. Crosstalk between RNA silencing and RNA quality control in plants. BMB Rep 2023; 56:321-325. [PMID: 37156633 PMCID: PMC10315563 DOI: 10.5483/bmbrep.2023-0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2024] Open
Abstract
RNAs are pivotal molecules acting as messengers of genetic information and regulatory molecules for cellular development and survival. From birth to death, RNAs face constant cellular decision for the precise control of cellular function and activity. Most eukaryotic cells employ conserved machineries for RNA decay including RNA silencing and RNA quality control (RQC). In plants, RQC monitors endogenous RNAs and degrades aberrant and dysfunctional species, whereas RNA silencing promotes RNA degradation to repress the expression of selected endogenous RNAs or exogenous RNA derived from transgenes and virus. Interestingly, emerging evidences have indicated that RQC and RNA silencing interact with each by sharing target RNAs and regulatory components. Such interaction should be tightly organized for proper cellular survival. However, it is still elusive that how each machinery specifically recognizes target RNAs. In this review, we summarize recent advances on RNA silencing and RQC pathway and discuss potential mechanisms underlying the interaction between the two machineries. [BMB Reports 2023; 56(6): 321-325].
Collapse
Affiliation(s)
- Yun Ju Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| |
Collapse
|
11
|
Mauro M, Berretta M, Palermo G, Cavalieri V, La Rocca G. The Multiplicity of Argonaute Complexes in Mammalian Cells. J Pharmacol Exp Ther 2023; 384:1-9. [PMID: 35667689 PMCID: PMC9827513 DOI: 10.1124/jpet.122.001158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
Argonautes (AGOs) are a highly conserved family of proteins found in most eukaryotes and involved in mechanisms of gene regulation, both at the transcriptional and post-transcriptional level. Among other functions, AGO proteins associate with microRNAs (miRNAs) to mediate the post-transcriptional repression of protein-coding genes. In this process, AGOs associate with members of the trinucleotide repeat containing 6 protein (TNRC6) family to form the core of the RNA-induced silencing complex (RISC), the effector machinery that mediates miRNA function. However, the description of the exact composition of the RISC has been a challenging task due to the fact the AGO's interactome is dynamically regulated in a cell type- and condition-specific manner. Here, we summarize some of the most significant studies that have identified AGO complexes in mammalian cells, as well as the approaches used to characterize them. Finally, we discuss possible opportunities to exploit what we have learned on the properties of the RISC to develop novel anti-cancer therapies. SIGNIFICANCE STATEMENT: The RNA-induced silencing complex (RISC) is the molecular machinery that mediates miRNA function in mammals. Studies over the past two decades have shed light on important biochemical and functional properties of this complex. However, many aspects of this complex await further elucidation, mostly due to technical limitations that have hindered full characterization. Here, we summarize some of the most significant studies on the mammalian RISC and discuss possible sources of biases in the approaches used to characterize it.
Collapse
Affiliation(s)
- Maurizio Mauro
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Massimiliano Berretta
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Giuseppe Palermo
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Vincenzo Cavalieri
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Gaspare La Rocca
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| |
Collapse
|
12
|
Nalavade R, Singh M. Intracellular Compartmentalization: A Key Determinant of MicroRNA Functions. Microrna 2023; 12:114-130. [PMID: 37638608 DOI: 10.2174/2211536612666230330184006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/26/2022] [Accepted: 01/19/2023] [Indexed: 08/29/2023]
Abstract
Being an integral part of the eukaryotic transcriptome, miRNAs are regarded as vital regulators of diverse developmental and physiological processes. Clearly, miRNA activity is kept in check by various regulatory mechanisms that control their biogenesis and decay pathways. With the increasing technical depth of RNA profiling technologies, novel insights have unravelled the spatial diversity exhibited by miRNAs inside a cell. Compartmentalization of miRNAs adds complexity to the regulatory circuits of miRNA expression, thereby providing superior control over the miRNA function. This review provides a bird's eye view of miRNAs expressed in different subcellular locations, thus affecting the gene regulatory pathways therein. Occurrence of miRNAs in diverse intracellular locales also reveals various unconventional roles played by miRNAs in different cellular organelles and expands the scope of miRNA functions beyond their traditionally known repressive activities.
Collapse
Affiliation(s)
- Rohit Nalavade
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Mohini Singh
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, India
| |
Collapse
|
13
|
Zhang M, Xiong F, Zhang S, Guo W, He Y. Crucial Roles of miR-625 in Human Cancer. Front Med (Lausanne) 2022; 9:845094. [PMID: 35308517 PMCID: PMC8931282 DOI: 10.3389/fmed.2022.845094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic and epigenetic characteristics are core factors of cancer. MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression at the post-transcriptional level via binding to corresponding mRNAs. Recently, increasing evidence has proven that miRNAs regulate the occurrence and development of human cancer. Here, we mainly review the abnormal expression of miR-625 in a variety of cancers. In summarizing the role and potential molecular mechanisms of miR-625 in various tumors in detail, we reveal that miR-625 is involved in a variety of biological processes, such as cell proliferation, invasion, migration, apoptosis, cell cycle regulation, and drug resistance. In addition, we discuss the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks and briefly explain the specific mechanisms of competing endogenous RNAs. In conclusion, we reveal the potential value of miR-625 in cancer diagnosis, treatment, and prognosis and hope to provide new ideas for the clinical application of miR-625.
Collapse
Affiliation(s)
- Menggang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Fei Xiong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
- *Correspondence: Wenzhi Guo
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
- Yuting He
| |
Collapse
|
14
|
Qi S, Zhang S, Islam MM, El-Sappah AH, Zhang F, Liang Y. Natural Resources Resistance to Tomato Spotted Wilt Virus (TSWV) in Tomato ( Solanum lycopersicum). Int J Mol Sci 2021; 22:ijms222010978. [PMID: 34681638 PMCID: PMC8538096 DOI: 10.3390/ijms222010978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
Tomato spotted wilt virus (TSWV) is one of the most destructive diseases affecting tomato (Solanum lycopersicum) cultivation and production worldwide. As defenses against TSWV, natural resistance genes have been identified in tomato, including Sw-1a, Sw-1b, sw-2, sw-3, sw-4, Sw-5, Sw-6, and Sw-7. However, only Sw-5 exhibits a high level of resistance to the TSWV. Thus, it has been cloned and widely used in the breeding of tomato with resistance to the disease. Due to the global spread of TSWV, resistance induced by Sw-5 decreases over time and can be overcome or broken by a high concentration of TSWV. How to utilize other resistance genes and identify novel resistance resources are key approaches for breeding tomato with resistance to TSWV. In this review, the characteristics of natural resistance genes, natural resistance resources, molecular markers for assisted selection, and methods for evaluating resistance to TSWV are summarized. The aim is to provide a theoretical basis for identifying, utilizing resistance genes, and developing tomato varieties that are resistant to TSWV.
