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Regateiro FJ, Silva H, Lemos MC, Moura G, Torres P, Pereira AD, Dias L, Ferreira PL, Amaral S, Santos MAS. Promoting advanced medical services in the framework of 3PM-a proof-of-concept by the "Centro" Region of Portugal. EPMA J 2024; 15:135-148. [PMID: 38463621 PMCID: PMC10923757 DOI: 10.1007/s13167-024-00353-9] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/02/2024] [Indexed: 03/12/2024]
Abstract
Multidisciplinary team from three universities based in the "Centro" Region of Portugal developed diverse approaches as parts of a project dedicated to enhancing and expanding Predictive, Preventive, and Personalized Medicine (3PM) in the Region. In a sense, outcomes acted as a proof-of-concept, in that they demonstrated the feasibility, but also the relevance of the approaches. The accomplishments comprise defining a new regional strategy for implementing 3PM within the Region, training of human resources in genomic sequencing, and generating good practices handbooks dedicated to diagnostic testing via next-generation sequencing, to legal and ethical concerns, and to knowledge transfer and entrepreneurship, aimed at increasing literacy on 3PM approaches. Further approaches also included support for entrepreneurship development and start-ups, and diverse and relevant initiatives aimed at increasing literacy relevant to 3PM. Efforts to enhance literacy encompassed citizens across the board, from patients and high school students to health professionals and health students. This focus on empowerment through literacy involved a variety of initiatives, including the creation of an illustrated book on genomics and the production of two theater plays centered on genetics. Additionally, authors stressed that genomic tools are relevant, but they are not the only resources 3PM is based on. Thus, they defend that other initiatives intended to enable citizens to take 3PM should include multi-omics and, having in mind the socio-economic burden of chronic diseases, suboptimal health status approaches in the 3PM framework should also be considered, in order to anticipate medical intervention in the subclinical phase. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00353-9.
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Affiliation(s)
- Fernando J. Regateiro
- University of Coimbra, Faculty of Medicine – Laboratory of Sequencing and Functional Genomics of UCGenomics and Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment, Genetics and Oncobiology (CIMAGO), and Centre for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
| | - Henriqueta Silva
- University of Coimbra, Faculty of Medicine – Laboratory of Sequencing and Functional Genomics of UCGenomics and Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment, Genetics and Oncobiology (CIMAGO), and Centre for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
| | - Manuel C. Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Gabriela Moura
- Genome Medicine Laboratory, Institute for Biomedicine (iBiMED) & Department of Medical Sciences (DCM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pedro Torres
- University of Coimbra, Centre for Business and Economics Research, Faculty of Economics, Av. Dias da Silva, 165, 3004-512 Coimbra, Portugal
| | - André Dias Pereira
- University of Coimbra, Centre for Biomedical Law, Faculty of Law, Pátio da Universidade, 3004-545 Coimbra, Portugal
| | - Luís Dias
- University of Coimbra, Centre for Business and Economics Research, Faculty of Economics, Av. Dias da Silva, 165, 3004-512 Coimbra, Portugal
| | - Pedro L. Ferreira
- University of Coimbra, Centre for Health Studies and Research and Faculty of Economics, Av. Dias da Silva 185, 3004-512 Coimbra, Portugal
| | - Sara Amaral
- University of Coimbra, Centre for Neuroscience and Cell Biology (CNC) and Centre for Innovative Biomedicine and Biotechnology (CIBB), Rua Larga, 3004-504 Coimbra, Portugal
| | - Manuel A. S. Santos
- University of Coimbra, Multidisciplinary Institute of Ageing, MIA-Portugal, Faculty of Medicine, Rua Larga, 3004-504 Coimbra, Portugal
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Santiago J, Silva JV, Santos MAS, Fardilha M. Age-Dependent Alterations in Semen Parameters and Human Sperm MicroRNA Profile. Biomedicines 2023; 11:2923. [PMID: 38001924 PMCID: PMC10669352 DOI: 10.3390/biomedicines11112923] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
The trend to delay parenthood is increasing, impacting fertility and reproductive outcomes. Advanced paternal age (APA), defined as men's age above 40 years at conception, has been linked with testicular impairment, abnormal semen parameters, and poor reproductive and birth outcomes. Recently, the significance of sperm microRNA for fertilization and embryonic development has emerged. This work aimed to investigate the effects of men's age on semen parameters and sperm microRNA profiles. The ejaculates of 333 Portuguese men were collected between 2018 and 2022, analyzed according to WHO guidelines, and a density gradient sperm selection was performed. For microRNA expression analysis, 16 normozoospermic human sperm samples were selected and divided into four age groups: ≤30, 31-35, 36-40, and >40 years. microRNA target genes were retrieved from the miRDB and TargetScan databases and Gene Ontology analysis was performed using the DAVID tool. No significant correlation was found between male age and conventional semen parameters, except for volume. Fifteen differentially expressed microRNAs (DEMs) between groups were identified. Enrichment analysis suggested the involvement of DEMs in the sperm of men with advanced age in critical biological processes like embryonic development, morphogenesis, and male gonad development. Targets of DEMs were involved in signaling pathways previously associated with the ageing process, including cellular senescence, autophagy, insulin, and mTOR pathways. These results suggest that although conventional semen parameters were not affected by men's age, alterations in microRNA regulation may occur and be responsible for poor fertility and reproductive outcomes associated with APA.
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Affiliation(s)
- Joana Santiago
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (J.V.S.); (M.A.S.S.)
| | - Joana V. Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (J.V.S.); (M.A.S.S.)
| | - Manuel A. S. Santos
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (J.V.S.); (M.A.S.S.)
- Multidisciplinary Institute of Ageing, MIA-Portugal, University of Coimbra, 3000-370 Coimbra, Portugal
| | - Margarida Fardilha
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (J.V.S.); (M.A.S.S.)
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Santos M, Fidalgo A, Varanda AS, Soares AR, Almeida GM, Martins D, Mendes N, Oliveira C, Santos MAS. Upregulation of tRNA-Ser-AGA-2-1 Promotes Malignant Behavior in Normal Bronchial Cells. Front Mol Biosci 2022; 9:809985. [PMID: 35586191 PMCID: PMC9108184 DOI: 10.3389/fmolb.2022.809985] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/30/2022] [Indexed: 11/25/2022] Open
Abstract
Serine tRNAs (tRNASer) are frequently overexpressed in tumors and associated with poor prognosis and increased risk of recurrence in breast cancer. Impairment of tRNA biogenesis and abundance also impacts proteome homeostasis, and activates protein quality control systems. Herein, we aimed at testing whether increasing tRNASer abundance could foster tumor establishment through activation of the UPR. In order to do so, firstly we confirmed that the expression of tRNA-Ser-AGA-2-1 [hereafter tRNASer(AGA)] was upregulated by 1.79-fold in Stage I NSCLC tumors when compared to normal adjacent tissue. To study the impact of tRNASer(AGA) in early stage tumorigenesis, we induced its upregulation in a non-tumoral bronchial cell line, BEAS-2B. Upregulation of this tRNA increased cellular proliferation and protein synthesis rate, driven by eIF2α dephosphorylation and ATF4 activation downstream of PERK signaling. Futhermore, tRNASer(AGA) enhanced transformation potential in vitro, and promoted the establishment of slow growing tumors with aggressive features in nude mice. Our work highlights the importance of studying tRNA deregulation on early stage tumorigenesis, as they may be potential malignancy and aggressiveness biomarkers.
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Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Raquel Soares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela M. Almeida
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department Pathology, Medical Faculty of Porto, Porto, Portugal
| | - Diana Martins
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
| | - Nuno Mendes
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department Pathology, Medical Faculty of Porto, Porto, Portugal
- *Correspondence: Carla Oliveira, ; Manuel A. S. Santos,
| | - Manuel A. S. Santos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- *Correspondence: Carla Oliveira, ; Manuel A. S. Santos,
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Francisco S, Martinho V, Ferreira M, Reis A, Moura G, Soares AR, Santos MAS. The Role of MicroRNAs in Proteostasis Decline and Protein Aggregation during Brain and Skeletal Muscle Aging. Int J Mol Sci 2022; 23:ijms23063232. [PMID: 35328652 PMCID: PMC8955204 DOI: 10.3390/ijms23063232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 01/14/2023] Open
Abstract
Aging can be defined as the progressive deterioration of cellular, tissue, and organismal function over time. Alterations in protein homeostasis, also known as proteostasis, are a hallmark of aging that lead to proteome imbalances and protein aggregation, phenomena that also occur in age-related diseases. Among the various proteostasis regulators, microRNAs (miRNAs) have been reported to play important roles in the post-transcriptional control of genes involved in maintaining proteostasis during the lifespan in several organismal tissues. In this review, we consolidate recently published reports that demonstrate how miRNAs regulate fundamental proteostasis-related processes relevant to tissue aging, with emphasis on the two most studied tissues, brain tissue and skeletal muscle. We also explore an emerging perspective on the role of miRNA regulatory networks in age-related protein aggregation, a known hallmark of aging and age-related diseases, to elucidate potential miRNA candidates for anti-aging diagnostic and therapeutic targets.
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Affiliation(s)
- Stephany Francisco
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Vera Martinho
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Margarida Ferreira
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Andreia Reis
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Gabriela Moura
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Ana Raquel Soares
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
- Correspondence: (A.R.S.); (M.A.S.S.)
| | - Manuel A. S. Santos
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
- Multidisciplinary Institute of Aging, MIA-Portugal, Faculty of Medicine, University of Coimbra, Rua Largo 2, 3º, 3000-370 Coimbra, Portugal
- Correspondence: (A.R.S.); (M.A.S.S.)
