AmiA and AliA peptide ligands, found in Klebsiella pneumoniae, are imported into pneumococci and alter the transcriptome

• Published in: Scientific reports 2024-05, Vol.14 (1), p.12416-11, Article 12416
• Main Authors: Lux, Janine, Sánchez García, Lucía, Chaparro Fernández, Patricia, Laloli, Laura, Licheri, Manon F., Gallay, Clement, Hermans, Peter W. M., Croucher, Nicholas J., Veening, Jan-Willem, Dijkman, Ronald, Straume, Daniel, Hathaway, Lucy J.
• Format: Article
• Language: English
• Subjects: 631/326; 631/80; ABC transporter; Amino acids; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biosynthesis; Epithelial cells; Gene expression; Gene Expression Regulation, Bacterial - drug effects; Gene regulation; Humanities and Social Sciences; Humans; Klebsiella pneumoniae; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - metabolism; Ligands; Membrane Transport Proteins - genetics; Membrane Transport Proteins - metabolism; Metabolism; multidisciplinary; Oligopeptide permease; Peptides; Peptides - metabolism; Peptides - pharmacology; Permease; Phenotypes; Protein transport; Science; Science (multidisciplinary); Serotypes; Streptococcus pneumoniae - drug effects; Streptococcus pneumoniae - genetics; Streptococcus pneumoniae - metabolism; Transcriptome; Transcriptomes; Transcriptomics
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-63217-2

Klebsiella pneumoniae releases the peptides AKTIKITQTR and FNEMQPIVDRQ, which bind the pneumococcal proteins AmiA and AliA respectively, two substrate-binding proteins of the ABC transporter Ami-AliA/AliB oligopeptide permease. Exposure to these peptides alters pneumococcal phenotypes such as growth. Using a mutant in which a permease domain of the transporter was disrupted, by growth analysis and epifluorescence microscopy, we confirmed peptide uptake via the Ami permease and intracellular location in the pneumococcus. By RNA-sequencing we found that the peptides modulated expression of genes involved in metabolism, as pathways affected were mostly associated with energy or synthesis and transport of amino acids. Both peptides downregulated expression of genes involved in branched-chain amino acid metabolism and the Ami permease; and upregulated fatty acid biosynthesis genes but differed in their regulation of genes involved in purine and pyrimidine biosynthesis. The transcriptomic changes are consistent with growth suppression by peptide treatment. The peptides inhibited growth of pneumococcal isolates of serotypes 3, 8, 9N, 12F and 19A, currently prevalent in Switzerland, and caused no detectable toxic effect to primary human airway epithelial cells. We conclude that pneumococci take up K. pneumoniae peptides from the environment via binding and transport through the Ami permease. This changes gene expression resulting in altered phenotypes, particularly reduced growth.