Collapse
Affiliation(s)
- Shiming Qi
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Shijie Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Md. Monirul Islam
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Ahmed H. El-Sappah
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Fei Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Yan Liang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
- Correspondence: ; Tel.: +86-29-8708-2613
| |
Collapse
|
15
|
Tarquini G, Pagliari L, Ermacora P, Musetti R, Firrao G. Trigger and Suppression of Antiviral Defenses by Grapevine Pinot Gris Virus (GPGV): Novel Insights into Virus-Host Interaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1010-1023. [PMID: 33983824 DOI: 10.1094/mpmi-04-21-0078-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is an emerging trichovirus that has been putatively associated with a novel grapevine disease known as grapevine leaf mottling and deformation (GLMD). Yet the role of GPGV in GLMD disease is poorly understood, since it has been detected both in symptomatic and symptomless grapevines. We exploited a recently constructed GPGV infectious clone (pRI::GPGV-vir) to induce an antiviral response in Nicotiana benthamiana plants. In silico prediction of virus-derived small interfering RNAs and gene expression analyses revealed the involvement of DCL4, AGO5, and RDR6 genes during GPGV infection, suggesting the activation of the posttranscriptional gene-silencing (PTGS) pathway as a plant antiviral defense. PTGS suppression assays in transgenic N. benthamiana 16c plants revealed the ability of the GPGV coat protein to suppress RNA silencing. This work provides novel insights on the interaction between GPGV and its host, revealing the ability of the virus to trigger and suppress antiviral RNA silencing.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Laura Pagliari
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Rita Musetti
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| |
Collapse
|
16
|
Santovito D, Egea V, Bidzhekov K, Natarelli L, Mourão A, Blanchet X, Wichapong K, Aslani M, Brunßen C, Horckmans M, Hristov M, Geerlof A, Lutgens E, Daemen MJAP, Hackeng T, Ries C, Chavakis T, Morawietz H, Naumann R, von Hundelshausen P, Steffens S, Duchêne J, Megens RTA, Sattler M, Weber C. Noncanonical inhibition of caspase-3 by a nuclear microRNA confers endothelial protection by autophagy in atherosclerosis. Sci Transl Med 2021; 12:12/546/eaaz2294. [PMID: 32493793 DOI: 10.1126/scitranslmed.aaz2294] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 04/02/2020] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are versatile regulators of gene expression with profound implications for human disease including atherosclerosis, but whether they can exert posttranslational functions to control cell adaptation and whether such noncanonical features harbor pathophysiological relevance is unknown. Here, we show that miR-126-5p sustains endothelial integrity in the context of high shear stress and autophagy. Bound to argonaute-2 (Ago2), miR-126-5p forms a complex with Mex3a, which occurs on the surface of autophagic vesicles and guides its transport into the nucleus. Mutational studies and biophysical measurements demonstrate that Mex3a binds to the central U- and G-rich regions of miR-126-5p with nanomolar affinity via its two K homology domains. In the nucleus, miR-126-5p dissociates from Ago2 and binds to caspase-3 in an aptamer-like fashion with its seed sequence, preventing dimerization of the caspase and inhibiting its activity to limit apoptosis. The antiapoptotic effect of miR-126-5p outside of the RNA-induced silencing complex is important for endothelial integrity under conditions of high shear stress promoting autophagy: ablation of Mex3a or ATG5 in vivo attenuates nuclear import of miR-126-5p, aggravates endothelial apoptosis, and exacerbates atherosclerosis. In human plaques, we found reduced nuclear miR-126-5p and active caspase-3 in areas of disturbed flow. The direct inhibition of caspase-3 by nuclear miR-126-5p reveals a noncanonical mechanism by which miRNAs can modulate protein function.
Collapse
Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Virginia Egea
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Kiril Bidzhekov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - André Mourão
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Xavier Blanchet
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Coy Brunßen
- Division of Vascular Endothelium and Microcirculation, Department of Medicine III, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Michael Horckmans
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles (ULB), B-1070 Brussels, Belgium
| | - Michael Hristov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Arie Geerlof
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany.,Department of Medical Biochemistry and Pathology, Amsterdam University Medical Centers, Amsterdam School of Cardiovascular Sciences (ACS), 1081HZ Amsterdam, Netherlands
| | - Mat J A P Daemen
- Department of Medical Biochemistry and Pathology, Amsterdam University Medical Centers, Amsterdam School of Cardiovascular Sciences (ACS), 1081HZ Amsterdam, Netherlands
| | - Tilman Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Christian Ries
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Triantafyllos Chavakis
- Institute of Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Henning Morawietz
- Division of Vascular Endothelium and Microcirculation, Department of Medicine III, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Ronald Naumann
- Max-Planck-Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Philipp von Hundelshausen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Sabine Steffens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Johan Duchêne
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Michael Sattler
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands.,Munich Cluster for Systems Neurology (SyNergy), D-81377 Munich, Germany
| |
Collapse
|
17
|
Han W, Niu L, Wang L, Liu J, Li H. Downregulation of long non-coding RNA B-Raf proto-oncogene-activated non-coding RNA reverses cisplatin resistance in laryngeal squamous cell carcinoma. Arch Med Sci 2021; 17:1164-1174. [PMID: 34522245 PMCID: PMC8425235 DOI: 10.5114/aoms.2019.91352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/14/2018] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION This study was performed to explore the function of B-Raf proto-oncogene-activated non-coding RNA (BANCR) in laryngeal squamous cell carcinoma (LSCC) and cisplatin resistance. MATERIAL AND METHODS The relative expression level of long non-coding RNA (lncRNA) BANCR was examined by qRT-PCR in tumor tissues and adjacent tissues, normal laryngeal cells (Het-1A) and laryngeal squamous carcinoma cells (TU686, TU177). Cisplatin-resistant laryngeal squamous carcinoma cell lines (TU686-DDP-R, TU177-DDP-R) were established. Next, we inhibited BANCR expression by transfecting siRNA-BANCR and enhanced BANCR expression by transfecting pcDNA3.1-BANCR into TU686, TU177, TU686-DDP-R and TU177-DDP-R cells. The CCK-8 assay and clone formation assay were performed to detect colony proliferation ability and formation ability of cells. Further, to investigate through which BANCR cell viability/formation is regulated, we detected the expression of MRP1, Bcl-2, p-PKB, and Bax by western blot. RESULTS BANCR was highly expressed in laryngeal squamous carcinoma tissues and cells. Chemoresistance was generated in TU686-DDP-R and TU177-DDP-R compared with TU686 and TU177 cells after cisplatin treatment. In addition, upregulated lncRNA BANCR reduced or postponed cell sensitivity to cisplatin by enhancing cell proliferation in TU686 and TU177 cells. Meanwhile, the expression of MRP1, Bcl-2, and p-PKB was increased, while Bax was reduced. After cisplatin treatment, down-regulation of BANCR could consequently attenuate TU686-DDP-R and TU177-DDP-R cell proliferation, and the expression of MRP1, Bcl-2, and p-PKB was decreased and Bax was increased. CONCLUSIONS Down-regulation of BANCR reverses cisplatin resistance of cisplatin-resistant LSCC cell lines.
Collapse
Affiliation(s)
- Weiwei Han
- Department of Otolaryngology Head and Neck Surgery, Tianjin Union Medicine Centre, Tianjin, China
| | - Lin Niu
- Department of Otolaryngology Head and Neck Surgery, Tianjin Union Medicine Centre, Tianjin, China
| | - Lin Wang
- Department of Otolaryngology Head and Neck Surgery, Tianjin Union Medicine Centre, Tianjin, China
| | - Jixiang Liu
- Department of Otolaryngology Head and Neck Surgery, Tianjin Union Medicine Centre, Tianjin, China
| | - Huanying Li
- Department of Otolaryngology Head and Neck Surgery, Tianjin Union Medicine Centre, Tianjin, China
| |
Collapse
|
18
|
Kumar S, Gonzalez EA, Rameshwar P, Etchegaray JP. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12:E3657. [PMID: 33291485 PMCID: PMC7762117 DOI: 10.3390/cancers12123657] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that regulate gene expressions. NcRNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), circular RNAs (cRNAs) and piwi-interacting RNAs (piRNAs). This review focuses on two types of ncRNAs: microRNAs (miRNAs) or short interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs). We highlight the mechanisms by which miRNAs and lncRNAs impact the epigenome in the context of cancer. Both miRNAs and lncRNAs have the ability to interact with numerous epigenetic modifiers and transcription factors to influence gene expression. The aberrant expression of these ncRNAs is associated with the development and progression of tumors. The primary reason for their deregulated expression can be attributed to epigenetic alterations. Epigenetic alterations can cause the misregulation of ncRNAs. The experimental evidence indicated that most abnormally expressed ncRNAs impact cellular proliferation and apoptotic pathways, and such changes are cancer-dependent. In vitro and in vivo experiments show that, depending on the cancer type, either the upregulation or downregulation of ncRNAs can prevent the proliferation and progression of cancer. Therefore, a better understanding on how ncRNAs impact tumorigenesis could serve to develop new therapeutic treatments. Here, we review the involvement of ncRNAs in cancer epigenetics and highlight their use in clinical therapy.