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Marçalo R, Neto S, Pinheiro M, Rodrigues AJ, Sousa N, Santos MAS, Simão P, Valente C, Andrade L, Marques A, Moura GR. Evaluation of the genetic risk for COVID-19 outcomes in COPD and differences among worldwide populations. PLoS One 2022; 17:e0264009. [PMID: 35196333 PMCID: PMC8865687 DOI: 10.1371/journal.pone.0264009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
Background Populations seem to respond differently to the global pandemic of severe acute respiratory syndrome coronavirus 2. Recent studies show individual variability in both susceptibility and clinical response to COVID-19 infection. People with chronic obstructive pulmonary disease (COPD) constitute one of COVID-19 risk groups, being already associated with a poor prognosis upon infection. This study aims contributing to unveil the underlying reasons for such prognosis in people with COPD and the variability in the response observed across worldwide populations, by looking at the genetic background as a possible answer to COVID-19 infection response heterogeneity. Methods SNPs already associated with susceptibility to COVID-19 infection (rs286914 and rs12329760) and severe COVID-19 with respiratory failure (rs657152 and rs11385942) were assessed and their allelic frequencies used to calculate the probability of having multiple risk alleles. This was performed on a Portuguese case-control COPD cohort, previously clinically characterized and genotyped from saliva samples, and also on worldwide populations (European, Spanish, Italian, African, American and Asian), using publicly available frequencies data. A polygenic risk analysis was also conducted on the Portuguese COPD cohort for the two mentioned phenotypes, and also for hospitalization and survival to COVID-19 infection. Findings No differences in genetic risk for COVID-19 susceptibility, hospitalization, severity or survival were found between people with COPD and the control group (all p-values > 0.01), either considering risk alleles individually, allelic combinations or polygenic risk scores. All populations, even those with European ancestry (Portuguese, Spanish and Italian), showed significant differences from the European population in genetic risk for both COVID-19 susceptibility and severity (all p-values < 0.0001). Conclusion Our results indicate a low genetic contribution for COVID-19 infection predisposition or worse outcomes observed in people with COPD. Also, our study unveiled a high genetic heterogeneity across major world populations for the same alleles, even within European sub-populations, demonstrating the need to build a higher resolution European genetic map, so that differences in the distribution of relevant alleles can be easily accessed and used to better manage diseases, ultimately, safeguarding populations with higher genetic predisposition to such diseases.
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Affiliation(s)
- Rui Marçalo
- Department of Medical Sciences, Genome Medicine Laboratory, Institute of Biomedicine—iBiMED, University of Aveiro, Aveiro, Portugal
- Lab3R-Respiratory Research and Rehabilitation, School for Health Sciences (ESSUA) and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
- * E-mail:
| | - Sonya Neto
- Department of Medical Sciences, Genome Medicine Laboratory, Institute of Biomedicine—iBiMED, University of Aveiro, Aveiro, Portugal
| | - Miguel Pinheiro
- Department of Medical Sciences, Genome Medicine Laboratory, Institute of Biomedicine—iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana J. Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho–Braga, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho–Braga, Portugal
| | - Manuel A. S. Santos
- Department of Medical Sciences, Genome Medicine Laboratory, Institute of Biomedicine—iBiMED, University of Aveiro, Aveiro, Portugal
| | - Paula Simão
- Pulmonology Department, Unidade Local de Saúde de Matosinhos—Porto, Porto, Portugal
| | - Carla Valente
- Pulmonology Department, Centro Hospitalar do Baixo Vouga–Aveiro, Aveiro, Portugal
| | - Lília Andrade
- Pulmonology Department, Centro Hospitalar do Baixo Vouga–Aveiro, Aveiro, Portugal
| | - Alda Marques
- Lab3R-Respiratory Research and Rehabilitation, School for Health Sciences (ESSUA) and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- Department of Medical Sciences, Genome Medicine Laboratory, Institute of Biomedicine—iBiMED, University of Aveiro, Aveiro, Portugal
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Santiago J, Silva JV, Howl J, Santos MAS, Fardilha M. All you need to know about sperm RNAs. Hum Reprod Update 2021; 28:67-91. [PMID: 34624094 DOI: 10.1093/humupd/dmab034] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 01/14/2021] [Revised: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Spermatogenesis generates a small and highly specialised type of cell that is apparently incapable of transcription and translation. For many years, this dogma was supported by the assumption that (i) the compact sperm nucleus, resulting from the substitution of histones by protamine during spermatogenesis, renders the genome inaccessible to the transcriptional machinery; and (ii) the loss of most organelles, including endoplasmic reticulum and ribosomes, limits or prevents translational activity. Despite these observations, several types of coding and non-coding RNAs have been identified in human sperm. Their functional roles, particularly during fertilisation and embryonic development, are only now becoming apparent. OBJECTIVE AND RATIONALE This review aimed to summarise current knowledge of the origin, types and functional roles of sperm RNAs, and to evaluate the clinical benefits of employing these transcripts as biomarkers of male fertility and reproductive outcomes. The possible contribution of sperm RNAs to intergenerational or transgenerational phenotypic inheritance is also addressed. SEARCH METHODS A comprehensive literature search on PubMed was conducted using the search terms 'sperm' AND 'RNA'. Searches focussed upon articles written in English and published prior to August 2020. OUTCOMES The development of more sensitive and accurate RNA technologies, including RNA sequencing, has enabled the identification and characterisation of numerous transcripts in human sperm. Though a majority of these RNAs likely arise during spermatogenesis, other data support an epididymal origin of RNA transmitted to maturing sperm by extracellular vesicles. A minority may also be synthesised by de novo transcription in mature sperm, since a small portion of the sperm genome remains packed by histones. This complex RNA population has important roles in paternal chromatin packaging, sperm maturation and capacitation, fertilisation, early embryogenesis and developmental maintenance. In recent years, additional lines of evidence from animal models support a role for sperm RNAs in intergenerational or transgenerational inheritance, modulating both the genotype and phenotype of progeny. Importantly, several reports indicate that the sperm RNA content of fertile and infertile men differs considerably and is strongly modulated by the environment, lifestyle and pathological states. WIDER IMPLICATIONS Transcriptional profiling has considerable potential for the discovery of fertility biomarkers. Understanding the role of sperm transcripts and comparing the sperm RNA fingerprint of fertile and infertile men could help to elucidate the regulatory pathways contributing to male factor infertility. Such data might also provide a molecular explanation for several causes of idiopathic male fertility. Ultimately, transcriptional profiling may be employed to optimise ART procedures and overcome some of the underlying causes of male infertility, ensuring the birth of healthy children.
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Affiliation(s)
- Joana Santiago
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Joana V Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal.,i3S-Institute for Innovation and Health Research, University of Porto, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - John Howl
- Research Institute in Healthcare Science, University of Wolverhampton, Wolverhampton, UK
| | - Manuel A S Santos
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Margarida Fardilha
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, 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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Direito I, Monteiro L, Melo T, Figueira D, Lobo J, Enes V, Moura G, Henrique R, Santos MAS, Jerónimo C, Amado F, Fardilha M, Helguero LA. Protein Aggregation Patterns Inform about Breast Cancer Response to Antiestrogens and Reveal the RNA Ligase RTCB as Mediator of Acquired Tamoxifen Resistance. Cancers (Basel) 2021; 13:cancers13133195. [PMID: 34206811 PMCID: PMC8269126 DOI: 10.3390/cancers13133195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Acquired resistance to antiestrogenic therapy remains the major obstacle to curing luminal subtype breast cancer. While current treatment in acquired endocrine-resistant settings includes combined therapy with receptor tyrosine kinase or cyclin-dependent kinase inhibitors, progression to incurable disease remains possible. In recent years, the antioxidant system and the protein quality control network have been associated with the enhanced resistance of breast cancer cells to hormonal therapy. In this work, we raise the hypothesis that antiestrogen treatment induces the accumulation of protein aggregates in sensitive cells, which in turn could hinder the activation of survival pathways. We present evidence concerning a novel way to identify antiestrogen response and disclose a novel protein, RTBC, that controls acquired antiestrogen resistance. This work opens a new avenue for research towards finding breast cancer prognostic markers and therapeutic targets, where the identification of proteins prone to aggregate could help to identify antiestrogen response and understand mechanisms of disease. Abstract The protein quality control network, including autophagy, the proteasome and the unfolded protein response (UPR), is triggered by stress and is overactive in acquired antiestrogen therapy resistance. We show for the first time that the aggresome load correlates with apoptosis and is increased in antiestrogen-sensitive cells compared to endocrine-resistant variants. LC-MS/MS analysis of the aggregated proteins obtained after 4OH-tamoxifen and Fulvestrant treatment identified proteins with essential function in protein quality control in antiestrogen-sensitive cells, but not in resistant variants. These include the UPR modulators RTCB and PDIA6, as well as many proteasome proteins such as PSMC2 and PSMD11. RTCB is a tRNA and XBP1 ligase and its aggregation induced by antiestrogens correlated with impaired XBP1s expression in sensitive cells. Knock down of RTCB was sufficient to restore sensitivity to tamoxifen in endocrine-resistant cells and increased the formation of aggresomes, leading to apoptotic cell death. Analysis of primary human breast cancer samples and their metastases appearing after endocrine treatment showed that RTCB is only localized to aggresomes in the primary tumors, while total aggresomes, including aggregated RTCB, were significantly reduced in the metastases. Therefore, different protein aggregation patterns may indicate loss of function of essential proteins resulting in enhanced protein aggregation that can be used to identify antiestrogen-resistant breast cancer cells and improve the response to antiestrogenic therapy.
