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Kramer S, Karolak NK, Odenwald J, Gabiatti B, Castañeda Londoño P, Zavřelová A, Freire E, Almeida K, Braune S, Moreira C, Eder A, Goos C, Field M, Carrington M, Holetz F, Górna M, Zoltner M. A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 2023; 51:7520-7540. [PMID: 37309887 PMCID: PMC10415143 DOI: 10.1093/nar/gkad497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5'-3'exoribonuclease Xrn1. Kinetoplastida lack Dcp2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. ALPH1 is composed of a catalytic domain flanked by C- and N-terminal extensions. We show that T. brucei ALPH1 is dimeric in vitro and functions within a complex composed of the trypanosome Xrn1 ortholog XRNA and four proteins unique to Kinetoplastida, including two RNA-binding proteins and a CMGC-family protein kinase. All ALPH1-associated proteins share a unique and dynamic localization to a structure at the posterior pole of the cell, anterior to the microtubule plus ends. XRNA affinity capture in T. cruzi recapitulates this interaction network. The ALPH1 N-terminus is not required for viability in culture, but essential for posterior pole localization. The C-terminus, in contrast, is required for localization to all RNA granule types, as well as for dimerization and interactions with XRNA and the CMGC kinase, suggesting possible regulatory mechanisms. Most significantly, the trypanosome decapping complex has a unique composition, differentiating the process from opisthokonts.
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Affiliation(s)
| | - Natalia Katarzyna Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Bernardo Gabiatti
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | | | - Anna Zavřelová
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | | | | | - Silke Braune
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Claudia Moreira
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Amelie Eder
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Mark Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Fabiola Holetz
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
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Cerqueira-Silva T, Shah SA, Robertson C, Sanchez M, Katikireddi SV, de Araujo Oliveira V, Paixão ES, Rudan I, Junior JB, Penna GO, Pearce N, Werneck GL, Barreto ML, Boaventura VS, Sheikh A, Barral-Netto M. Effectiveness of mRNA boosters after homologous primary series with BNT162b2 or ChAdOx1 against symptomatic infection and severe COVID-19 in Brazil and Scotland: A test-negative design case-control study. PLoS Med 2023; 20:e1004156. [PMID: 36630477 PMCID: PMC9879484 DOI: 10.1371/journal.pmed.1004156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 01/26/2023] [Accepted: 12/13/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Brazil and Scotland have used mRNA boosters in their respective populations since September 2021, with Omicron's emergence accelerating their booster program. Despite this, both countries have reported substantial recent increases in Coronavirus Disease 2019 (COVID-19) cases. The duration of the protection conferred by the booster dose against symptomatic Omicron cases and severe outcomes is unclear. METHODS AND FINDINGS Using a test-negative design, we analyzed national databases to estimate the vaccine effectiveness (VE) of a primary series (with ChAdOx1 or BNT162b2) plus an mRNA vaccine booster (with BNT162b2 or mRNA-1273) against symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and severe COVID-19 outcomes (hospitalization or death) during the period of Omicron dominance in Brazil and Scotland compared to unvaccinated individuals. Additional analyses included stratification by age group (18 to 49, 50 to 64, ≥65). All individuals aged 18 years or older who reported acute respiratory illness symptoms and tested for SARS-CoV-2 infection between January 1, 2022, and April 23, 2022, in Brazil and Scotland were eligible for the study. At 14 to 29 days after the mRNA booster, the VE against symptomatic SARS-CoV-2 infection of ChAdOx1 plus BNT162b2 booster was 51.6%, (95% confidence interval (CI): [51.0, 52.2], p < 0.001) in Brazil and 67.1% (95% CI [65.5, 68.5], p < 0.001) in Scotland. At ≥4 months, protection against symptomatic infection waned to 4.2% (95% CI [0.7, 7.6], p = 0.02) in Brazil and 37.4% (95% CI [33.8, 40.9], p < 0.001) in Scotland. VE against severe outcomes in Brazil was 93.5% (95% CI [93.0, 94.0], p < 0.001) at 14 to 29 days post-booster, decreasing to 82.3% (95% CI [79.7, 84.7], p < 0.001) and 98.3% (95% CI [87.3, 99.8], p < 0.001) to 77.8% (95% CI [51.4, 89.9], p < 0.001) in Scotland for the same periods. Similar results were obtained with the primary series of BNT162b2 plus homologous booster. Potential limitations of this study were that we assumed that all cases included in the analysis were due to the Omicron variant based on the period of dominance and the limited follow-up time since the booster dose. CONCLUSIONS We observed that mRNA boosters after a primary vaccination course with either mRNA or viral-vector vaccines provided modest, short-lived protection against symptomatic infection with Omicron but substantial and more sustained protection against severe COVID-19 outcomes for at least 3 months.
