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<p>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 <i>Escherichia coli</i> 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 <i>Escherichia coli</i> (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.</p>

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Leveraging existing knowledge about bacteria–protease relationships to predict existence of proteases across bacterial species

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月29日

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  • Xinling Li,
  • Peng Qiu

摘要

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.