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Affiliation(s)
- Inês Direito
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - Liliana Monteiro
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - Tânia Melo
- LaQV-REQUIMTE—Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (F.A.)
| | - Daniela Figueira
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal; (J.L.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Vera Enes
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - Gabriela Moura
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal; (J.L.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Manuel A. S. Santos
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - Carmen Jerónimo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal; (J.L.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Francisco Amado
- LaQV-REQUIMTE—Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (F.A.)
| | - Margarida Fardilha
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
| | - Luisa A. Helguero
- iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (I.D.); (L.M.); (D.F.); (V.E.); (G.M.); (M.A.S.S.); (M.F.)
- Correspondence:
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9
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Bezerra AR, Oliveira C, Correia I, Guimarães AR, Sousa G, Carvalho MJ, Moura G, Santos MAS. The role of non-standard translation in Candida albicans pathogenesis. FEMS Yeast Res 2021; 21:6280978. [PMID: 34021562 PMCID: PMC8178436 DOI: 10.1093/femsyr/foab032] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.
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Affiliation(s)
- Ana Rita Bezerra
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carla Oliveira
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Inês Correia
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana Rita Guimarães
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gonçalo Sousa
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maria João Carvalho
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gabriela Moura
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Manuel A S Santos
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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10
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Guimarães AR, Correia I, Sousa I, Oliveira C, Moura G, Bezerra AR, Santos MAS. tRNAs as a Driving Force of Genome Evolution in Yeast. Front Microbiol 2021; 12:634004. [PMID: 33776966 PMCID: PMC7990762 DOI: 10.3389/fmicb.2021.634004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 11/29/2022] Open
Abstract
Transfer RNAs (tRNAs) are widely known for their roles in the decoding of the linear mRNA information into amino acid sequences of proteins. They are also multifunctional platforms in the translation process and have other roles beyond translation, including sensing amino acid abundance, interacting with the general stress response machinery, and modulating cellular adaptation, survival, and death. In this mini-review, we focus on the emerging role of tRNA genes in the organization and modification of the genomic architecture of yeast and the role of tRNA misexpression and decoding infidelity in genome stability, evolution, and adaption. We discuss published work showing how quickly tRNA genes can mutate to meet novel translational demands, how tRNAs speed up genome evolution, and how tRNA genes can be sites of genomic instability. We highlight recent works showing that loss of tRNA decoding fidelity and small alterations in tRNA expression have unexpected and profound impacts on genome stability. By dissecting these recent evidence, we hope to lay the groundwork that prompts future investigations on the mechanistic interplay between tRNAs and genome modification that likely triggers genome evolution.
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Affiliation(s)
- Ana Rita Guimarães
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Inês Correia
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Inês Sousa
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela Moura
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Rita Bezerra
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
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11
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Santiago J, Santos MAS, Fardilha M, Silva JV. Stress response pathways in the male germ cells and gametes. Mol Hum Reprod 2021; 26:1-13. [PMID: 31814009 DOI: 10.1093/molehr/gaz063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/02/2019] [Revised: 10/31/2019] [Indexed: 12/20/2022] Open
Abstract
The unfolded protein response (UPR) is a conserved and essential cellular pathway involved in protein quality control that is activated in response to several cellular stressors such as diseases states, ageing, infection and toxins. The cytosol, endoplasmic reticulum (ER) and mitochondria are continuously exposed to new proteins and in situations of aberrant protein folding; one of three lines of defence may be activated: (i) heat-shock response, (ii) mitochondrial UPR and (iii) ER UPR. These pathways lead to different signal transduction mechanisms that activate or upregulate transcription factors that, in turn, regulate genes that increase the cell's ability to correct the conformation of poorly folded proteins or, ultimately, lead to apoptosis. Despite the recent progress in understanding such biological processes, few studies have focused on the implications of the UPR in male infertility, highlighting the need for a first approach concerning the presence of these components in the male reproductive system. In testis, there is a high rate of protein synthesis, and the UPR mechanisms are well described. However, the presence of these mechanisms in spermatozoa, apparently transcriptionally inactive cells, is contentious, and it is unclear how sperm cells deal with stress. Here, we review current concepts and mechanisms of the UPR and highlight the relevance of these stress response pathways in male fertility, especially the presence and functional activation of those components in male germinal cells and spermatozoa.
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Affiliation(s)
- J Santiago
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal
| | - M A S Santos
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal
| | - M Fardilha
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal
| | - J V Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal.,Reproductive Genetics and Embryo-fetal Development Group, Institute for Innovation and Health Research (I3S), University of Porto, 4200-135, Porto, Portugal.,Department of Microscopy, Laboratory of Cell Biology, and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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12
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Vitorino R, Guedes S, Trindade F, Correia I, Moura G, Carvalho P, Santos MAS, Amado F. De novo sequencing of proteins by mass spectrometry. Expert Rev Proteomics 2020; 17:595-607. [PMID: 33016158 DOI: 10.1080/14789450.2020.1831387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 12/24/2022]
Abstract
INTRODUCTION Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. AREAS COVERED De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. EXPERT OPINION As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification.
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Affiliation(s)
- Rui Vitorino
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal.,Unidade De Investigação Cardiovascular, Departamento De Cirurgia E Fisiologia, Faculdade De Medicina, Universidade Do Porto , Porto, Portugal
| | - Sofia Guedes
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal
| | - Fabio Trindade
- Unidade De Investigação Cardiovascular, Departamento De Cirurgia E Fisiologia, Faculdade De Medicina, Universidade Do Porto , Porto, Portugal
| | - Inês Correia
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Gabriela Moura
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Paulo Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, FIOCRUZ, Laboratory for Proteomics and Protein Engineering , Brazil
| | - Manuel A S Santos
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Francisco Amado
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal
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13
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Nunes A, Ribeiro DR, Marques M, Santos MAS, Ribeiro D, Soares AR. Emerging Roles of tRNAs in RNA Virus Infections. Trends Biochem Sci 2020; 45:794-805. [PMID: 32505636 DOI: 10.1016/j.tibs.2020.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 02/20/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Viruses rely on the host cell translation machinery for efficient synthesis of their own proteins. Emerging evidence highlights different roles for host transfer RNAs (tRNAs) in the process of virus replication. For instance, different RNA viruses manipulate host tRNA pools to favor viral protein translation. Interestingly, specific host tRNAs are used as reverse transcription primers and are packaged into retroviral virions. Recent data also demonstrate the formation of tRNA-derived fragments (tRFs) upon infection to facilitate viral replication. Here, we comprehensively discuss how RNA viruses exploit distinct aspects of the host tRNA biology for their benefit. In light of the recent advances in the field, we propose that host tRNA-related pathways and mechanisms represent promising cellular targets for the development of novel antiviral strategies.
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Affiliation(s)
- Alexandre Nunes
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Diana Roberta Ribeiro
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mariana Marques
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Daniela Ribeiro
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| | - Ana Raquel Soares
- iBiMED, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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14
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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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15
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Santos M, Fidalgo A, Varanda AS, Oliveira C, Santos MAS. tRNA Deregulation and Its Consequences in Cancer. Trends Mol Med 2019; 25:853-865. [PMID: 31248782 DOI: 10.1016/j.molmed.2019.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 04/17/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
The expression of transfer RNAs (tRNAs) is deregulated in cancer cells but the mechanisms and functional meaning of such deregulation are poorly understood. The proteome of cancer cells is not fully encoded by their transcriptome, however, the contribution of mRNA translation to such diversity remains to be elucidated. We review data supporting the hypothesis that tRNA expression deregulation and translational error rate is an important contributor to proteome diversity and cell population heterogeneity, genome instability, and drug resistance in tumors. This hypothesis is aligned with recent data in various model organisms, showing unanticipated adaptive roles of translational errors (adaptive mistranslation), expression control of specific gene subsets by tRNAs, and proteome diversification by elevation of translational error rates in tumors.
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Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - A Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Pathology, Medical Faculty 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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Cela M, Paulus C, Santos MAS, Moura GR, Frugier M, Rudinger-Thirion J. Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr. PLoS One 2018; 13:e0209805. [PMID: 30592748 PMCID: PMC6310243 DOI: 10.1371/journal.pone.0209805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The life cycle of Plasmodium falciparum, the agent responsible for malaria, depends on both cytosolic and apicoplast translation fidelity. Apicoplast aminoacyl-tRNA synthetases (aaRS) are bacterial-like enzymes devoted to organellar tRNA aminoacylation. They are all encoded by the nuclear genome and are translocated into the apicoplast only after cytosolic biosynthesis. Apicoplast aaRSs contain numerous idiosyncratic sequence insertions: An understanding of the roles of these insertions has remained elusive and they hinder efforts to heterologously overexpress these proteins. Moreover, the A/T rich content of the Plasmodium genome leads to A/U rich apicoplast tRNA substrates that display structural plasticity. Here, we focus on the P. falciparum apicoplast tyrosyl-tRNA synthetase (Pf-apiTyrRS) and its cognate tRNATyr substrate (Pf-apitRNATyr). Cloning and expression strategies used to obtain an active and functional recombinant Pf-apiTyrRS are reported. Functional analyses established that only three weak identity elements in the apitRNATyr promote specific recognition by the cognate Pf-apiTyrRS and that positive identity elements usually found in the tRNATyr acceptor stem are excluded from this set. This finding brings to light an unusual behavior for a tRNATyr aminoacylation system and suggests that Pf-apiTyrRS uses primarily negative recognition elements to direct tyrosylation specificity.