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Affiliation(s)
- Thiago Cerqueira-Silva
- LIB and LEITV Laboratories, Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
- Universidade Federal de Bahia (UFBA), Salvador, Bahia, Brazil
| | - Syed Ahmar Shah
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris Robertson
- Public Health Scotland, Glasgow, United Kingdom
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, United Kingdom
| | - Mauro Sanchez
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Srinivasa Vittal Katikireddi
- Public Health Scotland, Glasgow, United Kingdom
- MRC/CSO Social & Public Health Sciences Unit, University of Glasgow, Glasgow, United Kingdom
| | - Vinicius de Araujo Oliveira
- Universidade Federal de Bahia (UFBA), Salvador, Bahia, Brazil
- Center for Data Integration and Knowledge for Health (Cidacs), Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
| | - Enny S. Paixão
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Igor Rudan
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Juracy Bertoldo Junior
- Universidade Federal de Bahia (UFBA), Salvador, Bahia, Brazil
- Center for Data Integration and Knowledge for Health (Cidacs), Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
| | - Gerson O. Penna
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Neil Pearce
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Guilherme Loureiro Werneck
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauricio L. Barreto
- Universidade Federal de Bahia (UFBA), Salvador, Bahia, Brazil
- Center for Data Integration and Knowledge for Health (Cidacs), Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
| | - Viviane S. Boaventura
- LIB and LEITV Laboratories, Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
- Universidade Federal de Bahia (UFBA), Salvador, Bahia, Brazil
| | - Aziz Sheikh
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Manoel Barral-Netto
- LIB and LEITV Laboratories, Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
- Universidade Federal de Bahia (UFBA), Salvador, Bahia, Brazil
- Center for Data Integration and Knowledge for Health (Cidacs), Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil
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Finamore-Araujo P, Faier-Pereira A, Ramon do Nascimento Brito C, Gomes Peres E, Kazumy de Lima Yamaguchi K, Trotta Barroso Ferreira R, Moreira OC. Validation of a novel multiplex real-time PCR assay for Trypanosoma cruzi detection and quantification in açai pulp. PLoS One 2021; 16:e0246435. [PMID: 33529258 PMCID: PMC7853518 DOI: 10.1371/journal.pone.0246435] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/19/2021] [Indexed: 11/19/2022] Open
Abstract
In Brazil, orally acquired T. cruzi infection has become the most relevant transmission mechanisms from public health perspective. Around 70% of new Chagas disease cases have been associated with consumption of contaminated food or beverages. Açai (Euterpe oleracea and Euterpe precatoria) is currently one of the most commercialized Amazonian fruits in the Brazilian and international markets. Therefore, it has become important to incorporate in the production process some procedures to measure out effective hygiene and product quality control required by global market. Molecular methods have been developed for rapid detection and quantification of T. cruzi DNA in several biological samples, including food matrices, for epidemiological investigation of Chagas disease and food quality control. However, a high-performance molecular methodology since DNA extraction until detection and quantification of T. cruzi DNA in açai berry pulp is still needed. Herein, a simple DNA extraction methodology was standardized from the supernatant of açai berry pulp stabilized in a 6M Guanidine-HCl/0.2M EDTA buffer. In addition, a multiplex real time qPCR assay, targeting T. cruzi DNA and an Exogenous Internal Positive Control was developed and validated, using reference from all T. cruzi DTUs and commercial samples of açai pulp, from an endemic municipality with previous history of oral Chagas disease outbreak. Thus, a high-sensitivity qPCR assay, that could detect up to 0.01 parasite equivalents/mL in açai, was reached. As of the 45 commercial samples analyzed, 9 (20%) were positive for T. cruzi. This high-sensitive, fast, and easy-to-use molecular assay is compatible with most of the laboratories involved in the investigations of oral Chagas disease outbreaks, representing an important tool to the epidemiology, control, and surveillance of Chagas disease.
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Affiliation(s)
- Paula Finamore-Araujo
- Plataforma Fiocruz de PCR em Tempo Real RPT09A –Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda Faier-Pereira
- Plataforma Fiocruz de PCR em Tempo Real RPT09A –Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carlos Ramon do Nascimento Brito
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | | | | | - Otacilio Cruz Moreira
- Plataforma Fiocruz de PCR em Tempo Real RPT09A –Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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