Collapse
Affiliation(s)
- Subhasree Kumar
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Hematology/Oncology, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| |
Collapse
|
19
|
Extracellular MicroRNAs as Intercellular Mediators and Noninvasive Biomarkers of Cancer. Cancers (Basel) 2020; 12:cancers12113455. [PMID: 33233600 PMCID: PMC7699762 DOI: 10.3390/cancers12113455] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary There are an extensive number of publications regarding the role of endogenous miRNAs as regulators of gene expression in cancer. However, extracellular miRNAs have emerged as a novel mechanism of cell-to-cell communication in normal conditions and disease and have drawn a large amount of interest as regulators of gene expression and as potential non-invasive biomarkers in cancer. Despite this high interest and the abundance of research on the biology and role of extracellular miRNAs in cancer, they are not yet completely understood. The aim of this review is to highlight the relevant biological characteristics of extracellular miRNAs that enable them to function as intercellular mediators of gene expression regulation and provide the recently published evidence of the specific role of extracellular miRNAs in tumor development and progression. Abstract MicroRNAs (miRNAs) are released by different types of cells through highly regulated mechanisms under normal and pathological conditions. These extracellular miRNAs can be delivered into recipient cells for functional purposes, acting as cell-to-cell signaling mediators. It has been discovered that cancer cells release miRNAs into their surroundings, targeting normal cells or other cancer cells, presumably to promote tumor development and progression. These extracellular miRNAs are associated with oncogenic mechanisms and, because they can be quantified in blood and other bodily fluids, may be suitable noninvasive biomarkers for cancer detection. This review summarizes recent evidence of the role of extracellular miRNAs as intercellular mediators, with an emphasis on their role in the mechanisms of tumor development and progression and their potential value as biomarkers in solid tumors. It also highlights the biological characteristics of extracellular miRNAs that enable them to function as regulators of gene expression, such as biogenesis, gene silencing mechanisms, subcellular compartmentalization, and the functions and mechanisms of release.
Collapse
|
20
|
Starich TA, Bai X, Greenstein D. Gap junctions deliver malonyl-CoA from soma to germline to support embryogenesis in Caenorhabditis elegans. eLife 2020; 9:58619. [PMID: 32735213 PMCID: PMC7445009 DOI: 10.7554/elife.58619] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022] Open
Abstract
Gap junctions are ubiquitous in metazoans and play critical roles in important biological processes, including electrical conduction and development. Yet, only a few defined molecules passing through gap junction channels have been linked to specific functions. We isolated gap junction channel mutants that reduce coupling between the soma and germ cells in the Caenorhabditis elegans gonad. We provide evidence that malonyl-CoA, the rate-limiting substrate for fatty acid synthesis (FAS), is produced in the soma and delivered through gap junctions to the germline; there it is used in fatty acid synthesis to critically support embryonic development. Separation of malonyl-CoA production from its site of utilization facilitates somatic control of germline development. Additionally, we demonstrate that loss of malonyl-CoA production in the intestine negatively impacts germline development independently of FAS. Our results suggest that metabolic outsourcing of malonyl-CoA may be a strategy by which the soma communicates nutritional status to the germline.
Collapse
Affiliation(s)
- Todd A Starich
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Xiaofei Bai
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - David Greenstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| |
Collapse
|
21
|
Felaco P, Felaco M, Franceschelli S, Ferrone A, Gatta DMP, Speranza L, Patruno A, De Lutiis MA, Ballerini P, Sirolli V, Grilli A, Bonomini M, Pesce M. Erythropoietin induces miRNA-210 by JAK2/STAT5 signaling in PBMCs of End-stage Renal Disease patients. FEBS J 2020; 287:5167-5182. [PMID: 32196922 DOI: 10.1111/febs.15302] [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] [Received: 08/17/2019] [Revised: 02/03/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
Abstract
Anemia of chronic kidney disease is associated with blunted response/resistance to erythropoietin-stimulating agents (ESAs) in hemodialysis (HD) patients. Several molecules have been successfully associated with ESA responsiveness; however, none of them is now considered a valid therapeutic biomarker of erythropoietin resistance in these patients. We performed an evaluation of the level of specific plasma circulating miRNAs in blood samples of HD patients, in relation to ESA treatment, with a follow-up of 1 year (T0-T3). We found significantly lower circulating levels of all miRNAs analyzed at baseline (T0) in HD patients vs. healthy control (HC). The plasmatic levels of miRNA-210 resulted significantly and negatively associated with Erythropoietin Resistance Index (ERI), and the variance of ΔmiRNA-210 (miRNA-210T3 minus miRNA-210T0 ) explained significant percentage of ΔERI (ERIT3 minus ERIT0 ) variance. The receiver operating characteristic analysis at T0 showed that the plasmatic level of miRNA-210 could distinguish HD patients with positive or negative trend in ERI at T3. In vitro, recombinant human erythropoietin (EPO) induced significant release of miRNA-210 from cultured peripheral blood mononuclear cells, through the activation of Janus kinase 2 (JAK2)/ signal transducer and activator of transcription 5 (STAT5) signaling, but not by the activation of the MAPK protein 38α and extracellular signal-regulated kinase ½. Accordingly, HD patients with negative ΔERI showed higher level of phosphor-Janus kinase 2 and nuclear translocation of phosphor-signal transducer and activator of transcription 5. vs. patients with positive ΔERI or HC. Our data highlighted that chronic HD significantly reduces the circulating level of the miRNAs evaluated; within the targets analyzed, the miRNA-210 could be considered as a prognostic indicator of ESA responsiveness and index for anemia management.
Collapse
Affiliation(s)
- Paolo Felaco
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Mario Felaco
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Sara Franceschelli
- Department of Psychological, Health and Territorial Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Alessio Ferrone
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Daniela M P Gatta
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Lorenza Speranza
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Antonia Patruno
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Maria A De Lutiis
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Patrizia Ballerini
- Department Neurosciences, Imaging and Clinical Sciences, University G. d'Annunzio, Chieti, Italy
| | - Vittorio Sirolli
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Alfredo Grilli
- Department of Medical, Oral and Biotechnological Sciences, University G. d'Annunzio, Chieti, Italy
| | - Mario Bonomini
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| | - Mirko Pesce
- Department of Medicine and Aging Sciences, Medicine and Health Science School, University G. d'Annunzio, Chieti, Italy
| |
Collapse
|
22
|
Kloth KJ, Kormelink R. Defenses against Virus and Vector: A Phloem-Biological Perspective on RTM- and SLI1-Mediated Resistance to Potyviruses and Aphids. Viruses 2020; 12:E129. [PMID: 31979012 PMCID: PMC7077274 DOI: 10.3390/v12020129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/17/2020] [Accepted: 01/19/2020] [Indexed: 12/12/2022] Open
Abstract
Combining plant resistance against virus and vector presents an attractive approach to reduce virus transmission and virus proliferation in crops. RestrictedTobacco-etch virus Movement (RTM) genes confer resistance to potyviruses by limiting their long-distance transport. Recently, a close homologue of one of the RTM genes, SLI1, has been discovered but this gene instead confers resistance to Myzus persicae aphids, a vector of potyviruses. The functional connection between resistance to potyviruses and aphids, raises the question whether plants have a basic defense system in the phloem against biotic intruders. This paper provides an overview on restricted potyvirus phloem transport and restricted aphid phloem feeding and their possible interplay, followed by a discussion on various ways in which viruses and aphids gain access to the phloem sap. From a phloem-biological perspective, hypotheses are proposed on the underlying mechanisms of RTM- and SLI1-mediated resistance, and their possible efficacy to defend against systemic viruses and phloem-feeding vectors.
Collapse
Affiliation(s)
- Karen J. Kloth
- Laboratory of Entomology, Wageningen University and Research, 6700 AA Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research, 6700 AA Wageningen, The Netherlands;
| |
Collapse
|
23
|
Ré DA, Cambiagno DA, Arce AL, Tomassi AH, Giustozzi M, Casati P, Ariel FD, Manavella PA. CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants. MOLECULAR PLANT 2020; 13:72-87. [PMID: 31606467 DOI: 10.1016/j.molp.2019.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.
Collapse
Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Marisol Giustozzi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| |
Collapse
|
24
|
Naghizadeh S, Mansoori B, Mohammadi A, Sakhinia E, Baradaran B. Gene Silencing Strategies in Cancer Therapy: An Update for Drug Resistance. Curr Med Chem 2019; 26:6282-6303. [DOI: 10.2174/0929867325666180403141554] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/10/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
RNAi, post-transcriptional gene silencing mechanism, could be considered as one of the
most important breakthroughs and rapidly growing fields in science. Researchers are trying to use this
discovery in the treatment of various diseases and cancer is one of them although there are multiple
treatment procedures for treatment-resistant cancers, eradication of resistance remain as an unsolvable
problem yet. The current review summarizes both transcriptional and post-transcriptional gene silencing
mechanisms, and highlights mechanisms leading to drug-resistance such as, drug efflux, drug inactivation,
drug target alteration, DNA damages repair, and the epithelial-mesenchymal transition, as
well as the role of tumor cell heterogeneity and tumor microenvironment, involving genes in these
processes. It ultimately points out the obstacles of RNAi application for in vivo treatment of diseases
and progressions that have been achieved in this field.
