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Updated: Jun 23, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

The Cryptic Bacterial Microproteome.

Igor Fesenko¹, Harutyun Sahakyan¹, Svetlana A Shabalina¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Biorxiv : the Preprint Server for Biology

|June 21, 2024

Summary

This summary is machine-generated.

Researchers explored bacterial small open reading frames (smORFs) encoding microproteins, uncovering 67,297 clusters under selection. These microproteins may regulate neighboring gene activity, especially during stress.

Keywords:

bacteria bioinformatics de novo evolutionary analysis of smORFs intergenic microproteins protein structure prediction small open reading frames (smORFs)

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Genomics
Proteomics
Bacterial Biology

Background:

Microproteins encoded by small open reading frames (smORFs) represent a significant portion of proteomic 'dark matter'.
While functional microproteins are known across life domains, bacterial smORFs are understudied.
Intergenic smORFs (ismORFs) in bacteria are particularly poorly characterized.

Purpose of the Study:

To comprehensively identify and characterize intergenic small open reading frames (ismORFs) in the Enterobacteriaceae family.
To investigate the potential functions and interactions of microproteins encoded by bacterial ismORFs.
To create a catalog of predicted microprotein families for future research.

Main Methods:

Genome-wide analysis of 5,668 Enterobacteriaceae genomes to identify ismORFs (15-70 codons).
Computational analysis to detect purifying selection acting on ismORFs.
Structure prediction using AlphaFold Multimer to model microprotein interactions.
Synteny analysis, structure prediction, and transcription/translation data integration.

Main Results:

Identification of 67,297 clusters of bacterial ismORFs under purifying selection.
Characterization of encoded microproteins as predominantly hydrophobic, potentially transmembrane, and minimally structured.
Prediction of microprotein interactions with neighboring proteins, suggesting regulatory roles, especially under stress conditions.
Compilation of a catalog of predicted microprotein families with varying levels of supporting evidence.

Conclusions:

Bacterial ismORFs encode a diverse set of microproteins with potential regulatory functions.
Microproteins may play crucial roles in cellular processes, particularly in response to environmental stress.
The generated catalog provides a valuable resource for exploring the biological significance of bacterial microproteins.