Leveraging existing knowledge about bacteria–protease relationships to predict existence of proteases across bacterial species
- 1The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA USA
Abstract
Proteases perform essential functions in bacteria. While some bacterial genomes have been extensively studied, our understanding of protease distribution across bacterial genomes remains incomplete. In this study, we leveraged existing knowledge of bacterial proteases to investigate the existence of protease-encoding sequences across a diverse range of bacterial genomes. Currently, UniProt hosts over two million protease sequences from various bacterial species. To identify proteases associated with pathogenic bacteria, we used tBLASTn to align these sequences against the genomes of thirteen bacterial species known to cause severe infectious diseases. We identified hundreds to thousands of proteases with high sequence similarity to each of the thirteen bacterial genomes of interest. As expected, most of the aligned sequences corresponded to known protease-encoding genes within these genomes. Interestingly, some alignments suggested the existence of two proteases in Escherichia coli where such enzymes had not been previously reported, leading to novel hypotheses about the genome annotation. To confirm whether these two predicted regions represent functional units capable of being expressed, we analyzed three bulk RNA-seq samples. Specifically, we aligned three bulk RNA-seq samples from Escherichia coli (cultured in media with different nitrogen supplementations) to its respective genomes. The alignment results revealed expression of region with high sequency similarity to methionine aminopeptidase. The finding suggests potential new annotation in the genomes of the pathogen.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-64371-5.
Related
- Topoisomerase IIβ Kinase: A protein processed from HIV-1 envelope by cysteine proteases
- Protein polymers proliferate: polymerization of phosphatases and proteases
- Valorizing Pearl Mussel (Hyriopsis cumingii) into Hydrolysates: Impact of Different Ultrasonic Pretreatments and Proteases on Its Physicochemical and Functional Properties.
- Host Ubiquitin-Specific Proteases Regulate All Stages of Herpesvirus Infection
- Ubiquitin-specific proteases and the immune microenvironment in cervical cancer: mechanistic evidence, immunotherapy resistance, and therapeutic perspectives
BibTeX
@article{li2026leveraging,
title = {{Leveraging existing knowledge about bacteria–protease relationships to predict existence of proteases across bacterial species}},
author = {Xinling Li and Peng Qiu},
journal = {Scientific Reports},
year = {2026},
month = jul,
doi = {10.1038/s41598-026-64371-5},
url = {https://doi.org/10.1038/s41598-026-64371-5},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Leveraging existing knowledge about bacteria–protease relationships to predict existence of proteases across bacterial species
AU - Xinling Li
AU - Peng Qiu
PY - 2026
DA - 2026/07/29
JO - Scientific Reports
DO - 10.1038/s41598-026-64371-5
UR - https://doi.org/10.1038/s41598-026-64371-5
AB - Proteases perform essential functions in bacteria. While some bacterial genomes have been extensively studied, our understanding of protease distribution across bacterial genomes remains incomplete. In this study, we leveraged existing knowledge of bacterial proteases to investigate the existence of protease-encoding sequences across a diverse range of bacterial genomes. Currently, UniProt hosts over two million protease sequences from various bacterial species. To identify proteases associated with pathogenic bacteria, we used tBLASTn to align these sequences against the genomes of thirteen bacterial species known to cause severe infectious diseases. We identified hundreds to thousands of proteases with high sequence similarity to each of the thirteen bacterial genomes of interest. As expected, most of the aligned sequences corresponded to known protease-encoding genes within these genomes. Interestingly, some alignments suggested the existence of two proteases in Escherichia coli where such enzymes had not been previously reported, leading to novel hypotheses about the genome annotation. To confirm whether these two predicted regions represent functional units capable of being expressed, we analyzed three bulk RNA-seq samples. Specifically, we aligned three bulk RNA-seq samples from Escherichia coli (cultured in media with different nitrogen supplementations) to its respective genomes. The alignment results revealed expression of region with high sequency similarity to methionine aminopeptidase. The finding suggests potential new annotation in the genomes of the pathogen. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-64371-5.
SN - 2045-2322
ER -