Collapse
Affiliation(s)
- Sanaz Naghizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Sakhinia
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
25
|
Orfanidou CG, Mathioudakis MM, Katsarou K, Livieratos I, Katis N, Maliogka VI. Cucurbit chlorotic yellows virus p22 is a suppressor of local RNA silencing. Arch Virol 2019; 164:2747-2759. [PMID: 31502079 DOI: 10.1007/s00705-019-04391-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/04/2019] [Indexed: 01/20/2023]
Abstract
RNA silencing is a major antiviral mechanism in plants, which is counteracted by virus-encoded proteins with silencing suppression activity. ORFs encoding putative silencing suppressor proteins that share no structural or sequence homology have been identified in the genomes of four criniviruses. In this study, we investigated the RNA silencing suppression activity of several proteins encoded by the RNA1 (RdRp, p22) and RNA2 (CP, CPm and p26) of cucurbit chlorotic yellows virus (CCYV) using co-agroinfiltration assays on Nicotiana benthamiana plants. Our results indicate that p22 is a suppressor of local RNA silencing that does not interfere with cell-to-cell movement of the RNA silencing signal or with systemic silencing. Furthermore, comparisons of the suppression activity of CCYV p22 with that of two other well-known crinivirus suppressors (CYSDV p25 and ToCV p22) revealed that CCYV p22 is a weaker suppressor of local RNA silencing than the other two proteins. Finally, a comparative sequence analysis of the p22 genes of seven Greek CCYV isolates was performed, revealing a high level of conservation. Taken together, our research advances our knowledge about plant-virus interactions of criniviruses, an emergent group of pathogens that threatens global agriculture.
Collapse
Affiliation(s)
- Chrysoula G Orfanidou
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54 124, Thessaloniki, Greece
| | - Matthaios M Mathioudakis
- Department of Sustainable Agriculture, Mediterranean Agronomic Institute of Chania, Alsylio Agrokepio, 73100, Chania, Greece
- Institute for Olive tree, Subtropical crops and Viticulture, Plant Pathology Laboratory, Hellenic Agricultural Organization-"DEMETER", Karamanlis Ave. 167, 73134, Chania, Greece
| | | | - Ioannis Livieratos
- Department of Sustainable Agriculture, Mediterranean Agronomic Institute of Chania, Alsylio Agrokepio, 73100, Chania, Greece
| | - Nikolaos Katis
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54 124, Thessaloniki, Greece
| | - Varvara I Maliogka
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54 124, Thessaloniki, Greece.
| |
Collapse
|
26
|
The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1. Proc Natl Acad Sci U S A 2019; 116:22872-22883. [PMID: 31628252 PMCID: PMC6842623 DOI: 10.1073/pnas.1912222116] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The viral suppressor of RNA silencing P0 is known to target plant antiviral ARGONAUTE (AGO) proteins for degradation via an autophagy-related process. Here we utilized P0 to gain insight into the cellular degradation dynamics of AGO1, the major plant effector of RNA silencing. We revealed that P0 targets endoplasmic reticulum (ER)-associated AGO1 by inducing the formation of ER-related bodies that are delivered to the vacuole with both P0 and AGO1 as cargos. This process involves ATG8-interacting proteins 1 and 2 (ATI1 and ATI2) that interact with AGO1 and negatively regulate its transgene-silencing activity. Together, our results reveal a layer of ER-bound AGO1 posttranslational regulation that is manipulated by P0 to subvert plant antiviral defense. RNA silencing is a major antiviral defense mechanism in plants and invertebrates. Plant ARGONAUTE1 (AGO1) is pivotal in RNA silencing, and hence is a major target for counteracting viral suppressors of RNA-silencing proteins (VSRs). P0 from Turnip yellows virus (TuYV) is a VSR that was previously shown to trigger AGO1 degradation via an autophagy-like process. However, the identity of host proteins involved and the cellular site at which AGO1 and P0 interact were unknown. Here we report that P0 and AGO1 associate on the endoplasmic reticulum (ER), resulting in their loading into ER-associated vesicles that are mobilized to the vacuole in an ATG5- and ATG7-dependent manner. We further identified ATG8-Interacting proteins 1 and 2 (ATI1 and ATI2) as proteins that associate with P0 and interact with AGO1 on the ER up to the vacuole. Notably, ATI1 and ATI2 belong to an endogenous degradation pathway of ER-associated AGO1 that is significantly induced following P0 expression. Accordingly, ATI1 and ATI2 deficiency causes a significant increase in posttranscriptional gene silencing (PTGS) activity. Collectively, we identify ATI1 and ATI2 as components of an ER-associated AGO1 turnover and proper PTGS maintenance and further show how the VSR P0 manipulates this pathway.
Collapse
|
27
|
Rossi NF, Zenner Z, Rishi AK, Levi E, Maliszewska-Scislo M. AT 1 receptors in the subfornical organ modulate arterial pressure and the baroreflex in two-kidney, one-clip hypertensive rats. Am J Physiol Regul Integr Comp Physiol 2019; 316:R172-R185. [PMID: 30624974 DOI: 10.1152/ajpregu.00289.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The subfornical organ (SFO), a forebrain circumventricular organ that lies outside the blood-brain barrier, has been implicated in arterial pressure and baroreflex responses to angiotensin II (ANG II). We tested whether pharmacological inhibition or selective silencing of SFO ANG II type 1 receptors (AT1R) of two-kidney, one-clip rats with elevated plasma ANG II decreases resting arterial pressure and renal sympathetic nerve activity (RSNA) and/or modulates arterial baroreflex responses of heart rate (HR) and RSNA. Male Sprague-Dawley rats underwent renal artery clipping [2-kidney, 1-clip (2K,1C)] or sham clipping (sham). After 6 wk, conscious rats instrumented with vascular catheters, renal nerve electrodes, and a cannula directed to the SFO were studied. In another set of experiments, rats were instrumented with hemodynamic and nerve radio transmitters and injected with scrambled RNA or silencing RNA targeted against AT1R. Mean arterial pressure (MAP) was significantly higher in 2K,1C rats. Acute SFO injection with the AT1R inhibitor losartan did not change MAP in sham or 2K,1C rats. Baroreflex curves of HR and RSNA were shifted rightward in 2K,1C rats. Losartan exerted no effect. SFO AT1R knockdown did not influence MAP in sham rats but decreased MAP in 2K,1C rats, despite no change in plasma ANG II or resting RSNA. AT1R knockdown prevented the reduction in maximum gain and slope of baroreflex responses of HR and RSNA; the reduced RSNA response to baroreceptor unloading was partially restored in 2K,1C rats. These findings show that AT1R activation within the SFO contributes to hypertension and baroreflex dysfunction in 2K,1C rats and highlight the temporal requirement for reversal of these effects.
Collapse
Affiliation(s)
- Noreen F Rossi
- Departments of Internal Medicine and Physiology, Wayne State University School of Medicine , Detroit, Michigan.,John D. Dingell Veterans Administration Medical Center , Detroit, Michigan
| | - Zachary Zenner
- Departments of Internal Medicine and Physiology, Wayne State University School of Medicine , Detroit, Michigan
| | - Arun K Rishi
- Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan.,John D. Dingell Veterans Administration Medical Center , Detroit, Michigan
| | - Edi Levi
- Department of Pathology, Wayne State University School of Medicine , Detroit, Michigan.,John D. Dingell Veterans Administration Medical Center , Detroit, Michigan
| | - Maria Maliszewska-Scislo
- Departments of Internal Medicine and Physiology, Wayne State University School of Medicine , Detroit, Michigan
| |
Collapse
|
28
|
Trabucchi M, Mategot R. Subcellular Heterogeneity of the microRNA Machinery. Trends Genet 2018; 35:15-28. [PMID: 30503571 DOI: 10.1016/j.tig.2018.10.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/20/2018] [Accepted: 10/26/2018] [Indexed: 01/09/2023]
Abstract
Different methods have recently been developed to understand the subcellular localization and role of microRNAs (miRNAs) as well as small RNAs associated with Argonaute (AGO) proteins. The heterogeneity of the protein complexes associated with miRNAs, along with their subcellular localization, provides clues into their biochemical mechanism of function. Subcellular diversity indicates that miRNAs localized to different cellular regions could have different functions, including transcriptional regulation on chromatin or post-transcriptional control, providing global regulation of gene expression by miRNAs. Herein, I review the current knowledge and most recent discoveries relating to the subcellular function of miRNAs and other AGO-associated small RNAs, revealing the emergence of a multitude of functions of the miRNA pathway to control different steps of the gene expression program(s).