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Affiliation(s)
- Marta Cela
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
| | - Caroline Paulus
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
| | - Manuel A. S. Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Magali Frugier
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
- * E-mail:
| | - Joëlle Rudinger-Thirion
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
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17
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Araújo ARD, Melo T, Maciel EA, Pereira C, Morais CM, Santinha DR, Tavares JF, Oliveira H, Jurado AS, Costa V, Domingues P, Domingues MRM, Santos MAS. Errors in protein synthesis increase the level of saturated fatty acids and affect the overall lipid profiles of yeast. PLoS One 2018; 13:e0202402. [PMID: 30148852 PMCID: PMC6110467 DOI: 10.1371/journal.pone.0202402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/02/2018] [Indexed: 12/03/2022] Open
Abstract
The occurrence of protein synthesis errors (mistranslation) above the typical mean mistranslation level of 10−4 is mostly deleterious to yeast, zebrafish and mammal cells. Previous yeast studies have shown that mistranslation affects fitness and deregulates genes related to lipid metabolism, but there is no experimental proof that such errors alter yeast lipid profiles. We engineered yeast strains to misincorporate serine at alanine and glycine sites on a global scale and evaluated the putative effects on the lipidome. Lipids from whole cells were extracted and analysed by thin layer chromatography (TLC), liquid chromatography-mass spectrometry(LC-MS) and gas chromatography (GC). Oxidative damage, fatty acid desaturation and membrane fluidity changes were screened to identify putative alterations in lipid profiles in both logarithmic (fermentative) and post-diauxic shift (respiratory) phases. There were alterations in several lipid classes, namely lyso-phosphatidylcholine, phosphatidic acid, phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, and triglyceride, and in the fatty acid profiles, namely C16:1, C16:0, C18:1 and C18:0. Overall, the relative content of lipid species with saturated FA increased in detriment of those with unsaturated fatty acids. The expression of the OLE1 mRNA was deregulated, but phospholipid fluidity changes were not observed. These data expand current knowledge of mistranslation biology and highlight its putative roles in human diseases.
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Affiliation(s)
- Ana Rita D. Araújo
- Department of Medical Sciences and Institute of Biomedicine–iBiMED, University of Aveiro, Aveiro, Portugal
- Mass Spectrometry Center, Department of Chemistry, QOPNA, University of Aveiro, Aveiro, Portugal
| | - Tânia Melo
- Mass Spectrometry Center, Department of Chemistry, QOPNA, University of Aveiro, Aveiro, Portugal
| | - Elisabete A. Maciel
- Mass Spectrometry Center, Department of Chemistry, QOPNA, University of Aveiro, Aveiro, Portugal
- Department of Biology, CESAM, University of Aveiro, Aveiro, Portugal
| | - Clara Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Catarina M. Morais
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Deolinda R. Santinha
- Mass Spectrometry Center, Department of Chemistry, QOPNA, University of Aveiro, Aveiro, Portugal
| | - Joana F. Tavares
- Department of Medical Sciences and Institute of Biomedicine–iBiMED, University of Aveiro, Aveiro, Portugal
| | - Helena Oliveira
- Laboratory of Biotechnology and Cytomics, Department of Biology, CESAM, University of Aveiro, Aveiro, Portugal
| | - Amália S. Jurado
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Vítor Costa
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Pedro Domingues
- Mass Spectrometry Center, Department of Chemistry, QOPNA, University of Aveiro, Aveiro, Portugal
| | - Maria Rosário M. Domingues
- Mass Spectrometry Center, Department of Chemistry, QOPNA, University of Aveiro, Aveiro, Portugal
- * E-mail: (MASS); (MRMD)
| | - Manuel A. S. Santos
- Department of Medical Sciences and Institute of Biomedicine–iBiMED, University of Aveiro, Aveiro, Portugal
- * E-mail: (MASS); (MRMD)
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Santos M, Pereira PM, Varanda AS, Carvalho J, Azevedo M, Mateus DD, Mendes N, Oliveira P, Trindade F, Pinto MT, Bordeira-Carriço R, Carneiro F, Vitorino R, Oliveira C, Santos MAS. Codon misreading tRNAs promote tumor growth in mice. RNA Biol 2018; 15:773-786. [PMID: 29558247 DOI: 10.1080/15476286.2018.1454244] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 02/07/2023] Open
Abstract
Deregulation of tRNAs, aminoacyl-tRNA synthetases and tRNA modifying enzymes are common in cancer, raising the hypothesis that protein synthesis efficiency and accuracy (mistranslation) are compromised in tumors. We show here that human colon tumors and xenograft tumors produced in mice by two epithelial cancer cell lines mistranslate 2- to 4-fold more frequently than normal tissue. To clarify if protein mistranslation plays a role in tumor biology, we expressed mutant Ser-tRNAs that misincorporate Ser-at-Ala (frequent error) and Ser-at-Leu (infrequent error) in NIH3T3 cells and investigated how they responded to the proteome instability generated by the amino acid misincorporations. There was high tolerance to both misreading tRNAs, but the Ser-to-Ala misreading tRNA was a more potent inducer of cell transformation, stimulated angiogenesis and produced faster growing tumors in mice than the Ser-to-Leu misincorporating tRNA. Upregulation of the Akt pathway and the UPR were also observed. Most surprisingly, the relative expression of both misreading tRNAs increased during tumor growth, suggesting that protein mistranslation is advantageous in cancer contexts. These data highlight new features of protein synthesis deregulation in tumor biology.
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Affiliation(s)
- Mafalda Santos
- a Department of Medical Sciences and Institute of Biomedicine - iBiMED , University of Aveiro , Aveiro , Portugal.,b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Patricia M Pereira
- a Department of Medical Sciences and Institute of Biomedicine - iBiMED , University of Aveiro , Aveiro , Portugal.,b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal
| | - A Sofia Varanda
- a Department of Medical Sciences and Institute of Biomedicine - iBiMED , University of Aveiro , Aveiro , Portugal.,b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Joana Carvalho
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Mafalda Azevedo
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal
| | - Denisa D Mateus
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal
| | - Nuno Mendes
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Patricia Oliveira
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Fábio Trindade
- a Department of Medical Sciences and Institute of Biomedicine - iBiMED , University of Aveiro , Aveiro , Portugal.,d Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine , University of Porto , Porto , Portugal
| | - Marta Teixeira Pinto
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Renata Bordeira-Carriço
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal
| | - Fátima Carneiro
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal.,e Dept. of Pathology, Faculty of Medicine , University of Porto , Porto , Portugal
| | - Rui Vitorino
- a Department of Medical Sciences and Institute of Biomedicine - iBiMED , University of Aveiro , Aveiro , Portugal
| | - Carla Oliveira
- b Expression Regulation in Cancer, Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal.,c Instituto de Investigação e Inovação em Saúde, University of Porto , Porto , Portugal.,e Dept. of Pathology, Faculty of Medicine , University of Porto , Porto , Portugal
| | - Manuel A S Santos
- a Department of Medical Sciences and Institute of Biomedicine - iBiMED , University of Aveiro , Aveiro , Portugal
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19
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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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20
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Perego J, Mendes A, Bourbon C, Camosseto V, Combes A, Liu H, Manh TPV, Dalet A, Chasson L, Spinelli L, Bardin N, Chiche L, Santos MAS, Gatti E, Pierre P. Guanabenz inhibits TLR9 signaling through a pathway that is independent of eIF2α dephosphorylation by the GADD34/PP1c complex. Sci Signal 2018; 11:11/514/eaam8104. [PMID: 29363586 DOI: 10.1126/scisignal.aam8104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endoplasmic reticulum (ER) stress triggers or amplifies inflammatory signals and cytokine production in immune cells. Upon the resolution of ER stress, the inducible phosphatase 1 cofactor GADD34 promotes the dephosphorylation of the initiation factor eIF2α, thereby enabling protein translation to resume. Several aminoguanidine compounds, such as guanabenz, perturb the eIF2α phosphorylation-dephosphorylation cycle and protect different cell or tissue types from protein misfolding and degeneration. We investigated how pharmacological interference with the eIF2α pathway could be beneficial to treat autoinflammatory diseases dependent on proinflammatory cytokines and type I interferons (IFNs), the production of which is regulated by GADD34 in dendritic cells (DCs). In mouse and human DCs and B cells, guanabenz prevented the activation of Toll-like receptor 9 (TLR9) by CpG oligodeoxynucleotides or DNA-immunoglobulin complexes in endosomes. In vivo, guanabenz protected mice from CpG oligonucleotide-dependent cytokine shock and decreased autoimmune symptom severity in a chemically induced model of systemic lupus erythematosus. However, we found that guanabenz exerted its inhibitory effect independently of GADD34 activity on eIF2α and instead decreased the abundance of CH25H, a cholesterol hydroxylase linked to antiviral immunity. Our results therefore suggest that guanabenz and similar compounds could be used to treat type I IFN-dependent pathologies and that CH25H could be a therapeutic target to control these diseases.
