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An integrated landscape of mRNA and protein isoforms [NGS]

ABSTRACT: Current proteomic methods are not well suited to detect protein isoforms. On the one hand, standard shotgun (that is, bottom-up) proteomics involves digestion of proteins into peptides. While this approach identifies many proteins, it results in a loss of isoform information. On the other hand, mass spectrometric analysis of intact proteins (that is, top-down proteomics) distinguishes protein isoforms but only covers a small subset of the proteome. We developed peptide correlation profiling (PepCP) as a method to obtain protein-level information from peptide-centric (that is, bottom-up proteomic) data: First, proteins are fractionated by SDS-PAGE to polypeptides of different length. Second, individual protein fractions are digested into peptides. Third, peptides are identified and quantified in all fractions using quantitative mass spectrometry-based proteomics. Finally, peptide abundance profiles across fractions are analysed to obtain protein-level information.

ORGANISM(S): Homo sapiens

PROVIDER: GSE261379 | GEO | 2026/03/12

REPOSITORIES: GEO

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Project description:Specific Lactobacillus strains are marketed as probiotics i.e. health promoting organisms. As previously shown in vivo, L. plantarum WCFS1 modulates immune responses via nuclear factor (NF)kB in a growth phase dependent manner, likely caused by changed microbial cell surface characteristics. Here, we identified the differential cell-surface proteome composition of L. plantarum WCFS1 cells derived from the mid-logarithmic and late stationary growth phase by surface trypsination of intact bacterial cells, followed by a combined 1D- and 2D-LC-MS shotgun proteomics strategy, and growth phase dependent transcriptome analysis. Overall, these analyses led to the identification of 31 surface proteins differentially present in the logarithmic and stationary phase, whereas additional 17 and 33 proteins appeared solely present in stationary and logarithmic phase of growth, respectively. From 75% of predicted surface related genes displaying relatively high expression levels, the corresponding proteins were detected, demonstrating a high correlation between transcriptome and proteome profiles. The impact of cell-surface peptide fractions on cellular host responses was evaluated using NFkB promoter activation assays in intestinal epithelial cells, revealing that only late stationary phase derived peptides are capable of attenuating flagellin and cell envelope induced NFkB activation. Overall our data mechanistically expand earlier observations that revealed growth-phase dependent immunomodulation by L. plantarum WCFS1, leading to a typical adjuvant- or tolerance-like response after exposure to stationary phase harvested bacterial cells. Sub-fractionation of the late stationary phase peptide fraction revealed a sub-set of strong attenuator peptides able to manipulate NFkB related pathways to hereby attenuate pro-inflammatory signaling. Samples were hybridizedin a loop design linking each timepoint to the next as well as the previous timepoint. Additional hybridizations were introduced linking each sample three timepoints forward and three timepoints back. All samples were hybridized unsing at least each of the two dyes once.

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An integrated landscape of mRNA and protein isoforms [NGS]

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