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Article: Genetically divergent

Riera, Nadia / Salazar, Cecilia / Rivera, Bernardina / Galiana, Antonio / Durán, Rosario / Portela, María Magdalena / Antelo, Virginia / Pi, Beatriz / González, Óscar / Iraola, Gregorio

New microbes and new infections

2023 Volume 57, Page(s) 101210

Abstract: Here we report a case of septic arthritis associated with a genetically ... ...

Abstract	Here we report a case of septic arthritis associated with a genetically divergent
Language	English
Publishing date	2023-12-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2750179-6
ISSN	2052-2975
ISSN	2052-2975
DOI	10.1016/j.nmni.2023.101210
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals.

Lin, Amanda Dal / Fischer, Juliana de S da G / Santos, Marlon D M / Camillo-Andrade, Amanda Caroline / Kurt, Louise Ulrich / Souza, Tatiana A C B / Lajas, Ana Beatriz Lyrio / Rivera, Bernardina / Portela, Magdalena / Duran, Rosario / Mira, Marcelo Távora / Pillonetto, Marcelo / Carvalho, Paulo Costa

Journal of proteomics

2023 Volume 289, Page(s) 105012

Abstract: This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the ... ...

Abstract	This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ∼20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. SIGNIFICANCE: We present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general.
MeSH term(s)	Polymyxins/metabolism ; Anti-Bacterial Agents/pharmacology ; Acinetobacter baumannii/metabolism ; Proteomics/methods ; Proteome/metabolism ; Brazil ; Drug Resistance, Multiple, Bacterial ; Microbial Sensitivity Tests
Chemical Substances	Polymyxins ; Anti-Bacterial Agents ; Proteome
Language	English
Publishing date	2023-09-23
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2023.105012
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Article: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection

Rivera, Bernardina / Leyva, Alejandro / Portela, María Magdalena / Moratorio, Gonzalo / Moreno, Pilar / Durán, Rosario / Lima, Analía

Data in Brief. 2020 Oct., v. 32

2020

Abstract: Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a ... ...

Abstract	Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were “Guanylate-binding protein 1”, “Tapasin” and “HLA class II histocompatibility antigen DR beta chain”. The biological processes overrepresented in infected host cells were “SRP-dependent cotranslational protein targeting to membrane”, “nuclear-transcribed mRNA catabolic process, nonsense-mediated decay”, “viral transcription” and “translational initiation”. Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antigens ; catabolism ; computer software ; data collection ; genome ; humans ; nucleoproteins ; peptides ; proteomics ; spectrometers
Language	English
Dates of publication	2020-10
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2020.106121
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection.

Rivera, Bernardina / Leyva, Alejandro / Portela, María Magdalena / Moratorio, Gonzalo / Moreno, Pilar / Durán, Rosario / Lima, Analía

Data in brief

2020 Volume 32, Page(s) 106121

Abstract	Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were "Guanylate-binding protein 1", "Tapasin" and "HLA class II histocompatibility antigen DR beta chain". The biological processes overrepresented in infected host cells were "SRP-dependent cotranslational protein targeting to membrane", "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay", "viral transcription" and "translational initiation". Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.
Keywords	covid19
Language	English
Publishing date	2020-08-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2020.106121
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis

Bernardina Rivera / Alejandro Leyva / María Magdalena Portela / Gonzalo Moratorio / Pilar Moreno / Rosario Durán / Analía Lima

Data in Brief, Vol 32, Iss , Pp 106121- (2020)

Detection of viral proteins and host's biological processes altered by the infection

2020

Abstract	Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were “Guanylate-binding protein 1”, “Tapasin” and “HLA class II histocompatibility antigen DR beta chain”. The biological processes overrepresented in infected host cells were “SRP-dependent cotranslational protein targeting to membrane”, “nuclear-transcribed mRNA catabolic process, nonsense-mediated decay”, “viral transcription” and “translational initiation”. Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.
Keywords	SARS-CoV-2 ; COVID-19 ; Quantitative proteomics ; Shotgun proteomics ; Nucleoprotein ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390 ; covid19
Subject code	570
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis

Rivera, Bernardina / Leyva, Alejandro / Portela, María Magdalena / Moratorio, Gonzalo / Moreno, Pilar / Durán, Rosario / Lima, Analía

Data in Brief

Detection of viral proteins and host's biological processes altered by the infection

2020 Volume 32, Page(s) 106121

Keywords	Multidisciplinary ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2020.106121
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Proteome remodeling in the Mycobacterium tuberculosis PknG knockout: Molecular evidence for the role of this kinase in cell envelope biogenesis and hypoxia response.

Lima, Analía / Leyva, Alejandro / Rivera, Bernardina / Portela, María Magdalena / Gil, Magdalena / Cascioferro, Alessandro / Lisa, María-Natalia / Wehenkel, Annemarie / Bellinzoni, Marco / Carvalho, Paulo C / Batthyány, Carlos / Alvarez, María N / Brosch, Roland / Alzari, Pedro M / Durán, Rosario

Journal of proteomics

2021 Volume 244, Page(s) 104276

Abstract: Mycobacterium tuberculosis, the etiological agent of tuberculosis, is among the deadliest human pathogens. One of M. tuberculosis's pathogenic hallmarks is its ability to persist in a dormant state in the host. Thus, this pathogen has developed ... ...