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Affiliation(s)
- Jessica Perego
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Andreia Mendes
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France.,International Associated Laboratory (LIA) CNRS "Mistra," 13008 Marseille, France
| | - Clarisse Bourbon
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Voahirana Camosseto
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France.,International Associated Laboratory (LIA) CNRS "Mistra," 13008 Marseille, France
| | - Alexis Combes
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Hong Liu
- Sanofi, Cambridge, MA 02139, USA
| | - Thien-Phong Vu Manh
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Alexandre Dalet
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Lionel Chasson
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Lionel Spinelli
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France
| | - Nathalie Bardin
- Laboratoire d'Immunologie, Hôpital de la Conception, 13005 Marseille, France.,Aix Marseille Université, INSERM, VRCM, 13005 Marseille, France
| | | | - Manuel A S Santos
- International Associated Laboratory (LIA) CNRS "Mistra," 13008 Marseille, France.,Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program University of Aveiro, 3810-193 Aveiro, Portugal
| | - Evelina Gatti
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France. .,International Associated Laboratory (LIA) CNRS "Mistra," 13008 Marseille, France.,Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13008 Marseille, France. .,International Associated Laboratory (LIA) CNRS "Mistra," 13008 Marseille, France.,Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program University of Aveiro, 3810-193 Aveiro, Portugal
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21
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Bódi Z, Farkas Z, Nevozhay D, Kalapis D, Lázár V, Csörgő B, Nyerges Á, Szamecz B, Fekete G, Papp B, Araújo H, Oliveira JL, Moura G, Santos MAS, Székely T, Balázsi G, Pál C. Correction: Phenotypic heterogeneity promotes adaptive evolution. PLoS Biol 2017. [PMID: 28632738 PMCID: PMC5478090 DOI: 10.1371/journal.pbio.1002607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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22
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Bódi Z, Farkas Z, Nevozhay D, Kalapis D, Lázár V, Csörgő B, Nyerges Á, Szamecz B, Fekete G, Papp B, Araújo H, Oliveira JL, Moura G, Santos MAS, Székely T, Balázsi G, Pál C. Phenotypic heterogeneity promotes adaptive evolution. PLoS Biol 2017; 15:e2000644. [PMID: 28486496 PMCID: PMC5423553 DOI: 10.1371/journal.pbio.2000644] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [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: 08/04/2016] [Accepted: 04/06/2017] [Indexed: 11/22/2022] Open
Abstract
Genetically identical cells frequently display substantial heterogeneity in gene expression, cellular morphology and physiology. It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits, phenotypic heterogeneity (or plasticity) accelerates the rate of adaptive evolution in populations facing extreme environmental challenges. This issue is important as cell-to-cell phenotypic heterogeneity may initiate key steps in microbial evolution of drug resistance and cancer progression. Here, we study how stochastic transitions between cellular states influence evolutionary adaptation to a stressful environment in yeast Saccharomyces cerevisiae. We developed inducible synthetic gene circuits that generate varying degrees of expression stochasticity of an antifungal resistance gene. We initiated laboratory evolutionary experiments with genotypes carrying different versions of the genetic circuit by exposing the corresponding populations to gradually increasing antifungal stress. Phenotypic heterogeneity altered the evolutionary dynamics by transforming the adaptive landscape that relates genotype to fitness. Specifically, it enhanced the adaptive value of beneficial mutations through synergism between cell-to-cell variability and genetic variation. Our work demonstrates that phenotypic heterogeneity is an evolving trait when populations face a chronic selection pressure. It shapes evolutionary trajectories at the genomic level and facilitates evolutionary rescue from a deteriorating environmental stress. Phenotypic heterogeneity of genetically identical cells can generate nonheritable variation in a population. Is this heterogeneity favorable for microbes? In a changing environment, the answer is a definite yes. While scholars have argued that stochastically generated variation precedes genetic changes and thereby facilitate the evolution of complex traits, this idea has remained disputed, not least because of the shortage of experimental studies. We address this long-standing and controversial issue by integrating synthetic biology, laboratory experimental evolution, and genomic analyses. We explicitly tested the mechanisms whereby phenotypic heterogeneity may promote evolvability. Our work demonstrates that phenotypic heterogeneity facilitates evolutionary rescue from deteriorating environmental stress by generating individuals with exceptionally high fitness. Remarkably, elevated phenotypic heterogeneity evolves as a direct response to stress and thereby it promotes evolution of rare combinations of mutations. These results indicate that phenotypic heterogeneity might have an important role in the evolution of key innovations.
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Affiliation(s)
- Zoltán Bódi
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Zoltán Farkas
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Dmitry Nevozhay
- Department of Systems Biology - Unit 950, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Dorottya Kalapis
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Béla Szamecz
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
| | - Hugo Araújo
- DETI & IEETA, University of Aveiro, Aveiro, Portugal
| | | | - Gabriela Moura
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Tamás Székely
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America.,Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - Gábor Balázsi
- Department of Systems Biology - Unit 950, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.,The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America.,Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
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23
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Gaspar P, Moura G, Santos MAS, Oliveira JL. mRNA secondary structure optimization using a correlated stem–loop prediction. Nucleic Acids Res 2016; 44:5490. [PMID: 26917014 PMCID: PMC4914086 DOI: 10.1093/nar/gkw127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paulo Gaspar
- DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Gabriela Moura
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Manuel A S Santos
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - José Luís Oliveira
- DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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24
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25
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Simões J, Bezerra AR, Moura GR, Araújo H, Gut I, Bayes M, Santos MAS. The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons. Front Microbiol 2016; 7:401. [PMID: 27065968 PMCID: PMC4814463 DOI: 10.3389/fmicb.2016.00401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.
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Affiliation(s)
- João Simões
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Ana R Bezerra
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Gabriela R Moura
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Hugo Araújo
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Ivo Gut
- Centro Nacional de Análises Genómico, Parc Científic Barcelona, Spain
| | - Mónica Bayes
- Centro Nacional de Análises Genómico, Parc Científic Barcelona, Spain
| | - Manuel A S Santos
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
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26
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Rizzetto L, Ifrim DC, Moretti S, Tocci N, Cheng SC, Quintin J, Renga G, Oikonomou V, De Filippo C, Weil T, Blok BA, Lenucci MS, Santos MAS, Romani L, Netea MG, Cavalieri D. Fungal Chitin Induces Trained Immunity in Human Monocytes during Cross-talk of the Host with Saccharomyces cerevisiae. J Biol Chem 2016; 291:7961-72. [PMID: 26887946 DOI: 10.1074/jbc.m115.699645] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [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: 10/20/2015] [Indexed: 11/06/2022] Open
Abstract
The immune system is essential to maintain the mutualistic homeostatic interaction between the host and its micro- and mycobiota. Living as a commensal,Saccharomyces cerevisiaecould potentially shape the immune response in a significant way. We observed thatS. cerevisiaecells induce trained immunity in monocytes in a strain-dependent manner through enhanced TNFα and IL-6 production upon secondary stimulation with TLR ligands, as well as bacterial and fungal commensals. Differential chitin content accounts for the differences in training properties observed among strains, driving induction of trained immunity by increasing cytokine production and direct antimicrobial activity bothin vitroandin vivo These chitin-induced protective properties are intimately associated with its internalization, identifying a critical role of phagosome acidification to facilitate microbial digestion. This study reveals how commensal and passenger microorganisms could be important in promoting health and preventing mucosal diseases by modulating host defense toward pathogens and thus influencing the host microbiota-immune system interactions.
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Affiliation(s)
- Lisa Rizzetto
- From the Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige TN, Italy
| | - Daniela C Ifrim
- the Department of Internal Medicine, Division of Experimental Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Silvia Moretti
- the Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, 06123 Perugia PG, Italy
| | - Noemi Tocci
- From the Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige TN, Italy
| | - Shih-Chin Cheng
- the Department of Internal Medicine, Division of Experimental Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Jessica Quintin
- the Department of Internal Medicine, Division of Experimental Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Giorgia Renga
- the Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, 06123 Perugia PG, Italy
| | - Vasilis Oikonomou
- the Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, 06123 Perugia PG, Italy
| | - Carlotta De Filippo
- From the Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige TN, Italy, the Institute of Biometeorology, National Research Council, 50145 Florence, Italy
| | - Tobias Weil
- From the Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige TN, Italy
| | - Bastiaan A Blok
- the Department of Internal Medicine, Division of Experimental Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marcello S Lenucci
- the Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce LE, Italy
| | - Manuel A S Santos
- the Department of Biology and CESAM (Centro de Estudos do Ambiente e do Mar), University of Aveiro, 3810-193 Aveiro, Portugal, and
| | - Luigina Romani
- the Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, 06123 Perugia PG, Italy
| | - Mihai G Netea
- the Department of Internal Medicine, Division of Experimental Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Duccio Cavalieri
- From the Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige TN, Italy, the Institute of Biometeorology, National Research Council, 50145 Florence, Italy, the Department of Biology, University of Florence, 50019 Sesto Fiorentino FI, Italy
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27
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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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Soares AR, Fernandes N, Reverendo M, Araújo HR, Oliveira JL, Moura GMR, Santos MAS. Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Mol Biol 2015; 16:22. [PMID: 26694924 PMCID: PMC4688932 DOI: 10.1186/s12867-015-0050-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 05/27/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identification by next generation sequencing (NGS) we are still far from understanding their full diversity and functional repertoire. RESULTS Here we report the identification of tRNA derived fragments (tRFs) by NGS of the sncRNA fraction of zebrafish. The tRFs identified are 18-30 nt long, are derived from specific 5' and 3' processing of mature tRNAs and are differentially expressed during development and in differentiated tissues, suggesting that they are likely produced by specific processing rather than random degradation of tRNAs. We further show that a highly expressed tRF (5'tRF-Pro(CGG)) is cleaved in vitro by Dicer and has silencing ability, indicating that it can enter the RNAi pathway. A computational analysis of zebrafish tRFs shows that they are conserved among vertebrates and mining of publicly available datasets reveals that some 5'tRFs are differentially expressed in disease conditions, namely during infection and colorectal cancer. CONCLUSIONS tRFs constitute a class of conserved regulatory RNAs in vertebrates and may be involved in mechanisms of genome regulation and in some diseases.
