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Article: SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage.

Alonso, Andres Mariano / Diambra, Luis

Frontiers in cell and developmental biology

2020 Volume 8, Page(s) 831

Abstract: Severe acute respiratory syndrome has spread quickly throughout the world and was declared a pandemic by the World Health Organization (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In ...

Abstract	Severe acute respiratory syndrome has spread quickly throughout the world and was declared a pandemic by the World Health Organization (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral protein synthesis and its relationship with the protein synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could result in an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis can contribute to understanding how this virus evades the immune response and the etiology of some deleterious collateral effect as a result of the viral replication. In this manner, our finding contributes to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.
Keywords	covid19
Language	English
Publishing date	2020-08-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2020.00831
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Article ; Online: SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage

Andres Mariano Alonso / Luis Diambra

Frontiers in Cell and Developmental Biology, Vol

2020 Volume 8

Abstract	Severe acute respiratory syndrome has spread quickly throughout the world and was declared a pandemic by the World Health Organization (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral protein synthesis and its relationship with the protein synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could result in an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis can contribute to understanding how this virus evades the immune response and the etiology of some deleterious collateral effect as a result of the viral replication. In this manner, our finding contributes to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.
Keywords	SARS-CoV-2 ; codon usage bias ; codon optimality ; translational control ; pathogeny ; vaccine design ; Biology (General) ; QH301-705.5 ; covid19
Subject code	572
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage

Alonso, Andres Mariano / Diambra, Luis

Frontiers in Cell and Developmental Biology

2020 Volume 8

Keywords	covid19
Publisher	Frontiers Media SA
Publishing country	ch
Document type	Article ; Online
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2020.00831
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Article: Analysis of the Interactome of the

Munera López, Jonathan / Alonso, Andrés Mariano / Figueras, Maria Julia / Saldarriaga Cartagena, Ana María / Hortua Triana, Miryam A / Diambra, Luis / Vanagas, Laura / Deng, Bin / Moreno, Silvia N J / Angel, Sergio Oscar

Proteomes

2023 Volume 11, Issue 1

Abstract: Toxoplasma ... ...

Abstract	Toxoplasma gondii
Language	English
Publishing date	2023-03-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720995-7
ISSN	2227-7382
ISSN	2227-7382
DOI	10.3390/proteomes11010009
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Article ; Online: SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage

Alonso, Andres Mariano / Diambra, Luis

bioRxiv

Abstract: Severe acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great ... ...

Abstract	Severe acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.05.05.079087
Database	COVID19

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Article ; Online: MRI myositis sine myositis: the importance of the histopathology.

Andrés, Mariano / Sivera, Francisca / Alonso, Sonia / Pack, Christopher

Rheumatology (Oxford, England)

2015 Volume 54, Issue 1, Page(s) 76

MeSH term(s)	Aged ; Biopsy ; Diagnosis, Differential ; Female ; Humans ; Magnetic Resonance Imaging ; Muscle, Skeletal/pathology ; Myositis/diagnosis ; Myositis/pathology ; Vasculitis/diagnosis ; Vasculitis/pathology
Language	English
Publishing date	2015-01
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	1464822-2
ISSN	1462-0332 ; 1462-0324
ISSN (online)	1462-0332
ISSN	1462-0324
DOI	10.1093/rheumatology/keu370
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Article: PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders

Manso, José A. / Marcos, Tamara / Ruiz-Martín, Virginia / Casas, Javier / Alcón, Pablo / Sánchez Crespo, Mariano / Bayón, Yolanda / de Pereda, José M. / Alonso, Andrés

Cellular and molecular life sciences. 2022 Feb., v. 79, no. 2

2022

Abstract: Mutations in the adaptor protein PSTPIP1 cause a spectrum of autoinflammatory diseases, including PAPA and PAMI; however, the mechanism underlying these diseases remains unknown. Most of these mutations lie in PSTPIP1 F-BAR domain, which binds to LYP, a ... ...

Abstract	Mutations in the adaptor protein PSTPIP1 cause a spectrum of autoinflammatory diseases, including PAPA and PAMI; however, the mechanism underlying these diseases remains unknown. Most of these mutations lie in PSTPIP1 F-BAR domain, which binds to LYP, a protein tyrosine phosphatase associated with arthritis and lupus. To shed light on the mechanism by which these mutations generate autoinflammatory disorders, we solved the structure of the F-BAR domain of PSTPIP1 alone and bound to the C-terminal homology segment of LYP, revealing a novel mechanism of recognition of Pro-rich motifs by proteins in which a single LYP molecule binds to the PSTPIP1 F-BAR dimer. The residues R228, D246, E250, and E257 of PSTPIP1 that are mutated in immunological diseases directly interact with LYP. These findings link the disruption of the PSTPIP1/LYP interaction to these diseases, and support a critical role for LYP phosphatase in their pathogenesis.
Keywords	arthritis ; pathogenesis ; protein-tyrosine-phosphatase
Language	English
Dates of publication	2022-02
Size	p. 131.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-022-04173-w
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Article ; Online: The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection.