Collapse
Affiliation(s)
- Michele Trabucchi
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France.
| | - Raphael Mategot
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France
| |
Collapse
|
29
|
Liu L, Chen X. Intercellular and systemic trafficking of RNAs in plants. NATURE PLANTS 2018; 4:869-878. [PMID: 30390090 PMCID: PMC7155933 DOI: 10.1038/s41477-018-0288-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/21/2018] [Indexed: 05/14/2023]
Abstract
Plants have evolved dynamic and complex networks of cell-to-cell communication to coordinate and adapt their growth and development to a variety of environmental changes. In addition to small molecules, such as metabolites and phytohormones, macromolecules such as proteins and RNAs also act as signalling agents in plants. As information molecules, RNAs can move locally between cells through plasmodesmata, and over long distances through phloem. Non-cell-autonomous RNAs may act as mobile signals to regulate plant development, nutrient allocation, gene silencing, antiviral defence, stress responses and many other physiological processes in plants. Recent work has shed light on mobile RNAs and, in some cases, uncovered their roles in intercellular and systemic signalling networks. This review summarizes the current knowledge of local and systemic RNA movement, and discusses the potential regulatory mechanisms and biological significance of RNA trafficking in plants.
Collapse
Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| |
Collapse
|
30
|
Akgül B, Erdoğan İ. Intracytoplasmic Re-localization of miRISC Complexes. Front Genet 2018; 9:403. [PMID: 30298086 PMCID: PMC6160738 DOI: 10.3389/fgene.2018.00403] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/03/2018] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are a conserved class of non-coding RNAs of 22 nucleotides that post-transcriptionally regulate gene expression through translational repression and/or mRNA degradation. A great progress has been made regarding miRNA biogenesis and miRNA-mediated gene regulation. Additionally, an ample amount of information exists with respect to the regulation of miRNAs. However, the cytoplasmic localization of miRNAs and its effect on gene regulatory output is still in progress. We provide a current review of the cytoplasmic miRNA localization in metazoans. We then discuss the dynamic changes in the intracytoplasmic localization of miRNAs as a means to regulate their silencing activity. We then conclude our discussion with the potential molecules that could modulate miRNA localization.
Collapse
Affiliation(s)
- Bünyamin Akgül
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, İzmir Institute of Technology, Urla, Turkey
| | - İpek Erdoğan
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, İzmir Institute of Technology, Urla, Turkey
| |
Collapse
|
31
|
Naydenov NG, Joshi S, Feygin A, Saini S, Litovchick L, Ivanov AI. A membrane fusion protein, Ykt6, regulates epithelial cell migration via microRNA-mediated suppression of Junctional Adhesion Molecule A. Cell Cycle 2018; 17:1812-1831. [PMID: 30010460 DOI: 10.1080/15384101.2018.1496755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Vesicle trafficking regulates epithelial cell migration by remodeling matrix adhesions and delivering signaling molecules to the migrating leading edge. Membrane fusion, which is driven by soluble N-ethylmaleimide-sensitive factor associated receptor (SNARE) proteins, is an essential step of vesicle trafficking. Mammalian SNAREs represent a large group of proteins, but few have been implicated in the regulation of cell migration. Ykt6 is a unique SNARE existing in equilibrium between active membrane-bound and inactive cytoplasmic pools, and mediating vesicle trafficking between different intracellular compartments. The biological functions of this protein remain poorly understood. In the present study, we found that Ykt6 acts as a negative regulator of migration and invasion of human prostate epithelial cells. Furthermore, Ykt6 regulates the integrity of epithelial adherens and tight junctions. The observed anti-migratory activity of Ykt6 is mediated by a unique mechanism involving the expressional upregulation of microRNA 145, which selectively decreases the cellular level of Junctional Adhesion Molecule (JAM) A. This decreased JAM-A expression limits the activity of Rap1 and Rac1 small GTPases, thereby attenuating cell spreading and motility. The described novel functions of Ykt6 could be essential for the regulation of epithelial barriers, epithelial repair, and metastatic dissemination of cancer cells.
Collapse
Affiliation(s)
- Nayden G Naydenov
- a Department of Inflammation and Immunity , Lerner Research Institute of Cleveland Clinic Foundation , Cleveland , OH , USA.,b Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , VA , USA
| | - Supriya Joshi
- b Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , VA , USA
| | - Alex Feygin
- b Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , VA , USA
| | - Siddharth Saini
- c Department of Internal Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Larisa Litovchick
- c Department of Internal Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Andrei I Ivanov
- a Department of Inflammation and Immunity , Lerner Research Institute of Cleveland Clinic Foundation , Cleveland , OH , USA.,b Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , VA , USA
| |
Collapse
|
32
|
Silver J, Wadley G, Lamon S. Mitochondrial regulation in skeletal muscle: A role for non‐coding RNAs? Exp Physiol 2018; 103:1132-1144. [PMID: 29885080 DOI: 10.1113/ep086846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Jessica Silver
- Institute for Physical Activity and Nutrition (IPAN) Deakin University Geelong Victoria Australia
| | - Glenn Wadley
- Institute for Physical Activity and Nutrition (IPAN) Deakin University Geelong Victoria Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition (IPAN) Deakin University Geelong Victoria Australia
| |
Collapse
|
33
|
Zeng Z, Huang B, Huang S, Zhang R, Yan S, Yu X, Shu Y, Zhao C, Lei J, Zhang W, Yang C, Wu K, Wu Y, An L, Ji X, Gong C, Yuan C, Zhang L, Liu W, Feng Y, Zhang B, Dai Z, Shen Y, Wang X, Luo W, Haydon RC, Luu HH, Zhou L, Reid RR, He TC, Wu X. The development of a sensitive fluorescent protein-based transcript reporter for high throughput screening of negative modulators of lncRNAs. Genes Dis 2018; 5:62-74. [PMID: 30159383 PMCID: PMC6110536 DOI: 10.1016/j.gendis.2018.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
While the human genome is pervasively transcribed, <2% of the human genome is transcribed into protein-coding mRNAs, leaving most of the transcripts as noncoding RNAs, such as microRNAs and long-noncoding RNAs (lncRNAs), which are critical components of epigenetic regulation. lncRNAs are emerging as critical regulators of gene expression and genomic stability. However, it remains largely unknown about how lncRNAs are regulated. Here, we develop a highly sensitive and dynamic reporter that allows us to identify and/or monitor negative modulators of lncRNA transcript levels in a high throughput fashion. Specifically, we engineer a fluorescent fusion protein by fusing three copies of the PEST destruction domain of mouse ornithine decarboxylase (MODC) to the C-terminal end of the codon-optimized bilirubin-inducible fluorescent protein, designated as dBiFP, and show that the dBiFP protein is highly destabilized, compared with the commonly-used eGFP protein. We further demonstrate that the dBiFP signal is effectively down-regulated when the dBiFP and mouse lncRNA H19 chimeric transcript is silenced by mouse H19-specific siRNAs. Therefore, our results strongly suggest that the dBiFP fusion protein may serve as a sensitive and dynamic transcript reporter to monitor the inhibition of lncRNAs by microRNAs, synthetic regulatory RNA molecules, RNA binding proteins, and/or small molecule inhibitors so that novel and efficacious inhibitors targeting the epigenetic circuit can be discovered to treat human diseases such as cancer and other chronic disorders.
