Dataset Information

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

ABSTRACT: 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. 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.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Proteus Penneri Proteus Vulgaris Enterobacter Cloacae Ecwsu1 Enterobacter Sp. T3 Klebsiella Oxytoca Hafnia Alvei Stenotrophomonas Maltophilia Proteus Mirabilis Morganella Morganii (proteus Morganii) Raoultella Planticola

SUBMITTER: Mónica Carrera

LAB HEAD: Mónica Carrera

PROVIDER: PXD039320 | Pride | 2023-07-20

REPOSITORIES: Pride

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Publications

Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria.

Abril Ana González AG Calo-Mata Pilar P Böhme Karola K Villa Tomás G TG Barros-Velázquez Jorge J Pazos Manuel M Carrera Mónica M

International journal of molecular sciences 20230422 9

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 determine ...[more]

PMID: 37175409

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Project description:Background: With the increasing interest in metabolic engineering of plants using various genetic manipulation and gene editing technologies in order to enhance their growth, nutritional value and environmental adaptation, a major concern is the potential of broad and distant effects of manipulating the target gene or the metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses [PMID 19383098] The transcriptomes and metabolomes of a control and a high putrescine producing (HP) cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithineâputrescine) altered the expression of a broad spectrum of genes; many of them were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (P <0.05) in the HP cells on any day of analysis; the most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites. The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab regarding increased putrescine production causing an increased flux of glutamate into ornithine, with accompanied increase in glutamate production by additional nitrogen and carbon assimilation; the results may be useful in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production or for biofuels). 12 two-channel arrays directly comparing RNA from control and high putrescine producing (HP) cell lines of Populus nigra x maximowiczii at 3 and 5 days of growth. Three independent biological replicates derived from cells grown in three independent replicate cultures were used. In addition, each sample and time point included dye swap reciprocal two-color experiments for each biological replicate. Thus, six data points per cDNA are included (three biological replicates with two technical replicates each). Please note that experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array; barcode ID for each array is indicated in the sample title and raw data file names) but two idependent raw data files were generated from each slide (one for Cy3, the other for Cy5) and processed as though they are single channel (Cy3 and Cy5 signals are calculated and provided for each sample record). Therfore, each sample record is represented as single channel sample.

Project description:Background: With the increasing interest in metabolic engineering of plants using various genetic manipulation and gene editing technologies in order to enhance their growth, nutritional value and environmental adaptation, a major concern is the potential of broad and distant effects of manipulating the target gene or the metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses [PMID 19383098] The transcriptomes and metabolomes of a control and a high putrescine producing (HP) cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithine→putrescine) altered the expression of a broad spectrum of genes; many of them were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (P <0.05) in the HP cells on any day of analysis; the most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites. The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab regarding increased putrescine production causing an increased flux of glutamate into ornithine, with accompanied increase in glutamate production by additional nitrogen and carbon assimilation; the results may be useful in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production or for biofuels).

Dataset Information

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

Publications

Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria.

Similar Datasets

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