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Pereira M, Ribeiro DR, Berg M, Tsai AP, Dong C, Nho K, Kaiser S, Moutinho M, Soares AR. Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166857. [PMID: 37640114 DOI: 10.1016/j.bbadis.2023.166857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disorder characterized by accumulation of β-amyloid aggregates and loss of proteostasis. Transfer RNA (tRNA) modifications play a crucial role in maintaining proteostasis, but their impact in AD remains unclear. Here, we report that expression of the tRNA modifying enzyme ELP3 is reduced in the brain of AD patients and amyloid mouse models and negatively correlates with amyloid plaque mean density. We further show that SH-SY5Y neuronal cells carrying the amyloidogenic Swedish familial AD mutation (SH-SWE) display reduced ELP3 levels, tRNA hypomodifications and proteostasis impairments when compared to cells not carrying the mutation (SH-WT). Additionally, exposing SH-WT cells to the secretome of SH-SWE cells led to reduced ELP3 expression, wobble uridine tRNA hypomodification, and increased protein aggregation. Importantly, correcting tRNA deficits due to ELP3 reduction reverted proteostasis impairments. These findings suggest that amyloid pathology dysregulates proteostasis by reducing ELP3 expression and tRNA modification levels, and that targeting tRNA modifications may be a potential therapeutic avenue to restore neuronal proteostasis in AD and preserve neuronal function.
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Affiliation(s)
- Marisa Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Diana R Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Maximilian Berg
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, 60438, Germany
| | - Andy P Tsai
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Chuanpeng Dong
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stefanie Kaiser
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, 60438, Germany
| | - Miguel Moutinho
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ana R Soares
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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2
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Salazar SB, Pinheiro MJF, Sotti-Novais D, Soares AR, Lopes MM, Ferreira T, Rodrigues V, Fernandes F, Mira NP. Disclosing azole resistance mechanisms in resistant Candida glabrata strains encoding wild-type or gain-of-function CgPDR1 alleles through comparative genomics and transcriptomics. G3 (Bethesda) 2022; 12:jkac110. [PMID: 35532173 PMCID: PMC9258547 DOI: 10.1093/g3journal/jkac110] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/25/2022] [Indexed: 12/03/2022]
Abstract
The pathogenic yeast Candida glabrata is intrinsically resilient to azoles and rapidly acquires resistance to these antifungals, in vitro and in vivo. In most cases azole-resistant C. glabrata clinical strains encode hyperactive CgPdr1 variants, however, resistant strains encoding wild-type CgPDR1 alleles have also been isolated, although remaining to be disclosed the underlying resistance mechanism. In this study, we scrutinized the mechanisms underlying resistance to azoles of 8 resistant clinical C. glabrata strains, identified along the course of epidemiological surveys undertaken in Portugal. Seven of the strains were found to encode CgPdr1 gain-of-function variants (I392M, E555K, G558C, and I803T) with the substitutions I392M and I803T being herein characterized as hyper-activating mutations for the first time. While cells expressing the wild-type CgPDR1 allele required the mediator subunit Gal11A to enhance tolerance to fluconazole, this was dispensable for cells expressing the I803T variant indicating that the CgPdr1 interactome is shaped by different gain-of-function substitutions. Genomic and transcriptomic profiling of the sole azole-resistant C. glabrata isolate encoding a wild-type CgPDR1 allele (ISTB218) revealed that under fluconazole stress this strain over-expresses various genes described to provide protection against this antifungal, while also showing reduced expression of genes described to increase sensitivity to these drugs. The overall role in driving the azole-resistance phenotype of the ISTB218 C. glabrata isolate played by these changes in the transcriptome and genome of the ISTB218 isolate are discussed shedding light into mechanisms of resistance that go beyond the CgPdr1-signalling pathway and that may alone, or in combination, pave the way for the acquisition of resistance to azoles in vivo.