Collapse
Affiliation(s)
- Zongyue Zeng
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bo Huang
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Clinical Laboratory Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang 330031, China
| | - Shifeng Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ruyi Zhang
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Shujuan Yan
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Xinyi Yu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yi Shu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,The Children's Hospital, Chongqing Medical University, Chongqing 400014, China
| | - Chen Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jiayan Lei
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Wenwen Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Laboratory Medicine and Clinical Diagnostics, the Affiliated Yantai Hospital, Binzhou Medical University, Yantai 264100, China
| | - Chao Yang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,The Children's Hospital, Chongqing Medical University, Chongqing 400014, China
| | - Ke Wu
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Ying Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Immunology and Microbiology, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Liping An
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Key Laboratory of Orthopaedic Surgery of Gansu Province and the Department of Orthopaedic Surgery, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Xiaojuan Ji
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,The Children's Hospital, Chongqing Medical University, Chongqing 400014, China
| | - Cheng Gong
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Surgery, the Affiliated Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Chengfu Yuan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, China Three Gorges University School of Medicine, Yichang 443002, China
| | - Linghuan Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,The Children's Hospital, Chongqing Medical University, Chongqing 400014, China
| | - Wei Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yixiao Feng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Bo Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Key Laboratory of Orthopaedic Surgery of Gansu Province and the Department of Orthopaedic Surgery, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Zhengyu Dai
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Orthopaedic Surgery, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, China
| | - Yi Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Orthopaedic Surgery, Xiangya Second Hospital of Central South University, Changsha 410011, China
| | - Xi Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Wenping Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, and the Affiliated Hospital of Stomatology of Chongqing Medical University, Chongqing 401147, China
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lan Zhou
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Department of Surgery, Laboratory of Craniofacial Biology and Development, Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Xingye Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.,Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| |
Collapse
|
34
|
Poque S, Wu HW, Huang CH, Cheng HW, Hu WC, Yang JY, Wang D, Yeh SD. Potyviral Gene-Silencing Suppressor HCPro Interacts with Salicylic Acid (SA)-Binding Protein 3 to Weaken SA-Mediated Defense Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:86-100. [PMID: 29090655 DOI: 10.1094/mpmi-06-17-0128-fi] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The viral infection process is a battle between host defense response and pathogen antagonizing action. Several studies have established a tight link between the viral RNA silencing suppressor (RSS) and the repression of salicylic acid (SA)-mediated defense responses, nonetheless host factors directly linking an RSS and the SA pathway remains unidentified. From yeast two-hybrid analysis, we identified an interaction between the potyviral RSS helper-component proteinase (HCPro) and SA-binding protein SABP3. Co-localization and bimolecular fluorescence complementation analyses validated the direct in vivo interaction between Turnip mosaic virus (TuMV) HCPro and the Arabidopsis homologue of SABP3, AtCA1. Additionally, transient expression of TuMV HCPro demonstrated its ability to act as a negative regulator of AtCA1. When the plants of the AtCA1 knockout mutant line were inoculated with TuMV, our results indicated that AtCA1 is essential to restrict viral spreading and accumulation, induce SA accumulation, and trigger the SA pathway. Unexpectedly, the AtCA1 overexpression line also displayed a similar phenotype, suggesting that the constitutive expression of AtCA1 antagonizes the SA pathway. Taken together, our results depict AtCA1 as an essential regulator of SA defense responses. Moreover, the interaction of potyviral HCPro with this regulator compromises the SA pathway to weaken host defense responses and facilitate viral infection.
Collapse
Affiliation(s)
- Sylvain Poque
- 1 Department of Plant Pathology, National Chung-Hsing University, Taichung City 40227, Taiwan, R.O.C
| | - Hui-Wen Wu
- 2 Agricultural Biotechnology Center, National Chung-Hsing University
| | - Chung-Hao Huang
- 1 Department of Plant Pathology, National Chung-Hsing University, Taichung City 40227, Taiwan, R.O.C
| | - Hao-Wen Cheng
- 3 NCHU-UCD Plant and Food Biotechnology Center, National Chung-Hsing University
| | - Wen-Chi Hu
- 3 NCHU-UCD Plant and Food Biotechnology Center, National Chung-Hsing University
| | - Jun-Yi Yang
- 4 Institute of Biochemistry, National Chung-Hsing University; and
| | - David Wang
- 5 Department of Forestry, National Chung-Hsing University
| | - Shyi-Dong Yeh
- 1 Department of Plant Pathology, National Chung-Hsing University, Taichung City 40227, Taiwan, R.O.C
- 2 Agricultural Biotechnology Center, National Chung-Hsing University
- 3 NCHU-UCD Plant and Food Biotechnology Center, National Chung-Hsing University
| |
Collapse
|
35
|
McAlinden A, Im GI. MicroRNAs in orthopaedic research: Disease associations, potential therapeutic applications, and perspectives. J Orthop Res 2018; 36:33-51. [PMID: 29194736 PMCID: PMC5840038 DOI: 10.1002/jor.23822] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/27/2017] [Indexed: 02/04/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function to control many cellular processes by their ability to suppress expression of specific target genes. Tens to hundreds of target genes may be affected by one miRNA, thereby resulting in modulation of multiple pathways in any given cell type. Therefore, altered expression of miRNAs (i.e., during tissue development or in scenarios of disease or cellular stress) can have a profound impact on processes regulating cell differentiation, metabolism, proliferation, or apoptosis, for example. Over the past 5-10 years, thousands of reports have been published on miRNAs in cartilage and bone biology or disease, thus highlighting the significance of these non-coding RNAs in regulating skeletal development and homeostasis. For the purpose of this review, we will focus on miRNAs or miRNA families that have demonstrated function in vivo within the context of cartilage, bone or other orthopaedic-related tissues (excluding muscle). Specifically, we will discuss studies that have utilized miRNA transgenic mouse models or in vivo approaches to target a miRNA with the aim of altering conditions such as osteoarthritis, osteoporosis and bone fractures in rodents. We will not discuss miRNAs in the context skeletal cancers since this topic is worthy of a review of its own. Overall, we aim to provide a comprehensive description of where the field currently stands with respect to the therapeutic potential of specific miRNAs to treat orthopaedic conditions and current technologies to target and modify miRNA function in vivo. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:33-51, 2018.
Collapse
Affiliation(s)
- Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110
| | - Gun-Il Im
- Department of Orthopaedic Surgery, Dongguk University Ilsan Hospital, 814 Siksa-Dong, Goyang, Korea
| |
Collapse
|
36
|
Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH. The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One 2017; 12:e0189788. [PMID: 29244865 PMCID: PMC5731758 DOI: 10.1371/journal.pone.0189788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/03/2017] [Indexed: 11/26/2022] Open
Abstract
In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.
Collapse
Affiliation(s)
- Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dasuni Jayaweera
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| |
Collapse
|
37
|
Mongelli V, Saleh MC. Bugs Are Not to Be Silenced: Small RNA Pathways and Antiviral Responses in Insects. Annu Rev Virol 2017; 3:573-589. [PMID: 27741406 DOI: 10.1146/annurev-virology-110615-042447] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Like every other organism on Earth, insects are infected with viruses, and they rely on RNA interference (RNAi) mechanisms to circumvent viral infections. A remarkable characteristic of RNAi is that it is both broadly acting, because it is triggered by double-stranded RNA molecules derived from virtually any virus, and extremely specific, because it targets only the particular viral sequence that initiated the process. Reviews covering the different facets of the RNAi antiviral immune response in insects have been published elsewhere. In this review, we build a framework to guide future investigation. We focus on the remaining questions and avenues of research that need to be addressed to move the field forward, including issues such as the activity of viral suppressors of RNAi, comparative genomics, the development of detailed maps of the subcellular localization of viral replication complexes with the RNAi machinery, and the regulation of the antiviral RNAi response.