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Affiliation(s)
- Ana Raquel Soares
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Noémia Fernandes
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Marisa Reverendo
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
| | | | | | - Gabriela M R Moura
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Manuel A S Santos
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
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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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Bezerra AR, Guimarães AR, Santos MAS. Non-Standard Genetic Codes Define New Concepts for Protein Engineering. Life (Basel) 2015; 5:1610-28. [PMID: 26569314 PMCID: PMC4695839 DOI: 10.3390/life5041610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/12/2015] [Accepted: 10/21/2015] [Indexed: 11/16/2022] Open
Abstract
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.
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Affiliation(s)
- Ana R Bezerra
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Ana R Guimarães
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Manuel A S Santos
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
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Calejo AI, Reverendo M, Silva VS, Pereira PM, Santos MAS, Zorec R, Gonçalves PP. Differences in the expression pattern of HCN isoforms among mammalian tissues: sources and implications. Mol Biol Rep 2014; 41:297-307. [PMID: 24234751 DOI: 10.1007/s11033-013-2862-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 11/05/2013] [Indexed: 01/28/2023]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels play a critical role in a broad range of cell types, but the expression of the various HCN isoforms is still poorly understood. In the present study we have compared the expression of HCN isoforms in rat excitable and non-excitable tissues at both the mRNA and protein levels. Real-time PCR and Western blot analysis revealed distinct expression patterns of the four HCN isoforms in brain, heart, pituitary and kidney, with inconsistent mRNA-protein expression correlation. The HCN2 was the most abundant mRNA transcript (95.6, 78.0 and 59.0 % in kidney heart and pituitary, respectively) except in the brain (42.0 %) whereas HCN4 was the most abundant protein isoform. Our results suggest that HCN channels are mostly produced by the HCN4 isoform in heart, which contrasts with the sharp differences in the isoform stoichiometry in pituitary (15 HCN4:2 HCN2:1 HCN1:1 HCN3), kidney (24 HCN4:2 HCN3:1 HCN2:1 HCN1) and brain (3 HCN4:2 HCN2:1 HCN1:1 HCN3). Moreover, deviations of the electrophoretic molecular weight (MW) of the HCN isoforms relative to the theoretical MW were observed, suggesting that N-glycosylation and enzymatic proteolysis influences HCN channel surface expression. We hypothesize that selective cleavage of HCN channels by membrane bound metalloendopeptidases could account for the multiplicity of properties of native HCN channels in different tissues.
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Ribas de Pouplana L, Santos MAS, Zhu JH, Farabaugh PJ, Javid B. Protein mistranslation: friend or foe? Trends Biochem Sci 2014; 39:355-62. [PMID: 25023410 DOI: 10.1016/j.tibs.2014.06.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [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: 04/14/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 01/03/2023]
Abstract
The translation of genes into functional proteins involves error. Mistranslation is a known cause of disease, but, surprisingly, recent studies suggest that certain organisms from all domains of life have evolved diverse pathways that increase their tolerance of translational error. Although the reason for these high error rates are not yet clear, evidence suggests that increased mistranslation may have a role in the generation of diversity within the proteome and other adaptive functions. Error rates are regulated, and there appears to be an optimal mistranslation rate that varies by organism and environmental condition. Advances in unbiased interrogation of error types and experiments involving wild organisms may help our understanding of the potentially adaptive roles for protein translation errors.
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Affiliation(s)
- Liuís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), c/Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Manuel A S Santos
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Jun-Hao Zhu
- Centre for Infectious Diseases Research, Tsinghua University School of Medicine, Beijing, China
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Babak Javid
- Centre for Infectious Diseases Research, Tsinghua University School of Medicine, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China.
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Fernandes J, Vieira M, Carreto L, Santos MAS, Duarte CB, Carvalho AL, Santos AE. In vitro ischemia triggers a transcriptional response to down-regulate synaptic proteins in hippocampal neurons. PLoS One 2014; 9:e99958. [PMID: 24960035 PMCID: PMC4069008 DOI: 10.1371/journal.pone.0099958] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 02/19/2014] [Accepted: 05/20/2014] [Indexed: 11/26/2022] Open
Abstract
Transient global cerebral ischemia induces profound changes in the transcriptome of brain cells, which is partially associated with the induction or repression of genes that influence the ischemic response. However, the mechanisms responsible for the selective vulnerability of hippocampal neurons to global ischemia remain to be clarified. To identify molecular changes elicited by ischemic insults, we subjected hippocampal primary cultures to oxygen-glucose deprivation (OGD), an in vitro model for global ischemia that resulted in delayed neuronal death with an excitotoxic component. To investigate changes in the transcriptome of hippocampal neurons submitted to OGD, total RNA was extracted at early (7 h) and delayed (24 h) time points after OGD and used in a whole-genome RNA microarray. We observed that at 7 h after OGD there was a general repression of genes, whereas at 24 h there was a general induction of gene expression. Genes related with functions such as transcription and RNA biosynthesis were highly regulated at both periods of incubation after OGD, confirming that the response to ischemia is a dynamic and coordinated process. Our analysis showed that genes for synaptic proteins, such as those encoding for PICK1, GRIP1, TARPγ3, calsyntenin-2/3, SAPAP2 and SNAP-25, were down-regulated after OGD. Additionally, OGD decreased the mRNA and protein expression levels of the GluA1 AMPA receptor subunit as well as the GluN2A and GluN2B subunits of NMDA receptors, but increased the mRNA expression of the GluN3A subunit, thus altering the composition of ionotropic glutamate receptors in hippocampal neurons. Together, our results present the expression profile elicited by in vitro ischemia in hippocampal neurons, and indicate that OGD activates a transcriptional program leading to down-regulation in the expression of genes coding for synaptic proteins, suggesting that the synaptic proteome may change after ischemia.
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Affiliation(s)
- Joana Fernandes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Marta Vieira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 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
| | - Carlos B. Duarte
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Ana Luísa Carvalho
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
- * E-mail:
| | - Armanda E. Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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Bordeira-Carriço R, Ferreira D, Mateus DD, Pinheiro H, Pêgo AP, Santos MAS, Oliveira C. Rescue of wild-type E-cadherin expression from nonsense-mutated cancer cells by a suppressor-tRNA. Eur J Hum Genet 2014; 22:1085-92. [PMID: 24424122 DOI: 10.1038/ejhg.2013.292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 11/12/2013] [Accepted: 11/20/2013] [Indexed: 02/07/2023] Open
Abstract
Hereditary diffuse gastric cancer (HDGC) syndrome, although rare, is highly penetrant at an early age, and is severe and incurable because of ineffective screening tools and therapy. Approximately 45% of HDGC families carry germline CDH1/E-cadherin alterations, 20% of which are nonsense leading to premature protein truncation. Prophylactic gastrectomy is the only recommended approach for all asymptomatic CDH1 mutation carriers. Suppressor-tRNAs can replace premature stop codons (PTCs) with a cognate amino acid, inducing readthrough and generating full-length proteins. The use of suppressor-tRNAs in HDGC patients could therefore constitute a less invasive therapeutic option for nonsense mutation carriers, delaying the development of gastric cancer. Our analysis revealed that 23/108 (21.3%) of E-cadherin-mutant families carried nonsense mutations that could be potentially corrected by eight suppressor-tRNAs, and arginine was the most frequently affected amino acid. Using site-directed mutagenesis, we developed an arginine suppressor-tRNA vector to correct one HDGC nonsense mutation. E-cadherin- deficient cell lines were transfected with plasmids carrying simultaneously the suppressor-tRNA and wild-type or mutant CDH1 mini-genes. RT-PCR, western blot, immunofluorescence, flow cytometry and proximity ligation assay (PLA) were used to establish the model, and monitor mRNA and protein expression and function recovery from CDH1 vectors. Cells expressing a CDH1 mini-gene, carrying a nonsense mutation and the suppressor-tRNA, recovered full-length E-cadherin expression and its correct localization and incorporation into the adhesion complex. This is the first demonstration of functional recovery of a mutated causative gene in hereditary cancer by cognate amino acid replacement with suppressor-tRNAs. Of the HDGC families, 21.3% are candidates for correction with suppressor-tRNAs to potentially delay cancer onset.
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Affiliation(s)
- Renata Bordeira-Carriço
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Daniel Ferreira
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Denisa D Mateus
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Hugo Pinheiro
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Paula Pêgo
- 1] INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal [2] Universidade do Porto-Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal [3] Universidade do Porto-Faculdade de Engenharia, Porto, Portugal
| | - Manuel A S Santos
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- 1] Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal [2] Faculty of Medicine of the University of Porto, Porto, Portugal
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Silva A, Sampaio-Marques B, Fernandes Â, Carreto L, Rodrigues F, Holcik M, Santos MAS, Ludovico P. Involvement of yeast HSP90 isoforms in response to stress and cell death induced by acetic acid. PLoS One 2013; 8:e71294. [PMID: 23967187 PMCID: PMC3744546 DOI: 10.1371/journal.pone.0071294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 03/21/2013] [Accepted: 06/27/2013] [Indexed: 11/18/2022] Open
Abstract
Acetic acid-induced apoptosis in yeast is accompanied by an impairment of the general protein synthesis machinery, yet paradoxically also by the up-regulation of the two isoforms of the heat shock protein 90 (HSP90) chaperone family, Hsc82p and Hsp82p. Herein, we show that impairment of cap-dependent translation initiation induced by acetic acid is caused by the phosphorylation and inactivation of eIF2α by Gcn2p kinase. A microarray analysis of polysome-associated mRNAs engaged in translation in acetic acid challenged cells further revealed that HSP90 mRNAs are over-represented in this polysome fraction suggesting preferential translation of HSP90 upon acetic acid treatment. The relevance of HSP90 isoform translation during programmed cell death (PCD) was unveiled using genetic and pharmacological abrogation of HSP90, which suggests opposing roles for HSP90 isoforms in cell survival and death. Hsc82p appears to promote survival and its deletion leads to necrotic cell death, while Hsp82p is a pro-death molecule involved in acetic acid-induced apoptosis. Therefore, HSP90 isoforms have distinct roles in the control of cell fate during PCD and their selective translation regulates cellular response to acetic acid stress.
