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Updated: May 27, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

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Published on: January 10, 2025

The hidden bacterial microproteome.

Igor Fesenko¹, Harutyun Sahakyan¹, Rajat Dhyani²

¹Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

|February 20, 2025

Summary

This summary is machine-generated.

Researchers identified 67,297 microprotein families from bacterial genomes. Many of these microproteins, encoded by intergenic small open reading frames (ismORFs), are expressed and may have diverse functions.

Keywords:

bacterial microproteins evolution of microproteins intergenic regions protein structure prediction smORFs small open reading frames

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Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

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Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Published on: May 23, 2021

Area of Science:

Microbiology
Proteomics
Bioinformatics

Background:

Microproteins, encoded by small open reading frames, represent a significant portion of the proteome, often termed 'dark matter'.
While detected across life domains, many microproteins remain unidentified and functionally uncharacterized.

Purpose of the Study:

To comprehensively identify and characterize microproteins encoded by intergenic small open reading frames (ismORFs) in the Enterobacteriaceae family.
To assess the evolutionary conservation and potential functions of these newly identified bacterial microproteins.

Main Methods:

Bioinformatic analysis of 5,668 bacterial genomes from the Enterobacteriaceae family to identify ismORFs (15-70 codons).
Computational prediction of purifying selection acting on identified ismORFs.
Experimental validation of predicted microprotein expression in Escherichia coli using tagged proteins.

Main Results:

Identification of 67,297 clusters of ismORFs under purifying selection within the Enterobacteriaceae.
Experimental detection of expression for 11 out of 16 tested microproteins in Escherichia coli, validating computational predictions.
Predicted microproteins are often hydrophobic, transmembrane, or unstructured, but some exhibit globular folds and potential for oligomerization or interaction with neighboring proteins.

Conclusions:

A vast repertoire of bacterial microproteins encoded by ismORFs has been identified, suggesting a significant, previously underappreciated component of bacterial proteomes.
The study provides a searchable resource of predicted microprotein families, including evidence of transcription, translation, and structure, facilitating future functional investigations.