Dataset.

Shotgun Proteomics Analysis, Functional Networks and Peptide Biomarkers for Biogenic Amine-producing Bacteria [Dataset]

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/355103
Digital.CSIC. Repositorio Institucional del CSIC
  • Carrera, Mónica
This repository may be useful for further studies, for the development of new therapeutic treatments for food intoxication and for tracking microbial sources in foodstuffs, Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds, such as histamine, cadaverine, tyramine and putrescine, after foods spoil due to microorganisms. In the present work, we applied a shotgun proteomics approach to quickly and easily characterize 15 different foodborne strains of biogenic amine-producing bacteria. A total of 10673 peptide spectrum matches (PSMs) belonging to 4081 nonredundant peptides and corresponding to 1811 annotated proteins were identified. With the results, relevant functional pathways were determined and the strains were differentiated into different Euclidean hierarchical clusters. Moreover, a predicted protein‒protein interaction network of biogenic amine foodborne strains was created. The whole confidence network contains 260 nodes and 1973 interactions. Most of the identified proteins were related to pathways and networks of energy, putrescine metabolism and host‒virus interaction. In addition, a total of 556 nonredundant peptides were identified as virulence factors, and most of these peptides corresponded to functions such as toxins, antimicrobial compound production, antimicrobial resistance, additional resistances and tolerances, host colonization and immune evasion, ABC transporters, phage proteins, and alternative virulence factors and proteins involved in horizontal transfer. Potential species-specific peptide biomarkers were screened. Thus, 77 species-specific peptide biomarkers belonging to 64 different proteins were proposed to identify 10 species (Enterobacter aerogenes, Enterobacter cloacae, Hafnia alvei, Klebsiella oxytoca, Morganella morganii, Proteus mirabilis, Proteus penneri, Proteus vulgaris, Raoutella planticola, Stenotrophomonas maltophilia). All of these results constitute the first major dataset of peptides and proteins of seafood biogenic amine-producing strains, Peer reviewed
 
DOI: http://hdl.handle.net/10261/355103
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/355103

HANDLE: http://hdl.handle.net/10261/355103
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/355103
 
Ver en: http://hdl.handle.net/10261/355103
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/355103

Investigo. Repositorio Institucional de la Universidade de Vigo
oai:www.investigo.biblioteca.uvigo.es:11093/8315
Artículo científico (article). 2025

SHOTGUN PROTEOMICS ANALYSIS, FUNCTIONAL NETWORKS, AND PEPTIDE BIOMARKERS FOR SEAFOOD-ORIGINATING BIOGENIC-AMINE-PRODUCING BACTERIA

Investigo. Repositorio Institucional de la Universidade de Vigo
  • González Abril, Ana
  • Calo-Mata, Pilar
  • Böhme, Karola
  • Villa, Tomás G.
  • Barros-Velázquez, Jorge
  • Pazos, Manuel
  • Carrera, Mónica
Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs., Xunta de Galicia, Ministerio de Economía y Competitividad | Ref. AGL 2.013-48.244-R, Agencia Estatal de Investigación | Ref. PID2019-103845RB-C21, Ministerio de Ciencia e Innovación | Ref. ACAM 2022020038




Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/348659
Artículo científico (article). 2023

SHOTGUN PROTEOMICS ANALYSIS, FUNCTIONAL NETWORKS, AND PEPTIDE BIOMARKERS FOR SEAFOOD-ORIGINATING BIOGENIC-AMINE-PRODUCING BACTERIA

Digital.CSIC. Repositorio Institucional del CSIC
  • Abril, Ana G.
  • Calo-Mata, Pilar
  • Böhme, K.
  • Villa, Tomás G.
  • Barros-Velázquez, Jorge
  • Pazos Palmeiro, Manuel
  • Carrera, Mónica
23 pages, 4 tables, 5 figures.-- This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs, A.G.A. thanks the USC for the “Convocatoria de Recualificación do Sistema Universitario Español-Margarita Salas” postdoc grant under the “Plan de Recuperación Transformación” program funded by the Spanish Ministry of Universities through the European Union’s NextGeneration EU funds. This work has received financial support from the Xunta de Galicia and the European Union (European Social Fund2013ESF), the Spanish Ministry of Economy and Competitivity Project AGL 2.013-48.244-R, and the European Regional Development Fund (ERDF) (2007–2013). This study was also financed by the GAIN-Xunta de Galicia Project (IN607D 2017/01) and the Spanish AEI/EU-FEDER PID2019-103845RB-C21 project. It was also supported by the Plan Complementario en Ciencias Marinas (PCCM) funded by the Ministry of Science and Innovation (Activity 3.6.B. NANOSEAOMICS), Peer reviewed




Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/355103
Dataset. 2023

SHOTGUN PROTEOMICS ANALYSIS, FUNCTIONAL NETWORKS AND PEPTIDE BIOMARKERS FOR BIOGENIC AMINE-PRODUCING BACTERIA [DATASET]

Digital.CSIC. Repositorio Institucional del CSIC
  • Carrera, Mónica
This repository may be useful for further studies, for the development of new therapeutic treatments for food intoxication and for tracking microbial sources in foodstuffs, Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds, such as histamine, cadaverine, tyramine and putrescine, after foods spoil due to microorganisms. In the present work, we applied a shotgun proteomics approach to quickly and easily characterize 15 different foodborne strains of biogenic amine-producing bacteria. A total of 10673 peptide spectrum matches (PSMs) belonging to 4081 nonredundant peptides and corresponding to 1811 annotated proteins were identified. With the results, relevant functional pathways were determined and the strains were differentiated into different Euclidean hierarchical clusters. Moreover, a predicted protein‒protein interaction network of biogenic amine foodborne strains was created. The whole confidence network contains 260 nodes and 1973 interactions. Most of the identified proteins were related to pathways and networks of energy, putrescine metabolism and host‒virus interaction. In addition, a total of 556 nonredundant peptides were identified as virulence factors, and most of these peptides corresponded to functions such as toxins, antimicrobial compound production, antimicrobial resistance, additional resistances and tolerances, host colonization and immune evasion, ABC transporters, phage proteins, and alternative virulence factors and proteins involved in horizontal transfer. Potential species-specific peptide biomarkers were screened. Thus, 77 species-specific peptide biomarkers belonging to 64 different proteins were proposed to identify 10 species (Enterobacter aerogenes, Enterobacter cloacae, Hafnia alvei, Klebsiella oxytoca, Morganella morganii, Proteus mirabilis, Proteus penneri, Proteus vulgaris, Raoutella planticola, Stenotrophomonas maltophilia). All of these results constitute the first major dataset of peptides and proteins of seafood biogenic amine-producing strains, Peer reviewed




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