Co-Evolutionary Characterization of PBP2 as the Predominant Siderophore Recognizer in Diverse Gram-Positive Bacteria

Iron is a scarce yet essential nutrient for bacteria, which often acquire it by secreting siderophores, diverse small molecules that form high-affinity complexes with iron for microbial uptake. Understanding microbial iron interaction networks requires characterizing the specificity of siderophore recognition. In Gram-positive bacteria, substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver them to ABC transporters for import. However, the SBPs responsible for selective recognition remain poorly characterized, hindering large-scale data mining and network reconstruction. Here, we systematically analyzed siderophore uptake systems in five representative Gram-positive genera. Through genome mining and co-evolutionary analysis, we characterized Peripla_BP_2 subtype SBPs as the predominant recognizer family, exhibiting strong co-evolutionary signals with siderophore synthetase genes. Unlike their counterparts in Gram-negative bacteria, synthetase and recognizer genes in Gram-positive bacteria are sometimes genomically distant yet display coordinated transcriptional regulation, indicating a spatially decoupled but transcriptionally synchronized mechanism. Our findings underscore key differences between Gram-positive and -negative iron acquisition systems, providing foundational knowledge for large-scale inference of siderophore-mediated microbial interactions.