Collapse
Affiliation(s)
- Vanesa Mongelli
- Viruses and RNA Interference Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France;
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France;
| |
Collapse
|
38
|
Khan NM, Haqqi TM. Epigenetics in osteoarthritis: Potential of HDAC inhibitors as therapeutics. Pharmacol Res 2017; 128:73-79. [PMID: 28827187 DOI: 10.1016/j.phrs.2017.08.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/09/2017] [Accepted: 08/12/2017] [Indexed: 12/19/2022]
Abstract
Osteoarthritis (OA) is the most common joint disease and the leading cause of chronic disability in middle-aged and older populations worldwide. The development of disease modifying therapy for OA is in its infancy largely because the regulatory mechanisms for the molecular effectors of OA pathogenesis are poorly understood. Recent studies identified epigenetic events as a critical regulator of molecular players involved in the induction and development of OA. Epigenetic mechanisms include DNA methylation, non-coding RNA and histone modifications. The aim of this review is to briefly highlight the recent advances in the epigenetics of cartilage and potential of HDACs (Histone deacetylases) inhibitors in the therapeutic management of OA. We summarize the recent studies utilizing HDAC inhibitors as potential therapeutics for inhibiting disease progression and preventing the cartilage destruction in OA. HDACs control normal cartilage development and homeostasis and understanding the impact of HDACs inhibitors on the disease pathogenesis is of interest because of its importance in affecting overall cartilage health and homeostasis. These findings also shed new light on cartilage disease pathophysiology and provide substantial evidence that HDACs may be potential novel therapeutic targets in OA.
Collapse
Affiliation(s)
- Nazir M Khan
- Department of Anatomy & Neurobiology, Northeast Ohio Medical University, 4209 St Rt 44, Rootstown, OH 44272, USA
| | - Tariq M Haqqi
- Department of Anatomy & Neurobiology, Northeast Ohio Medical University, 4209 St Rt 44, Rootstown, OH 44272, USA.
| |
Collapse
|
39
|
Ziebell H, MacDiarmid R. Prospects for engineering and improvement of cross-protective virus strains. Curr Opin Virol 2017; 26:8-14. [PMID: 28743041 DOI: 10.1016/j.coviro.2017.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/21/2017] [Indexed: 11/17/2022]
Abstract
Mild strain cross-protection is currently an important method for the production of high quality plant products; despite challenge from severe virus isolates the initial protecting strain precludes symptom development. The mechanism of cross-protection is not yet resolved as RNA silencing does not sufficiently explain the phenomenon. Six requirements have been put forward to ensure long-lasting protection. We propose two additional requirements for effective and durable mild strain cross-protection; mild strains based on knowledge of the mechanism and consideration of impacts to consumers. Future research on predicting phenotype from genotype and understanding virus-plant and virus-vector interactions will enable improvement of cross-protective strains. Shared international databases of whole ecosystem interactions across a wide range of virus patho- and symbiotic-systems will form the basis for making step-change advances towards our collective ability to engineer and improve mild strain cross-protection.
Collapse
Affiliation(s)
- Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Messeweg 11-12, 38104 Braunschweig, Germany.
| | - Robin MacDiarmid
- New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, New Zealand
| |
Collapse
|
40
|
Chakrabarty Y, Bhattacharyya SN. Leishmania donovani restricts mitochondrial dynamics to enhance miRNP stability and target RNA repression in host macrophages. Mol Biol Cell 2017; 28:2091-2105. [PMID: 28539410 PMCID: PMC5509422 DOI: 10.1091/mbc.e16-06-0388] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs), the tiny regulatory RNAs, form complexes with Argonaute (Ago) proteins and inhibit gene expression in metazoan cells. While studying parasite-invaded macrophages, we identify a unique mode of gene regulation in which the parasite Leishmania donovani (Ld) causes mitochondrial depolarization, reduces mitochondrial dynamics, and restricts turnover of cellular microRNA ribonucleoprotein (miRNP) complexes in infected host cells. This leads to increased stability of miRNPs along with elevated levels of Ago2-bound cytokine mRNA in Ld-infected macrophages. Thus the increase of miRNP stability in Ld-infected cells curtails production of proinflammatory cytokines, which are otherwise detrimental for survival of the parasite within the infected macrophages. Loss of mitochondrial membrane potential is accompanied by reduced juxtaposition of endoplasmic reticulum (ER) and mitochondria as well as endosomes. This is likely coupled with enhanced sequestration and stabilization of ER- associated miRNPs observed in infected macrophage cells. Mitofusin 2 (Mfn2), a membrane protein implicated in ER-mitochondria tethering, also shows reduced expression in Ld-infected cells. A mitochondrial role in Ld-induced alteration of miRNA activity and stability is further corroborated by impaired compartmentalization and stabilization of miRNP components in Mfn2-depleted mammalian cells.
Collapse
Affiliation(s)
- Yogaditya Chakrabarty
- RNA Biology Research Laboratories, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Suvendra N Bhattacharyya
- RNA Biology Research Laboratories, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| |
Collapse
|
41
|
Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes. Nat Commun 2017; 8:15690. [PMID: 28585547 PMCID: PMC5467174 DOI: 10.1038/ncomms15690] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/19/2017] [Indexed: 02/06/2023] Open
Abstract
Understanding the function of the thousands of cellular proteins is a central question in molecular cell biology. As proteins are typically part of multiple dynamic and often overlapping macromolecular complexes exerting distinct functions, the identification of protein–protein interactions (PPI) and their assignment to specific complexes is a crucial but challenging task. We present a protein fragments complementation assay integrated with the proximity-dependent biotinylation technique BioID. Activated on the interaction of two proteins, split-BioID is a conditional proteomics approach that allows in a single and simple assay to both experimentally validate binary PPI and to unbiasedly identify additional interacting factors. Applying our method to the miRNA-mediated silencing pathway, we can probe the proteomes of two distinct functional complexes containing the Ago2 protein and uncover the protein GIGYF2 as a regulator of miRNA-mediated translation repression. Hence, we provide a novel tool to study dynamic spatiotemporally defined protein complexes in their native cellular environment. The BioID approaches takes advantage of the promiscuous biotinylation enzyme (BirA*) to identify proteins that closely interact. Here the authors improve the resolution of BioID using a protein fragment complementation approach that allows the assignment of protein-protein interactions to specific complexes within a common interactome.
Collapse
|
42
|
Donlin-Asp PG, Rossoll W, Bassell GJ. Spatially and temporally regulating translation via mRNA-binding proteins in cellular and neuronal function. FEBS Lett 2017; 591:1508-1525. [PMID: 28295262 DOI: 10.1002/1873-3468.12621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/20/2022]
Abstract
Coordinated regulation of mRNA localization and local translation are essential steps in cellular asymmetry and function. It is increasingly evident that mRNA-binding proteins play critical functions in controlling the fate of mRNA, including when and where translation occurs. In this review, we discuss the robust and complex roles that mRNA-binding proteins play in the regulation of local translation that impact cellular function in vertebrates. First, we discuss the role of local translation in cellular polarity and possible links to vertebrate development and patterning. Next, we discuss the expanding role for local protein synthesis in neuronal development and function, with special focus on how a number of neurological diseases have given us insight into the importance of translational regulation. Finally, we discuss the ever-increasing set of tools to study regulated translation and how these tools will be vital in pushing forward and addressing the outstanding questions in the field.
Collapse
Affiliation(s)
- Paul G Donlin-Asp
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Wilfried Rossoll
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
43
|
Bradford BJ, Cooper CA, Tizard ML, Doran TJ, Hinton TM. RNA interference-based technology: what role in animal agriculture? ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15437] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animal agriculture faces a broad array of challenges, ranging from disease threats to adverse environmental conditions, while attempting to increase productivity using fewer resources. RNA interference (RNAi) is a biological phenomenon with the potential to provide novel solutions to some of these challenges. Discovered just 20 years ago, the mechanisms underlying RNAi are now well described in plants and animals. Intracellular double-stranded RNA triggers a conserved response that leads to cleavage and degradation of complementary mRNA strands, thereby preventing production of the corresponding protein product. RNAi can be naturally induced by expression of endogenous microRNA, which are critical in the regulation of protein synthesis, providing a mechanism for rapid adaptation of physiological function. This endogenous pathway can be co-opted for targeted RNAi either through delivery of exogenous small interfering RNA (siRNA) into target cells or by transgenic expression of short hairpin RNA (shRNA). Potentially valuable RNAi targets for livestock include endogenous genes such as developmental regulators, transcripts involved in adaptations to new physiological states, immune response mediators, and also exogenous genes such as those encoded by viruses. RNAi approaches have shown promise in cell culture and rodent models as well as some livestock studies, but technical and market barriers still need to be addressed before commercial applications of RNAi in animal agriculture can be realised. Key challenges for exogenous delivery of siRNA include appropriate formulation for physical delivery, internal transport and eventual cellular uptake of the siRNA; additionally, rigorous safety and residue studies in target species will be necessary for siRNA delivery nanoparticles currently under evaluation. However, genomic incorporation of shRNA can overcome these issues, but optimal promoters to drive shRNA expression are needed, and genetic engineering may attract more resistance from consumers than the use of exogenous siRNA. Despite these hurdles, the convergence of greater understanding of RNAi mechanisms, detailed descriptions of regulatory processes in animal development and disease, and breakthroughs in synthetic chemistry and genome engineering has created exciting possibilities for using RNAi to enhance the sustainability of animal agriculture.