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Affiliation(s)
- Sara B Salazar
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Maria Joana F Pinheiro
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Danielle Sotti-Novais
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Ana R Soares
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro 3810, Portugal
| | - Maria M Lopes
- Departamento de Microbiologia e Imunologia, Faculdade de Farmácia da Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Teresa Ferreira
- Laboratório de Microbiologia, Hospital Dona Estefânia (Centro Hospitalar Universitário Lisboa Central), Lisboa 1169-045, Portugal
| | - Vitória Rodrigues
- Seção de Microbiologia, Laboratório SYNLAB—Lisboa, Grupo SYNLAB Portugal, Lisboa 1070-061, Portugal
| | - Fábio Fernandes
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
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Ferreira M, Francisco S, Soares AR, Nobre A, Pinheiro M, Reis A, Neto S, Rodrigues AJ, Sousa N, Moura G, Santos MAS. Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. Aging (Albany NY) 2021; 13:18150-18190. [PMID: 34330884 PMCID: PMC8351669 DOI: 10.18632/aging.203379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023]
Abstract
Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.
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Affiliation(s)
- Margarida Ferreira
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Stephany Francisco
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana R. Soares
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana Nobre
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Andreia Reis
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Sonya Neto
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana João Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gabriela Moura
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Manuel A. S. Santos
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
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Tavares JF, Davis NK, Poim A, Reis A, Kellner S, Sousa I, Soares AR, Moura GMR, Dedon PC, Santos M. tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. RNA Biol 2021; 18:563-575. [PMID: 32893724 PMCID: PMC7971265 DOI: 10.1080/15476286.2020.1819671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/28/2023] Open
Abstract
Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.
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Affiliation(s)
- Joana F Tavares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Nick K. Davis
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Ana Poim
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Inês Sousa
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana R. Soares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela M R Moura
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise – CREATE, Singapore
| | - Manuel Santos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
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5
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Pereira M, Ribeiro DR, Pinheiro MM, Ferreira M, Kellner S, Soares AR. m 5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Int J Mol Sci 2021; 22:ijms22062941. [PMID: 33799331 PMCID: PMC8001983 DOI: 10.3390/ijms22062941] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
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Affiliation(s)
- Marisa Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Diana R. Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Miguel M. Pinheiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Margarida Ferreira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, 81377 Munich, Germany;
- Institute of Pharmaceutical Chemistry, Goethe-University, 60438 Frankfurt, Germany
| | - Ana R. Soares
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
- Correspondence:
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6
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Cunha AM, Teixeira FG, Guimarães MR, Esteves M, Pereira-Mendes J, Soares AR, Almeida A, Sousa N, Salgado AJ, Leite-Almeida H. Unilateral accumbal dopamine depletion affects decision-making in a side-specific manner. Exp Neurol 2020; 327:113221. [PMID: 32027930 DOI: 10.1016/j.expneurol.2020.113221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/21/2020] [Accepted: 02/01/2020] [Indexed: 01/16/2023]
Abstract
Mechanisms underlying affective and cognitive deficits in Parkinson's disease (PD) remain less studied than motor symptoms. Nucleus accumbens (NAc) is affected in PD and due to its well-known involvement in motivation is an interesting target in this context. Furthermore, PD is frequently asymmetrical, with side-specific deficits aligning with evidences of accumbal laterality. We therefore used a 6-hydroxydopamine (6-OHDA) model to study the role of left and right NAc dopamine depletion in a battery of behavioral tasks. 2 months old male rats were used in all experiments. Habitual-based and goal-directed decision-making, impulsivity, anxiety- and depressive-like behavior and motor performance were tested 3 weeks after left (6-OHDA L) or right (6-OHDA R) NAc lesion was induced. Upon contingency degradation, 6-OHDA R decrease their lever press rate less than Sham and 6-OHDA L, indicating an impairment in the shift from habit-based to goal-directed strategies. On the other hand, 6-OHDA L lesions lead to increased rates of premature responding when delays where increased in the variable delay-to-signal test. Importantly, in both paradigms task acquisition was similar between groups. In the same line we found no differences in the amount of sugared pellets eaten when freely available as well as in both general and fine motor behaviors. In conclusion, left and right NAc play distinct roles in the contingency degradation and impulsivity. More studies are needed to understand the mechanisms behind this functional lateralization and its implications for PD patients.