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Affiliation(s)
- Alexandra Silva
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ângela Fernandes
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Laura Carreto
- Department of Biology and Centre d’Enseignement de la Statistique Appliquée à la Médecine, University of Aveiro, Aveiro, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Martin Holcik
- Apoptosis Research Centre, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Manuel A. S. Santos
- Department of Biology and Centre d’Enseignement de la Statistique Appliquée à la Médecine, University of Aveiro, Aveiro, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail:
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Mateus DD, Paredes JA, Español Y, Ribas de Pouplana L, Moura GR, Santos MAS. Molecular reconstruction of a fungal genetic code alteration. RNA Biol 2013; 10:969-80. [PMID: 23619021 DOI: 10.4161/rna.24683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 11/19/2022] Open
Abstract
Fungi of the CTG clade translate the Leu CUG codon as Ser. This genetic code alteration is the only eukaryotic sense-to-sense codon reassignment known to date, is mediated by an ambiguous serine tRNA (tRNACAG(Ser)), exposes unanticipated flexibility of the genetic code and raises major questions about its selection and fixation in this fungal lineage. In particular, the origin of the tRNACAG(Ser) and the evolutionary mechanism of CUG reassignment from Leu to Ser remain poorly understood. In this study, we have traced the origin of the tDNACAG(Ser) gene and studied critical mutations in the tRNACAG(Ser) anticodon-loop that modulated CUG reassignment. Our data show that the tRNACAG(Ser) emerged from insertion of an adenosine in the middle position of the 5'-CGA-3'anticodon of a tRNACGA(Ser) ancestor, producing the 5'-CAG-3' anticodon of the tRNACAG(Ser), without altering its aminoacylation properties. This mutation initiated CUG reassignment while two additional mutations in the anticodon-loop resolved a structural conflict produced by incorporation of the Leu 5'-CAG-3'anticodon in the anticodon-arm of a tRNA(Ser). Expression of the mutant tRNACAG(Ser) in yeast showed that it cannot be expressed at physiological levels and we postulate that such downregulation was essential to maintain Ser misincorporation at sub-lethal levels during the initial stages of CUG reassignment. We demonstrate here that such low level CUG ambiguity is advantageous in specific ecological niches and we propose that misreading tRNAs are targeted for degradation by an unidentified tRNA quality control pathway.
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Affiliation(s)
- Denisa D Mateus
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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Quintela T, Gonçalves I, Carreto LC, Santos MAS, Marcelino H, Patriarca FM, Santos CRA. Analysis of the effects of sex hormone background on the rat choroid plexus transcriptome by cDNA microarrays. PLoS One 2013; 8:e60199. [PMID: 23585832 PMCID: PMC3622009 DOI: 10.1371/journal.pone.0060199] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 11/16/2012] [Accepted: 02/22/2013] [Indexed: 01/20/2023] Open
Abstract
The choroid plexus (CP) are highly vascularized branched structures that protrude into the ventricles of the brain, and form a unique interface between the blood and the cerebrospinal fluid (CSF), the blood-CSF barrier, that are the main site of production and secretion of CSF. Sex hormones are widely recognized as neuroprotective agents against several neurodegenerative diseases, and the presence of sex hormones cognate receptors suggest that it may be a target for these hormones. In an effort to provide further insight into the neuroprotective mechanisms triggered by sex hormones we analyzed gene expression differences in the CP of female and male rats subjected to gonadectomy, using microarray technology. In gonadectomized female and male animals, 3045 genes were differentially expressed by 1.5-fold change, compared to sham controls. Analysis of the CP transcriptome showed that the top-five pathways significantly regulated by the sex hormone background are olfactory transduction, taste transduction, metabolism, steroid hormone biosynthesis and circadian rhythm pathways. These results represent the first overview of global expression changes in CP of female and male rats induced by gonadectomy and suggest that sex hormones are implicated in pathways with central roles in CP functions and CSF homeostasis.
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Affiliation(s)
- Telma Quintela
- CICS-UBI – Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Isabel Gonçalves
- CICS-UBI – Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Laura C. Carreto
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Manuel A. S. Santos
- CICS-UBI – Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Helena Marcelino
- CICS-UBI – Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Filipa M. Patriarca
- CICS-UBI – Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Cecília R. A. Santos
- CICS-UBI – Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- * E-mail:
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Abstract
Secondary structure of messenger RNA plays an important role in the bio-synthesis of proteins. Its negative impact on translation can reduce the yield of protein by slowing or blocking the initiation and movement of ribosomes along the mRNA, becoming a major factor in the regulation of gene expression. Several algorithms can predict the formation of secondary structures by calculating the minimum free energy of RNA sequences, or perform the inverse process of obtaining an RNA sequence for a given structure. However, there is still no approach to redesign an mRNA to achieve minimal secondary structure without affecting the amino acid sequence. Here we present the first strategy to optimize mRNA secondary structures, to increase (or decrease) the minimum free energy of a nucleotide sequence, without changing its resulting polypeptide, in a time-efficient manner, through a simplistic approximation to hairpin formation. Our data show that this approach can efficiently increase the minimum free energy by >40%, strongly reducing the strength of secondary structures. Applications of this technique range from multi-objective optimization of genes by controlling minimum free energy together with CAI and other gene expression variables, to optimization of secondary structures at the genomic level.
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Affiliation(s)
- Paulo Gaspar
- DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Lousado JP, Oliveira JL, Moura G, Santos MAS. An integrative approach for codon repeats evolutionary analyses. INT J DATA MIN BIOIN 2012; 6:369-81. [PMID: 23155768 DOI: 10.1504/ijdmb.2012.049294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relationship between genome characteristics and several human diseases has been a central research goal in genomics. Many studies have shown that specific gene patterns, such as amino acid repetitions, are associated with human diseases. However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. In this paper, we present a computational solution that facilitates comparative studies of orthologous genes from various organisms. The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering.
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Affiliation(s)
- José Paulo Lousado
- Centro de Estudos em Educação, Tecnologias e Saúde, ESTGL, Instituto Politécnico de Viseu, Campus Politécnico de Viseu, 3504-510 Viseu, Portugal.
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40
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Abstract
UNLABELLED Numerous software applications exist to deal with synthetic gene design, granting the field of heterologous expression a significant support. However, their dispersion requires the access to different tools and online services in order to complete one single project. Analyzing codon usage, calculating codon adaptation index (CAI), aligning orthologs and optimizing genes are just a few examples. A software application, EuGene, was developed for the optimization of multiple gene synthetic design algorithms. In a seamless automatic form, EuGene calculates or retrieves genome data on codon usage (relative synonymous codon usage and CAI), codon context (CPS and codon pair bias), GC content, hidden stop codons, repetitions, deleterious sites, protein primary, secondary and tertiary structures, gene orthologs, species housekeeping genes, performs alignments and identifies genes and genomes. The main function of EuGene is analyzing and redesigning gene sequences using multi-objective optimization techniques that maximize the coding features of the resulting sequence. AVAILABILITY EuGene is freely available for non-commercial use, at http://bioinformatics.ua.pt/eugene.
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Affiliation(s)
- Paulo Gaspar
- DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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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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Paredes JA, Carreto L, Simões J, Bezerra AR, Gomes AC, Santamaria R, Kapushesky M, Moura GR, Santos MAS. Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast. BMC Biol 2012; 10:55. [PMID: 22715922 PMCID: PMC3391182 DOI: 10.1186/1741-7007-10-55] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 06/01/2012] [Accepted: 06/20/2012] [Indexed: 11/21/2022] Open
Abstract
Background Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this, low level gene translational errors induced by mutations and environmental factors cause neurodegeneration and premature death in mice and mitochondrial disorders in humans. Paradoxically, such errors can generate advantageous phenotypic diversity in fungi and bacteria through poorly understood molecular processes. Results In order to clarify the biological relevance of gene translational errors we have engineered codon misreading in yeast and used profiling of total and polysome-associated mRNAs, molecular and biochemical tools to characterize the recombinant cells. We demonstrate here that gene translational errors, which have negligible impact on yeast growth rate down-regulate protein synthesis, activate the unfolded protein response and environmental stress response pathways, and down-regulate chaperones linked to ribosomes. Conclusions We provide the first global view of transcriptional and post-transcriptional responses to global gene translational errors and we postulate that they cause gradual cell degeneration through synergistic effects of overloading protein quality control systems and deregulation of protein synthesis, but generate adaptive phenotypes in unicellular organisms through activation of stress cross-protection. We conclude that these genome wide gene translational infidelities can be degenerative or adaptive depending on cellular context and physiological condition.