Collapse
|
44
|
Achkar NP, Cambiagno DA, Manavella PA. miRNA Biogenesis: A Dynamic Pathway. TRENDS IN PLANT SCIENCE 2016; 21:1034-1044. [PMID: 27793495 DOI: 10.1016/j.tplants.2016.09.003] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) modulate plant homeostasis through the inactivation of specific mRNAs, especially those encoding transcription factors. A delicate spatial/temporal balance between a miRNA and its targets is central to achieving the appropriate biological outcomes. In this review we discuss our growing understanding of the dynamic regulation of miRNA biogenesis. We put special emphasis on crosstalk between miRNA biogenesis and other cellular processes such as transcription and splicing. We also discuss how the pathway is regulated in specific tissues to achieve harmonious plant development through a subtle balance between gene expression and silencing.
Collapse
Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Damián A Cambiagno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina.
| |
Collapse
|
45
|
Guay C, Regazzi R. New emerging tasks for microRNAs in the control of β-cell activities. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:2121-2129. [DOI: 10.1016/j.bbalip.2016.05.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/22/2016] [Accepted: 05/02/2016] [Indexed: 12/26/2022]
|
46
|
Brosseau C, El Oirdi M, Adurogbangba A, Ma X, Moffett P. Antiviral Defense Involves AGO4 in an Arabidopsis-Potexvirus Interaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:878-888. [PMID: 27762650 DOI: 10.1094/mpmi-09-16-0188-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In plants, RNA silencing regulates gene expression through the action of Dicer-like (DCL) and Argonaute (AGO) proteins via micro RNAs and RNA-dependent DNA methylation (RdDM). In addition, RNA silencing functions as an antiviral defense mechanism by targeting virus-derived double-stranded RNA. Plants encode multiple AGO proteins with specialized functions, including AGO4-like proteins that affect RdDM and AGO2, AGO5, and AGO1, which have antiviral activities. Here, we show that AGO4 is also required for defense against the potexvirus Plantago asiatica mosaic virus (PlAMV), most likely independent of RdDM components such as DCL3, Pol IV, and Pol V. Transient assays showed that AGO4 has direct antiviral activity on PlAMV and, unlike RdDM, this activity does not require nuclear localization of AGO4. Furthermore, although PlAMV infection causes a decrease in AGO4 expression, PlAMV causes a change in AGO4 localization from a largely nuclear to a largely cytoplasmic distribution. These results indicate an important role for AGO4 in targeting plant RNA viruses as well as demonstrating novel mechanisms of regulation of and by AGO4, independent of its canonical role in regulating gene expression by RdDM.
Collapse
Affiliation(s)
- Chantal Brosseau
- 1 Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Mohamed El Oirdi
- 1 Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
- 2 Current address: Department of Biology, PYD, King Faisal University, Al Hasa, Kingdom of Saudi Arabia; and
| | - Ayooluwa Adurogbangba
- 1 Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Xiaofang Ma
- 1 Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
- 3 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Peter Moffett
- 1 Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| |
Collapse
|
47
|
Abstract
Understanding the molecular mechanisms behind the capacity of cancer cells to adapt to the tumor microenvironment and to anticancer therapies is a major challenge. In this context, cancer is believed to be an evolutionary process where random mutations and the selection process shape the mutational pattern and phenotype of cancer cells. This article challenges the notion of randomness of some cancer-associated mutations by describing molecular mechanisms involving stress-mediated biogenesis of mRNA-derived small RNAs able to target and increase the local mutation rate of the genomic loci they originate from. It is proposed that the probability of some mutations at specific loci could be increased in a stress-specific and RNA-depending manner. This would increase the probability of generating mutations that could alleviate stress situations, such as those triggered by anticancer drugs. Such a mechanism is made possible because tumor- and anticancer drug-associated stress situations trigger both cellular reprogramming and inflammation, which leads cancer cells to express molecular tools allowing them to “attack” and mutate their own genome in an RNA-directed manner.
Collapse
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
| |
Collapse
|
48
|
Abstract
Micro ribonucleic acid (microRNA) regulation and expression has become an emerging field in determining the mechanisms regulating a variety of inflammation-mediated diseases. Several studies have focused on specific microRNAs that are differentially expressed in cases of osteoarthritis. Furthermore, several targets of these miRNAs important in disease progression have also been identified. In this review, we focus on microRNA biogenesis, regulation, detection, and quantification with an emphasis on cellular localization and how these concepts may be linked to disease processes such as osteoarthritis. Next, we review the relationships of specific microRNAs to certain features and risk factors associated with osteoarthritis such as inflammation, obesity, autophagy, and cartilage homeostasis. We also identify certain microRNAs that are differentially expressed in osteoarthritis but have unidentified targets and functions in the disease state. Lastly, we identify the potential use of microRNAs for therapeutic purposes and also mention certain remedies that regulate microRNA expression.
Collapse
Affiliation(s)
- Gregory R Sondag
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University (NEOMED), 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Tariq M Haqqi
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University (NEOMED), 4209 State Route 44, Rootstown, OH, 44272, USA.
| |
Collapse
|
49
|
Hedil M, Kormelink R. Viral RNA Silencing Suppression: The Enigma of Bunyavirus NSs Proteins. Viruses 2016; 8:v8070208. [PMID: 27455310 PMCID: PMC4974542 DOI: 10.3390/v8070208] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
The Bunyaviridae is a family of arboviruses including both plant- and vertebrate-infecting representatives. The Tospovirus genus accommodates plant-infecting bunyaviruses, which not only replicate in their plant host, but also in their insect thrips vector during persistent propagative transmission. For this reason, they are generally assumed to encounter antiviral RNA silencing in plants and insects. Here we present an overview on how tospovirus nonstructural NSs protein counteracts antiviral RNA silencing in plants and what is known so far in insects. Like tospoviruses, members of the related vertebrate-infecting bunyaviruses classified in the genera Orthobunyavirus, Hantavirus and Phlebovirus also code for a NSs protein. However, for none of them RNA silencing suppressor activity has been unambiguously demonstrated in neither vertebrate host nor arthropod vector. The second part of this review will briefly describe the role of these NSs proteins in modulation of innate immune responses in mammals and elaborate on a hypothetical scenario to explain if and how NSs proteins from vertebrate-infecting bunyaviruses affect RNA silencing. If so, why this discovery has been hampered so far.
Collapse
Affiliation(s)
- Marcio Hedil
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Wageningen, 6708PB, The Netherlands.
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Wageningen, 6708PB, The Netherlands.
| |
Collapse
|
50
|
Leung AKL. The Whereabouts of microRNA Actions: Cytoplasm and Beyond. Trends Cell Biol 2016; 25:601-610. [PMID: 26410406 DOI: 10.1016/j.tcb.2015.07.005] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/23/2015] [Accepted: 07/17/2015] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are a conserved class of approximately 22 nucleotide (nt) short noncoding RNAs that normally silence gene expression via translational repression and/or degradation of targeted mRNAs in plants and animals. Identifying the whereabouts of miRNAs potentially informs miRNA functions, some of which are perhaps specialized to specific cellular compartments. In this review, the significance of miRNA localizations in the cytoplasm, including those at RNA granules and endomembranes, and the export of miRNAs to extracellular space will be discussed. How miRNA localizations and functions are regulated by protein modifications on the core miRNA-binding protein Argonaute (AGO) during normal and stress conditions will be explored, and in conclusion new AGO partners, non-AGO miRNA-binding proteins, and the emergent understanding of miRNAs found in the nucleoplasm, nucleoli, and mitochondria will be discussed.
Collapse
Affiliation(s)
- Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
| |
Collapse
|