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Affiliation(s)
- A M Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - F G Teixeira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - M R Guimarães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - M Esteves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - J Pereira-Mendes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - A R Soares
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - A Almeida
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - N Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - A J Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - H Leite-Almeida
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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7
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Varanda AS, Santos M, Soares AR, Vitorino R, Oliveira P, Oliveira C, Santos MAS. Human cells adapt to translational errors by modulating protein synthesis rate and protein turnover. RNA Biol 2020; 17:135-149. [PMID: 31570039 PMCID: PMC6948982 DOI: 10.1080/15476286.2019.1670039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 02/08/2023] Open
Abstract
Deregulation of tRNAs, aminoacyl-tRNA synthetases (aaRS) or tRNA modifying enzymes, increase the level of protein synthesis errors (PSE) and are associated with several diseases, but the cause-effect mechanisms of these pathologies remain elusive. To clarify the role of PSE in human biology, we have engineered a HEK293 cell line to overexpress a wild type (Wt) tRNASer and two tRNASer mutants that misincorporate serine at non-cognate codon sites. Then, we followed long-term adaptation to PSE of such recombinant cells by analysing cell viability, protein synthesis rate and activation of protein quality control mechanisms (PQC). Engineered cells showed higher level of misfolded and aggregated proteins; activated the ubiquitin-proteasome system (UPS) and the unfolded protein response (UPR), indicative of proteotoxic stress. Adaptation to PSE involved increased protein turnover, UPR up-regulation and altered protein synthesis rate. Gene expression analysis showed that engineered cells presented recurrent alterations in the endoplasmic reticulum, cell adhesion and calcium homeostasis. Herein, we unveil new phenotypic consequences of protein synthesis errors in human cells and identify the protein quality control processes that are necessary for long-term adaptation to PSE and proteotoxic stress. Our data provide important insight on how chronic proteotoxic stress may cause disease and highlight potential biological pathways that support the association of PSE with disease.
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Affiliation(s)
- Ana Sofia Varanda
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Mafalda Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Ana R. Soares
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Patrícia Oliveira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Carla Oliveira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Manuel A. S. Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
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8
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Guimarães MR, Soares AR, Cunha AM, Esteves M, Borges S, Magalhães R, Moreira PS, Rodrigues AJ, Sousa N, Almeida A, Leite‐Almeida H. Evidence for lack of direct causality between pain and affective disturbances in a rat peripheral neuropathy model. Genes, Brain and Behavior 2018; 18:e12542. [DOI: 10.1111/gbb.12542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/22/2018] [Accepted: 11/26/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Marco R. Guimarães
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Ana R. Soares
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Ana M. Cunha
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Madalena Esteves
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Sónia Borges
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Ricardo Magalhães
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
- Clinical Academic Center – Braga Braga Portugal
| | - Pedro S. Moreira
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
- Clinical Academic Center – Braga Braga Portugal
| | - Ana J. Rodrigues
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
- Clinical Academic Center – Braga Braga Portugal
| | - Armando Almeida
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
| | - Hugo Leite‐Almeida
- Life and Health Sciences Research Institute, School of Health Sciences University of Minho Braga Portugal
- ICVS/3B's – PT Government Associate Laboratory Braga Portugal
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Pereira M, Tomé D, Domingues AS, Varanda AS, Paulo C, Santos MAS, Soares AR. A Fluorescence-Based Sensor Assay that Monitors General Protein Aggregation in Human Cells. Biotechnol J 2018; 13:e1700676. [PMID: 29345424 DOI: 10.1002/biot.201700676] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/19/2017] [Indexed: 12/17/2022]
Abstract
Protein conformational disorders are characterized by disruption of protein folding and toxic accumulation of protein aggregates. Here we describe a sensitive and simple method to follow and monitor general protein aggregation in human cells. Heat shock protein 27 (HSP27) is an oligomeric small heat shock protein that binds and keeps unfolded proteins in a folding competent state. This high specificity of HSP27 for aggregated proteins can be explored to monitor aggregation in living cells by fusing it to a fluorescent protein as Green Fluorescent Protein (GFP). We have constructed a HeLa stable cell line expressing a HSP27:GFP chimeric reporter protein and after validation, this stable cell line is exposed to different agents that interfere with proteostasis, namely Arsenite, MG132, and Aβ-peptide. Exposure to proteome destabilizers lead to re-localization of HSP27:GFP fluorescence to foci, confirming that our reporter system is functional and can be used to detect and follow protein aggregation in living cells. This reporter is a valuable tool to setup wide-genetic screens to identify genes and pathways involved in protein misfolding and aggregation.