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Affiliation(s)
- João A Paredes
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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Carvalho J, van Grieken NC, Pereira PM, Sousa S, Tijssen M, Buffart TE, Diosdado B, Grabsch H, Santos MAS, Meijer G, Seruca R, Carvalho B, Oliveira C. Lack of microRNA-101 causes E-cadherin functional deregulation through EZH2 up-regulation in intestinal gastric cancer. J Pathol 2012; 228:31-44. [PMID: 22450781 DOI: 10.1002/path.4032] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/10/2012] [Accepted: 03/20/2012] [Indexed: 12/21/2022]
Abstract
E-cadherin expression disruption is commonly observed in metastatic epithelial cancers and is a crucial step in gastric cancer (GC) initiation and progression. As aberrant expression of microRNAs often perturb the normal expression/function of pivotal cancer-related genes, we characterized and dissected a pathway that causes E-cadherin dysfunction via loss of microRNA-101 and up-regulation of EZH2 expression in GC. MicroRNA microarray expression profiling and array-CGH were used to reinforce miR-101 involvement in GC. By using quantitative real-time PCR and quantitative SNaPshot genomic PCR, we confirmed that miR-101 was significantly down-regulated in GC (p < 0.0089) in comparison with normal gastric mucosas and, at least in 65% of the GC cases analysed, this down-regulation was caused by deletions and/or microdeletions at miR-101 genomic loci. Moreover, around 40% of cases showing miR-101 down-regulation displayed concomitant EZH2 over-expression (at the RNA and protein levels), which, in turn, was associated with loss/aberrant expression of E-cadherin. Interestingly, this occurred preferentially in intestinal-type GCs, retaining allele(s) untargeted by classical CDH1-inactivating mechanisms. We also demonstrated that miR-101 gain of function or direct inhibition of EZH2 in Kato III GC cells led to a strong depletion of endogenous EZH2 and consequent rescue of E-cadherin membranous localization, mimicking results obtained in clinical GC samples. In conclusion, we show that deletions and/or microdeletions at both miR-101 genomic loci cause mature miR-101 down-regulation, subsequent EZH2 over-expression and E-cadherin dysfunction, specifically in intestinal-type GC.
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Affiliation(s)
- Joana Carvalho
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Portugal; Faculty of Medicine, University of Porto, Portugal
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Schuller D, Cardoso F, Sousa S, Gomes P, Gomes AC, Santos MAS, Casal M. Genetic diversity and population structure of Saccharomyces cerevisiae strains isolated from different grape varieties and winemaking regions. PLoS One 2012; 7:e32507. [PMID: 22393409 PMCID: PMC3290581 DOI: 10.1371/journal.pone.0032507] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [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: 08/03/2011] [Accepted: 01/30/2012] [Indexed: 11/18/2022] Open
Abstract
We herein evaluate intraspecific genetic diversity of fermentative vineyard-associated S. cerevisiae strains and evaluate relationships between grape varieties and geographical location on populational structures. From the musts obtained from 288 grape samples, collected from two wine regions (16 vineyards, nine grape varieties), 94 spontaneous fermentations were concluded and 2820 yeast isolates were obtained that belonged mainly (92%) to the species S. cerevisiae. Isolates were classified in 321 strains by the use of ten microsatellite markers. A high strain diversity (8-43 strains per fermentation) was associated with high percentage (60-100%) of fermenting samples per vineyard, whereas a lower percentage of spontaneous fermentations (0-40%) corresponded to a rather low strain diversity (1-10 strains per fermentation).For the majority of the populations, observed heterozygosity (Ho) was about two to five times lower than the expected heterozygosity (He). The inferred ancestry showed a very high degree of admixture and divergence was observed between both grape variety and geographical region. Analysis of molecular variance showed that 81-93% of the total genetic variation existed within populations, while significant differentiation within the groups could be detected. Results from AMOVA analysis and clustering of allelic frequencies agree in the distinction of genetically more dispersed populations from the larger wine region compared to the less extended region. Our data show that grape variety is a driver of populational structures, because vineyards with distinct varieties harbor genetically more differentiated S. cerevisiae populations. Conversely, S. cerevisiae strains from vineyards in close proximity (5-10 km) that contain the same grape variety tend to be less divergent. Populational similarities did not correlate with the distance between vineyards of the two wine regions. Globally, our results show that populations of S. cerevisiae in vineyards may occur locally due to multi-factorial influences, one of them being the grape variety.
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Affiliation(s)
- Dorit Schuller
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.
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45
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Soares AR, Pereira PM, Ferreira V, Reverendo M, Simões J, Bezerra AR, Moura GR, Santos MAS. Ethanol exposure induces upregulation of specific microRNAs in zebrafish embryos. Toxicol Sci 2012; 127:18-28. [PMID: 22298809 DOI: 10.1093/toxsci/kfs068] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Prenatal exposure to ethanol leads to a myriad of developmental disorders known as fetal alcohol spectrum disorder, often characterized by growth and mental retardation, central nervous system damage, and specific craniofacial dysmorphic features. The mechanisms of ethanol toxicity are not fully understood, but exposure during development affects the expression of several genes involved in cell cycle control, apoptosis, and transcriptional regulation. MicroRNAs (miRNAs) are implicated in some of these processes, however, it is not yet clear if they are involved in ethanol-induced toxicity. In order to clarify this question, we have exposed zebrafish embryos to ethanol and evaluated whether a miRNA deregulation signature could be obtained. Zebrafish embryos were exposed to 1 and 1.5% of ethanol from 4 h postfertilization (hpf) to 24 hpf. The miRNA expression profiles obtained reveal significant miRNA deregulation and show that both ethanol concentrations upregulate miR-153a, miR-725, miR-30d, let-7k, miR-100, miR-738, and miR-732. Putative gene targets of deregulated miRNAs are involved in cell cycle control, apoptosis, and transcription, which are the main processes affected by ethanol toxicity. The conservation of affected mechanisms among vertebrates leads us to postulate that similar miRNA deregulation occurs in humans, highlighting a relevant role of miRNAs in ethanol toxicology.
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Affiliation(s)
- Ana Raquel Soares
- RNA Biology Laboratory, Department of Biology, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
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Soares AR, Pereira PM, Santos MAS. Next-generation sequencing of miRNAs with Roche 454 GS-FLX technology: steps for a successful application. Methods Mol Biol 2012; 822:189-204. [PMID: 22144200 DOI: 10.1007/978-1-61779-427-8_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs (sRNAs) of approximately 22 nucleotides in length that control eukaryotic gene expression at the translational level. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, the immune response, and infection. Their identification is essential to understand eukaryotic biology. Their small size, low abundance, and high instability complicated early identification, however new generation genome sequencing approaches, such as the Roche 454 Pyrosequencer, allow for both miRNA identification and for generating miRNA profiles in a given sample. This technique avoids cloning steps in bacteria and is a fast and bias-minimized tool to discover novel miRNAs and other sRNAs on a genome-wide scale. Prior to sequencing, cDNA libraries are built for each sample using total RNA as starter material. Each cDNA library can be tagged with specific identifier sequences that allow sequencing different samples in the same chip run. Here, we describe the protocols for the construction of sRNA cDNA libraries for 454 sequencing, and we include tips for overcoming problems often encountered during cDNA library preparation.
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Affiliation(s)
- Ana Raquel Soares
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal.
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Novais SC, Howcroft CF, Carreto L, Pereira PM, Santos MAS, De Coen W, Soares AMVM, Amorim MJB. Differential gene expression analysis in Enchytraeus albidus exposed to natural and chemical stressors at different exposure periods. Ecotoxicology 2012; 21:213-224. [PMID: 21892792 DOI: 10.1007/s10646-011-0780-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/20/2011] [Indexed: 05/31/2023]
Abstract
The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on E. albidus gene expression, during exposure periods of 2, 4 and 21 days, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al. 2011). The main objectives of this study were: (1) to assess changes in gene expression of E. albidus over time, and (2) to identify molecular markers for natural and chemical exposures. Results showed an influence of exposure time on gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects in the energy metabolism and cell growth.
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Affiliation(s)
- Sara C Novais
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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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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Franco-Duarte R, Mendes I, Gomes AC, Santos MAS, de Sousa B, Schuller D. Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics. Electrophoresis 2011; 32:1447-55. [DOI: 10.1002/elps.201000640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/24/2011] [Accepted: 02/22/2011] [Indexed: 11/06/2022]
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50
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Carreto L, Eiriz MF, Domingues I, Schuller D, Moura GR, Santos MAS. Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains. BMC Genomics 2011; 12:201. [PMID: 21507216 PMCID: PMC3094312 DOI: 10.1186/1471-2164-12-201] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [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: 12/06/2010] [Accepted: 04/20/2011] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae (Baker's yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments. In spite of recent advances on the study of yeast genome diversity, little is known about the underlying gene expression plasticity. In order to shed new light onto this biological question, we have compared transcriptome profiles of five environmental isolates, clinical and laboratorial strains at different time points of fermentation in synthetic must medium, during exponential and stationary growth phases. RESULTS Our data unveiled diversity in both intensity and timing of gene expression. Genes involved in glucose metabolism and in the stress response elicited during fermentation were among the most variable. This gene expression diversity increased at the onset of stationary phase (diauxic shift). Environmental isolates showed lower average transcript abundance of genes involved in the stress response, assimilation of nitrogen and vitamins, and sulphur metabolism, than other strains. Nitrogen metabolism genes showed significant variation in expression among the environmental isolates. CONCLUSIONS Wild type yeast strains respond differentially to the stress imposed by nutrient depletion, ethanol accumulation and cell density increase, during fermentation of glucose in synthetic must medium. Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.
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Affiliation(s)
- Laura Carreto
- RNA Biology Laboratory, CESAM & Department of Biology, Universidade de Aveiro, Portugal
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