Dataset Information

Streptococcus pneumoniae biomarker identification by surface shaving and bottom-up mass spectrometry-based proteomics

ABSTRACT: In this study, genomics- and proteomics-based approaches were used for the identification of Streptococcus pneumoniae potential biomarkers for diagnostics and prospective targets for treatment. Through a Pan-genome analyses 11 strains from the CCUG demonstrating genetic variability within the species were selected for a proteomic characterization. Mass spectrometry-based proteomics in combination with bacterial surface shaving were used to study the surface proteome of S. pneumoniae. The 11 strains were analyzed in triplicates by proteotyping (typing and characterization of species by mass spectrometry-based proteomics) and bioinformatic approaches, including the Microorganism Identification and Classification, were used to validate the expressed proteins and peptide biomarkers.

INSTRUMENT(S):

ORGANISM(S): Bacteria Streptococcus Pneumoniae

SUBMITTER: Roger Karlsson

LAB HEAD: Roger Karlsson

PROVIDER: PXD063486 | Pride | 2025-12-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Exp_221123_84_CCUG28588.mgf	Mgf
	Exp_221123_84_CCUG28588.mzML	Mzml
	Exp_221123_84_CCUG28588.mzTab	Mztab
	Exp_221123_84_CCUG28588_1.raw	Raw
	Exp_221123_87_CCUG28588_2.raw	Raw

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Publications

Identification of Streptococcus pneumoniae-Specific Proteins by Surface-Shaving Proteomics.

Acha Alarcon Leonarda L Seguí Guillem G Piñeiro-Iglesias Beatriz B Svetlicic Ema E Kondori Nahid N Gomila Margarita M Moore Edward R B ERB Karlsson Roger R

Journal of proteome research 20251110 12

Streptococcus pneumoniae (pneumococcus) is a prominent cause of bacterial pneumonia, meningitis, and septicemia, causing high morbidity and high mortality, particularly in children and the elderly. In this study, proteomics- and genomics-based approaches were used for the identification of pneumococcal protein and peptide biomarkers of S. pneumoniae for diagnostics and prospective targets for treatment. Through a pan-genome analysis, 11 S. pneumoniae strains, d ...[more]

PMID: 41212599

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Project description:Otitis media, pneumonia, sinusitis and as well as severe diseases such as meningitis and bacteraemia are related to biofilm-like diseases, in which Streptococcus pneumoniae demonstrated differential and tissue specific gene expressions. In this study, we reported the differential gene expression profile of early in vitro biofilm and planktonic cell in c-DNA microarray analysis. The microarray analysis was performed on total RNA extracted from biofilms grown in 24-well microtiter plate and mid-log grown planktonic cells. To validate the results of microarray, real-time RT-PCR was performed on 13 differentially expressed genes and one constitutively expressed gene from six different functional groups. cDNA-microarray analyses indicated 89 genes that were significantly differentially expressed in biofilm and planktonic cells. Among total differentially expressed gene, almost 50% were hypothetical genes. Of the 46 protein coding genes, 34 showed up-regulation and 16 showed down-regulation in biofilm. The functional annotation showed that many functional categories were differentially regulated in biofilm and planktonic cells, such as genes involve in purine, pyrimidine nucleotide metabolism, RNA/DNA metabolism, amino acid transport and metabolism, translation, transporter protein, carbohydrate transport and metabolism, cell wall biosynthesis, isoprenoid biosynthesis, transcription regulator and cellular process. Streptococcus pneumoniae R6 strain used in this is an unencapsulated and avirulent strain derived from encapsulated serotype 2 pathogenic strain D39. In vitro biofilm formation was carried out in 24-well, flat-bottom, polystyrene microtiter plate (BD falcon, MD, USA) in static model. S. pneumoniae grown up to mid-logarithmic phase in TSB medium was diluted 1:100 with fresh sterile TSB medium supplied with 1% glucose, inoculated 1.5 mL in 24-well microtiter plate and, incubated for 15 hours at 37M-BM-0C in 5% CO2. After incubation medium was discarded, and the plates were gently washed three times with 1.5 mL sterile, cold phosphate buffer saline (PBS). Adherent cell were scraped and immediately processed for RNA extraction. For planktonic cells RNA extraction, five ml of mid-logarithmic phase cell suspension was pelleted by centrifugation and wash three times with sterile PBS and immediately processed for RNA extraction. All experiments were performed in triplicate (3 independent biological replicates)

Dataset Information

Streptococcus pneumoniae biomarker identification by surface shaving and bottom-up mass spectrometry-based proteomics

Dataset's files

Publications

Identification of <i>Streptococcus pneumoniae</i><i>-</i>Specific Proteins by Surface-Shaving Proteomics.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Streptococcus pneumoniae biomarker identification by surface shaving and bottom-up mass spectrometry-based proteomics

Dataset's files

Publications

Identification of &lt;i&gt;Streptococcus pneumoniae&lt;/i&gt;&lt;i&gt;-&lt;/i&gt;Specific Proteins by Surface-Shaving Proteomics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Identification of <i>Streptococcus pneumoniae</i><i>-</i>Specific Proteins by Surface-Shaving Proteomics.