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Affiliation(s)
- Marisa Pereira
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
| | - Diogo Tomé
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana S Domingues
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana S Varanda
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristiana Paulo
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
| | - Manuel A S Santos
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana R Soares
- iBiMED - Institute of Biomedicine Department of Medical Sciences University of Aveiro, 3810-193 Aveiro, Portugal
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10
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Lopes AJ, Marinho CL, Alves UD, Gonçalves CEA, Silva PO, Botelho EC, Bedirian R, Soares AR, Maioli MCP. Relationship between ventilation heterogeneity and exercise intolerance in adults with sickle cell anemia. ACTA ACUST UNITED AC 2017; 50:e6512. [PMID: 28746470 PMCID: PMC5520223 DOI: 10.1590/1414-431x20176512] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022]
Abstract
Sickle cell anemia (SCA) causes dysfunction of multiple organs, with pulmonary involvement as a major cause of mortality. Recently, there has been growing interest in the nitrogen single-breath washout (N2SBW) test, which is able to detect ventilation heterogeneity and small airway disease when the results of other pulmonary function tests (PFTs) are still normal. Thus, the objectives of the present study were to assess the heterogeneity in the ventilation distribution in adults with SCA and to determine the association between the ventilation distribution and the clinical, cardiovascular, and radiological findings. This cross-sectional study included 38 adults with SCA who underwent PFTs, echocardiography, computed tomography (CT), and 6-min walk test. To evaluate the ventilation heterogeneity, the patients were categorized according to the phase III slope of the N2SBW (SIIIN2). Compared with adults with lower SIIIN2 values, adults with higher SIIIN2 values showed lower hemoglobin levels (P=0.048), a history of acute chest syndrome (P=0.001), an elevated tricuspid regurgitation velocity (P=0.039), predominance of a reticular pattern in the CT (P=0.002), a shorter 6-min walking distance (6MWD) (P=0.002), and lower peripheral oxygen saturation (SpO2) after exercise (P=0.03). SIIIN2 values correlated significantly with hemoglobin (rs=-0.344; P=0.034), forced vital capacity (rs=-0.671; P<0.0001), diffusing capacity for carbon monoxide (rs=-0.376; P=0.019), 6MWD (rs=-0.554; P=0.0003), and SpO2 after exercise (P=0.040). Heterogeneity in the ventilation distribution is one of the most common pulmonary dysfunctions in adults with SCA. Moreover, relationships exist between ventilation heterogeneity, worsening of pulmonary structural damage, and reduced tolerance for exercise.
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Affiliation(s)
- A J Lopes
- Programa de Pós-Graduação em Ciências da Reabilitação, Centro Universitário Augusto Motta, Rio de Janeiro, RJ, Brasil.,Programa de Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - C L Marinho
- Programa de Pós-Graduação em Fisiopatologia Clínica e Experimental, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - U D Alves
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - C E A Gonçalves
- Programa de Pós-Graduação em Ciências da Reabilitação, Centro Universitário Augusto Motta, Rio de Janeiro, RJ, Brasil
| | - P O Silva
- Programa de Pós-Graduação em Ciências da Reabilitação, Centro Universitário Augusto Motta, Rio de Janeiro, RJ, Brasil
| | - E C Botelho
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R Bedirian
- Disciplina de Clínica Médica, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - A R Soares
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil.,Disciplina de Hematologia e Hemoterapia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - M C P Maioli
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil.,Disciplina de Hematologia e Hemoterapia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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11
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Ferreira C, Soares AR, Lamosa P, Santos MA, da Costa MS. Comparison of the compatible solute pool of two slightly halophilic planctomycetes species, Gimesia maris and Rubinisphaera brasiliensis. Extremophiles 2016; 20:811-820. [PMID: 27502056 DOI: 10.1007/s00792-016-0868-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/30/2016] [Indexed: 11/29/2022]
Abstract
Gimesia maris and Rubinisphaera brasiliensis are slightly halophilic representatives of the deep-branching phylum Planctomycetes. For osmoadaptation both species accumulated α-glutamate, sucrose, ectoine and hydroxyectoine. A major role was found for ectoine, hydroxyectoine as well as sucrose under hyper-osmotic shock conditions. Nevertheless, the levels of sucrose were up-regulated by the increased salinity levels and also by low nitrogen availability. Additionally, G. maris accumulated glucosylglycerate (GG) as major solute specifically under low nitrogen levels, which prompted us to analyse the transcript abundance of two homologues genes known for the biosynthesis of GG, namely glucosyl-3-phosphoglycerate synthase (GpgS) and glucosyl-3-phosphoglycerate phosphatase (GpgP). By qPCR using a suitable reference gene selected in this study, the transcript abundance of the biosynthetic genes was quantified in G. maris cells under hyper-osmotic shock or under low nitrogen conditions. The gpgS gene was induced under nitrogen-limiting conditions suggesting that GG synthesis is regulated primarily at the transcription level. Moreover, the expression of a gene coding for a putative sucrose-phosphorylase (Spase) located upstream the gpgS and gpgP genes was up-regulated, predicting a metabolic role of Spase probably related to GG synthesis.