Abstract	Mycobacterium tuberculosis, the etiological agent of tuberculosis, is among the deadliest human pathogens. One of M. tuberculosis's pathogenic hallmarks is its ability to persist in a dormant state in the host. Thus, this pathogen has developed mechanisms to withstand stressful conditions found in the human host. Particularly, the Ser/Thr-protein kinase PknG has gained relevance since it regulates nitrogen metabolism and facilitates bacterial survival inside macrophages. Nevertheless, the molecular mechanisms underlying these effects are far from being elucidated. To further investigate these issues, we performed quantitative proteomic analyses of protein extracts from M. tuberculosis H37Rv and a mutant lacking pknG. We found that in the absence of PknG the mycobacterial proteome was remodeled since 5.7% of the proteins encoded by M. tuberculosis presented significant changes in its relative abundance compared with the wild-type. The main biological processes affected by pknG deletion were cell envelope components biosynthesis and response to hypoxia. Thirteen DosR-regulated proteins were underrepresented in the pknG deletion mutant, including Hrp-1, which was 12.5-fold decreased according to Parallel Reaction Monitoring experiments. Altogether, our results allow us to postulate that PknG regulation of bacterial adaptation to stress conditions might be an important mechanism underlying its reported effect on intracellular bacterial survival. SIGNIFICANCE: PknG is a Ser/Thr kinase from Mycobacterium tuberculosis with key roles in bacterial metabolism and bacterial survival within the host. However, at present the molecular mechanisms underlying these functions remain largely unknown. In this work, we evaluate the effect of pknG deletion on M. tuberculosis proteome using different approaches. Our results clearly show that the global proteome was remodeled in the absence of PknG and shed light on new molecular mechanism underlying PknG role. Altogether, this work contributes to a better understanding of the molecular bases of the adaptation of M. tuberculosis, one of the most deadly human pathogens, to its host.
MeSH term(s)	Bacterial Proteins/genetics ; Biological Phenomena ; Humans ; Hypoxia ; Mycobacterium tuberculosis/genetics ; Protein-Serine-Threonine Kinases/genetics ; Proteome ; Proteomics
Chemical Substances	Bacterial Proteins ; Proteome ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2021-05-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2021.104276
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Proteome remodeling in the Mycobacterium tuberculosis PknG knockout: Molecular evidence for the role of this kinase in cell envelope biogenesis and hypoxia response

Journal of proteomics. 2021 July 30, v. 244

2021

Abstract	Mycobacterium tuberculosis, the etiological agent of tuberculosis, is among the deadliest human pathogens. One of M. tuberculosis's pathogenic hallmarks is its ability to persist in a dormant state in the host. Thus, this pathogen has developed mechanisms to withstand stressful conditions found in the human host. Particularly, the Ser/Thr-protein kinase PknG has gained relevance since it regulates nitrogen metabolism and facilitates bacterial survival inside macrophages. Nevertheless, the molecular mechanisms underlying these effects are far from being elucidated. To further investigate these issues, we performed quantitative proteomic analyses of protein extracts from M. tuberculosis H37Rv and a mutant lacking pknG. We found that in the absence of PknG the mycobacterial proteome was remodeled since 5.7% of the proteins encoded by M. tuberculosis presented significant changes in its relative abundance compared with the wild-type. The main biological processes affected by pknG deletion were cell envelope components biosynthesis and response to hypoxia. Thirteen DosR-regulated proteins were underrepresented in the pknG deletion mutant, including Hrp-1, which was 12.5-fold decreased according to Parallel Reaction Monitoring experiments. Altogether, our results allow us to postulate that PknG regulation of bacterial adaptation to stress conditions might be an important mechanism underlying its reported effect on intracellular bacterial survival.PknG is a Ser/Thr kinase from Mycobacterium tuberculosis with key roles in bacterial metabolism and bacterial survival within the host. However, at present the molecular mechanisms underlying these functions remain largely unknown. In this work, we evaluate the effect of pknG deletion on M. tuberculosis proteome using different approaches. Our results clearly show that the global proteome was remodeled in the absence of PknG and shed light on new molecular mechanism underlying PknG role. Altogether, this work contributes to a better understanding of the molecular bases of the adaptation of M. tuberculosis, one of the most deadly human pathogens, to its host.
Keywords	Mycobacterium tuberculosis ; biogenesis ; biosynthesis ; humans ; hypoxia ; macrophages ; mutants ; nitrogen metabolism ; proteome ; proteomics ; tuberculosis
Language	English
Dates of publication	2021-0730
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2021.104276
Database	NAL-Catalogue (AGRICOLA)

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Article: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection

Rivera, Bernardina / Leyva, Alejandro / Portela, María Magdalena / Moratorio, Gonzalo / Moreno, Pilar / Durán, Rosario / Lima, Analía

Data Brief

Abstract	Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were “Guanylate-binding protein 1”, “Tapasin” and “HLA class II histocompatibility antigen DR beta chain”. The biological processes overrepresented in infected host cells were “SRP-dependent cotranslational protein targeting to membrane”, “nuclear-transcribed mRNA catabolic process, nonsense-mediated decay”, “viral transcription” and “translational initiation”. Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #694582
Database	COVID19

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Article ; Online: Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay.

Rego, Natalia / Costábile, Alicia / Paz, Mercedes / Salazar, Cecilia / Perbolianachis, Paula / Spangenberg, Lucía / Ferrés, Ignacio / Arce, Rodrigo / Fajardo, Alvaro / Arleo, Mailen / Possi, Tania / Reyes, Natalia / Bentancor, Ma Noel / Lizasoain, Andrés / Benítez, María José / Bortagaray, Viviana / Moller, Ana / Bello, Gonzalo / Arantes, Ighor /

Emerging infectious diseases

2021 Volume 27, Issue 11, Page(s) 2957–2960

Abstract: We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARS-CoV-2 VOCs, the surveillance workflow, and ... ...

Abstract	We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARS-CoV-2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of the SARS-CoV-2 P.1 VOC in Uruguay.
MeSH term(s)	COVID-19 ; Genomics ; Humans ; SARS-CoV-2 ; Uruguay/epidemiology
Language	English
Publishing date	2021-08-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2711.211198
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