Fernández, Jose Javier / Marín, Arturo / Rosales, Romel / Penrice-Randal, Rebekah / Mlcochova, Petra / Alvarez, Yolanda / Villalón-Letelier, Fernando / Yildiz, Soner / Pérez, Enrique / Rathnasinghe, Raveen / Cupic, Anastasija / Kehrer, Thomas / Uccellini, Melissa B / Alonso, Sara / Martínez, Fernando / McGovern, Briana Lynn / Clark, Jordan J / Sharma, Parul / Bayón, Yolanda /

Alonso, Andrés / Albrecht, Randy A / White, Kris M / Schotsaert, Michael / Miorin, Lisa / Stewart, James P / Hiscox, Julian A / Gupta, Ravindra K / Irigoyen, Nerea / García-Sastre, Adolfo / Crespo, Mariano Sánchez / Fernández, Nieves

Biochimica et biophysica acta. Molecular basis of disease

2024 Volume 1870, Issue 5, Page(s) 167193

Abstract: SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state ... ...

Abstract	SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.
Language	English
Publishing date	2024-04-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	60-7
ISSN	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbadis.2024.167193
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Article ; Online: PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders.

Manso, José A / Marcos, Tamara / Ruiz-Martín, Virginia / Casas, Javier / Alcón, Pablo / Sánchez Crespo, Mariano / Bayón, Yolanda / de Pereda, José M / Alonso, Andrés

Cellular and molecular life sciences : CMLS

2022 Volume 79, Issue 2, Page(s) 131

Abstract	Mutations in the adaptor protein PSTPIP1 cause a spectrum of autoinflammatory diseases, including PAPA and PAMI; however, the mechanism underlying these diseases remains unknown. Most of these mutations lie in PSTPIP1 F-BAR domain, which binds to LYP, a protein tyrosine phosphatase associated with arthritis and lupus. To shed light on the mechanism by which these mutations generate autoinflammatory disorders, we solved the structure of the F-BAR domain of PSTPIP1 alone and bound to the C-terminal homology segment of LYP, revealing a novel mechanism of recognition of Pro-rich motifs by proteins in which a single LYP molecule binds to the PSTPIP1 F-BAR dimer. The residues R228, D246, E250, and E257 of PSTPIP1 that are mutated in immunological diseases directly interact with LYP. These findings link the disruption of the PSTPIP1/LYP interaction to these diseases, and support a critical role for LYP phosphatase in their pathogenesis.
MeSH term(s)	Adaptor Proteins, Signal Transducing/chemistry ; Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/physiology ; Crystallization ; Cytoskeletal Proteins/chemistry ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/physiology ; Diabetes Mellitus, Type 1/etiology ; HEK293 Cells ; Humans ; Immune System Diseases/etiology ; Mutation ; Protein Domains ; Protein Multimerization ; Protein Tyrosine Phosphatase, Non-Receptor Type 22/chemistry ; Protein Tyrosine Phosphatase, Non-Receptor Type 22/genetics ; Protein Tyrosine Phosphatase, Non-Receptor Type 22/physiology
Chemical Substances	Adaptor Proteins, Signal Transducing ; Cytoskeletal Proteins ; PSTPIP1 protein, human ; Protein Tyrosine Phosphatase, Non-Receptor Type 22 (EC 3.1.3.48)
Language	English
Publishing date	2022-02-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-022-04173-w
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Article ; Online: Serological reactivity against T. cruzi-derived antigens: Evaluation of their suitability for the assessment of response to treatment in chronic Chagas disease.

Alonso-Padilla, Julio / López, Manuel Carlos / Esteva, Mónica / Zrein, Maan / Casellas, Aina / Gómez, Inmaculada / Granjon, Elodie / Méndez, Susana / Benítez, Celia / Ruiz, Andres Mariano / Sanz, Sergi / Gascón, Joaquim / Thomas, M Carmen / Pinazo, Maria-Jesus

Acta tropica

2021 Volume 221, Page(s) 105990

Abstract: Chagas disease, caused by the protozoan Trypanosoma cruzi, affects more than 6 million people worldwide. Following a mostly asymptomatic acute phase, the disease progresses to a long-lasting chronic phase throughout which life-threatening disorders to ... ...

Abstract	Chagas disease, caused by the protozoan Trypanosoma cruzi, affects more than 6 million people worldwide. Following a mostly asymptomatic acute phase, the disease progresses to a long-lasting chronic phase throughout which life-threatening disorders to the heart and/or gastrointestinal tract will manifest in about 30% of those chronically infected. During the chronic phase, the parasitemia is low and intermittent, while a high level of anti-T. cruzi antibodies persist for years. These two features hamper post-chemotherapeutic follow-up of patients with the tools available. The lack of biomarkers for timely assessment of therapeutic response discourages a greater use of the two available anti-parasitic drugs, and complicates the evaluation of new drugs in clinical trials. Herein, we investigated in a blinded case-control study the serological reactivity over time of a group of parasite-derived antigens to potentially address follow up of T. cruzi chronically infected subjects after treatment. We tested PFR2, KMP11, HSP70, 3973, F29 and the InfYnity multiplexed antigenic array, by means of serological assays on a multi-national retrospective collection of samples. Some of the antigens exhibited promising results, underscoring the need for further studies to determine their potential role as treatment response biomarkers.
MeSH term(s)	Antibodies, Protozoan ; Antigens, Protozoan ; Case-Control Studies ; Chagas Disease/diagnosis ; Chagas Disease/drug therapy ; Chronic Disease ; Humans ; Retrospective Studies ; Trypanosoma cruzi/immunology
Chemical Substances	Antibodies, Protozoan ; Antigens, Protozoan
Language	English
Publishing date	2021-06-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2021.105990
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