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Affiliation(s)
- Catarina Ferreira
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Ana R Soares
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Pedro Lamosa
- Centro de Ressonância Magnética António Xavier, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901, Oeiras, Portugal
| | - Manuel A Santos
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Milton S da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.
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Santos RM, Weber L, Souza VL, Soares AR, Petry AC. Effects of water-soluble fraction of petroleum on growth and prey consumption of juvenile Hoplias aff. malabaricus (Osteichthyes: Erythrinidae). BRAZ J BIOL 2016; 76:10-7. [PMID: 26871747 DOI: 10.1590/1519-6984.06714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 10/23/2014] [Indexed: 11/22/2022] Open
Abstract
The influence of the water-soluble fraction of petroleum (WSF) on prey consumption and growth of juvenile trahira Hoplias aff. malabaricus was investigated. Juveniles were submitted to either WSF or Control treatment over 28 days, and jewel tetra Hyphessobrycon eques adults were offered daily as prey for each predator. Total prey consumption ranged from 16 to 86 individuals. Despite the initially lower prey consumption under WSF exposure, there were no significant differences in overall feeding rates between the two treatments. Water-soluble fraction of petroleum had a negative effect on the growth in length of H. aff. malabaricus juveniles. Although unaffected, prey consumption suggested a relative resistance in H. aff. malabaricus to WSF exposition and the lower growth of individuals exposed to WSF than the Control possibly reflects metabolic costs. The implications of the main findings for the individual and the food chain are discussed, including behavioral aspects and the role played by this predator in shallow aquatic systems.
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Affiliation(s)
- R M Santos
- Pós-graduação em Ciências Ambientais e Conservação, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - L Weber
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - V L Souza
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - A R Soares
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - A C Petry
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
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13
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Terawaki S, Camosseto V, Prete F, Wenger T, Papadopoulos A, Rondeau C, Combes A, Rodriguez Rodrigues C, Vu Manh TP, Fallet M, English L, Santamaria R, Soares AR, Weil T, Hammad H, Desjardins M, Gorvel JP, Santos MAS, Gatti E, Pierre P. RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4. J Cell Biol 2015; 210:1133-52. [PMID: 26416964 PMCID: PMC4586740 DOI: 10.1083/jcb.201501059] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a key degradative pathway coordinated by external cues, including starvation, oxidative stress, or pathogen detection. Rare are the molecules known to contribute mechanistically to the regulation of autophagy and expressed specifically in particular environmental contexts or in distinct cell types. Here, we unravel the role of RUN and FYVE domain-containing protein 4 (RUFY4) as a positive molecular regulator of macroautophagy in primary dendritic cells (DCs). We show that exposure to interleukin-4 (IL-4) during DC differentiation enhances autophagy flux through mTORC1 regulation and RUFY4 induction, which in turn actively promote LC3 degradation, Syntaxin 17-positive autophagosome formation, and lysosome tethering. Enhanced autophagy boosts endogenous antigen presentation by MHC II and allows host control of Brucella abortus replication in IL-4-treated DCs and in RUFY4-expressing cells. RUFY4 is therefore the first molecule characterized to date that promotes autophagy and influences endosome dynamics in a subset of immune cells.
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Affiliation(s)
- Seigo Terawaki
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Voahirana Camosseto
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Francesca Prete
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Till Wenger
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Alexia Papadopoulos
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Christiane Rondeau
- Département de pathologie et biologie cellulaire, Université de Montréal, Québec H3C 3J7, Canada
| | - Alexis Combes
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Christian Rodriguez Rodrigues
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Thien-Phong Vu Manh
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Mathieu Fallet
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Luc English
- Département de pathologie et biologie cellulaire, Université de Montréal, Québec H3C 3J7, Canada
| | - Rodrigo Santamaria
- Departamento de Informática y Automática, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Ana R Soares
- RNA Biology Laboratory, Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal Institute for Research in Biomedicine (iBiMED), Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Tobias Weil
- RNA Biology Laboratory, Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Hamida Hammad
- Laboratory of Immunoregulation and Mucosal Immunology, Department for Molecular Biomedical Research, VIB, Ghent 9050, Belgium
| | - Michel Desjardins
- Département de pathologie et biologie cellulaire, Université de Montréal, Québec H3C 3J7, Canada Département de microbiologie, infectiologie, et immunologie, Université de Montréal, Québec H3C 3J7, Canada
| | - Jean-Pierre Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France
| | - Manuel A S Santos
- RNA Biology Laboratory, Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal Institute for Research in Biomedicine (iBiMED), Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Evelina Gatti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France Institute for Research in Biomedicine (iBiMED), Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Institut National de la Santé et de la Recherche Médicale U1104, Centre National de la Recherche Scientifique UMR7280, 13288 Marseille, France Institute for Research in Biomedicine (iBiMED), Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
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14
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Moura GR, Pinheiro M, Freitas A, Oliveira JL, Frommlet JC, Carreto L, Soares AR, Bezerra AR, Santos MAS. Correction: Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations. PLoS One 2015; 10:e0145593. [PMID: 26678389 PMCID: PMC4683089 DOI: 10.1371/journal.pone.0145593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Reverendo M, Soares AR, Pereira PM, Carreto L, Ferreira V, Gatti E, Pierre P, Moura GR, Santos MA. TRNA mutations that affect decoding fidelity deregulate development and the proteostasis network in zebrafish. RNA Biol 2015; 11:1199-213. [PMID: 25483040 DOI: 10.4161/rna.32199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Mutations in genes that encode tRNAs, aminoacyl-tRNA syntheases, tRNA modifying enzymes and other tRNA interacting partners are associated with neuropathies, cancer, type-II diabetes and hearing loss, but how these mutations cause disease is unclear. We have hypothesized that levels of tRNA decoding error (mistranslation) that do not fully impair embryonic development can accelerate cell degeneration through proteome instability and saturation of the proteostasis network. To test this hypothesis we have induced mistranslation in zebrafish embryos using mutant tRNAs that misincorporate Serine (Ser) at various non-cognate codon sites. Embryo viability was affected and malformations were observed, but a significant proportion of embryos survived by activating the unfolded protein response (UPR), the ubiquitin proteasome pathway (UPP) and downregulating protein biosynthesis. Accumulation of reactive oxygen species (ROS), mitochondrial and nuclear DNA damage and disruption of the mitochondrial network, were also observed, suggesting that mistranslation had a strong negative impact on protein synthesis rate, ER and mitochondrial homeostasis. We postulate that mistranslation promotes gradual cellular degeneration and disease through protein aggregation, mitochondrial dysfunction and genome instability.
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16
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Soares AR, Reverendo M, Pereira PM, Nivelles O, Pendeville H, Bezerra AR, Moura GR, Struman I, Santos MAS. Dre-miR-2188 targets Nrp2a and mediates proper intersegmental vessel development in zebrafish embryos. PLoS One 2012; 7:e39417. [PMID: 22761789 PMCID: PMC3382224 DOI: 10.1371/journal.pone.0039417] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 05/24/2012] [Indexed: 12/30/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small RNAs that are implicated in the control of eukaryotic gene expression by binding to the 3′UTR of target mRNAs. Several algorithms have been developed for miRNA target prediction however, experimental validation is still essential for the correct identification of miRNA targets. We have recently predicted that Neuropilin2a (Nrp2a), a vascular endothelial growth factor receptor which is essential for normal developmental angiogenesis in zebrafish, is a dre-miR-2188 target. Methodology Here we show that dre-miR-2188 targets the 3′-untranslated region (3′UTR) of Nrp2a mRNA and is implicated in proper intersegmental vessel development in vivo. Over expression of miR-2188 in zebrafish embryos down regulates Nrp2a expression and results in intersegmental vessel disruption, while its silencing increases Nrp2a expression and intersegmental vessel sprouting. An in vivo GFP sensor assay based on a fusion between the GFP coding region and the Nrp2a 3′UTR confirms that miR-2188 binds to the 3′UTR of Nrp2a and inhibits protein translation. Conclusions We demonstrate that miR-2188 targets Nrp2a and affects intersegmental vessel development in zebrafish embryos.
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Affiliation(s)
- Ana R. Soares
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Marisa Reverendo
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Patrícia M. Pereira
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Olivier Nivelles
- Unit of Molecular Biology and Genetic Engineering, GIGA-Research, University of Liège, Sart Tilman, Liège, Belgium
| | - Hélène Pendeville
- Unit of Molecular Biology and Genetic Engineering, GIGA-Research, University of Liège, Sart Tilman, Liège, Belgium
| | - Ana Rita Bezerra
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Ingrid Struman
- Unit of Molecular Biology and Genetic Engineering, GIGA-Research, University of Liège, Sart Tilman, Liège, Belgium
| | - Manuel A. S. Santos
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
- * E-mail:
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17
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Moura GR, Pinheiro M, Freitas A, Oliveira JL, Frommlet JC, Carreto L, Soares AR, Bezerra AR, Santos MAS. Species-specific codon context rules unveil non-neutrality effects of synonymous mutations. PLoS One 2011; 6:e26817. [PMID: 22046369 PMCID: PMC3202573 DOI: 10.1371/journal.pone.0026817] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/05/2011] [Indexed: 11/18/2022] Open
Abstract
Background Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution. Methodologies/Principal Findings Here we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases. Conclusions Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life.
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Affiliation(s)
- Gabriela R Moura
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal.
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Abstract
MicroRNAs (miRNAs) are short (∼22 nt) non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. Cervical cancer is one of the most common cancers in women worldwide and there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform containing probes for mature miRNAs. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL) and 9 low-grade squamous intraepithelial lesion (LSIL) samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, deregulated miRNAs were identified in malignant and pre-malignant cervical tissues after tackling the high expression variability observed. We were also able to identify putative target genes of relevant candidate miRNAs. Our results show that miRNA expression shows natural variability among human samples, which complicates miRNA data profiling analysis. However, such expression noise can be filtered and does not prevent the identification of deregulated miRNAs that play a role in the malignant transformation of cervical squamous cells. Deregulated miRNAs highlight new candidate gene targets allowing for a better understanding of the molecular mechanism underlying the development of this tumour type.
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Affiliation(s)
- Patrícia M. Pereira
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Ana R. Soares
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
- Experimental Biology and Biomedicine PhD Program, Centre for Neurosciences, Coimbra, Portugal
| | - Laura Carreto
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Manuel A. S. Santos
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
- * E-mail:
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19
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Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MAS. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 2009; 10:195. [PMID: 19397817 PMCID: PMC2684549 DOI: 10.1186/1471-2164-10-195] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 04/27/2009] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification, however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. Results We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from miRNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics. Twenty five novel miRNAs were predicted, 107 miRNA star sequences and also 41 candidate miRNA targets were identified. A miRNA expression profile built on the basis of pyrosequencing read numbers showed high expression of most miRNAs throughout zebrafish development and identified tissue specific miRNAs. Conclusion This study increases the number of zebrafish miRNAs from 192 to 217 and demonstrates that a single DNA mini-chip pyrosequencing run is effective in miRNA identification in zebrafish. This methodology also produced sufficient information to elucidate miRNA expression patterns during development and in differentiated organs. Moreover, some zebrafish miRNA star sequences were more abundant than their corresponding miRNAs, suggesting a functional role for the former in gene expression control in this vertebrate model organism.
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Affiliation(s)
- Ana R Soares
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro 3810-193, Portugal.
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Abstract
Salmonella enterica serotype Enteritidis is an important serovar comprising 76 % of Salmonella isolates in Portugal in 2001. For better understand the epidemiology of salmonellosis, a total of 47 isolates of S. Enteritidis phage type (PT) 1b and 6a were analysed by pulsed-field gel electrophoresis (PFGE) and genomic DNA was subjected to macro restriction with XbaI. For PT 1b isolates, only three different patterns were observed, and PT6a showed a total of 10 digestion patterns. Curiously, the main pattern among PT1b isolates seams quite similar to main pattern of PT6a isolates, but when the two patterns were analysed with Bionumerics, we observed that they exhibited some differences. It was concluded that, in 2001, there was one predominant pattern for PT1b and PT6a and, possibly, we were in presence of clonal strains that exists all over the country.
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Affiliation(s)
- A R Soares
- Enterobactereaceae Unity, Bacteriology Center, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
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