Comparative in silico analysis of transporters coded within biosynthetic genes clusters for ramoplanin and related antibiotics

Glycopeptide antibiotics (GPAs), like teicoplanin and vancomycin, have been the first-line treatment for infections caused by Gram-positive multidrug-resistant pathogens. GPAs appear to be related to ramoplanin-like lipodepsipeptides (LDPs), yet another signi­ficant class of lipid II binders. Major compounds among LDPs are ramoplanin (the key representative), enduracidin, and chersinamycin; each with known biosynthetic gene clusters (BGCs). Five additional BGCs for the putative LDPs were recently described. LDP BGCs are poorly investigated; one particular aspect that deserves further investigation is transporters coded within BGCs. These proteins most likely take part in the export of antibiotics out of the cell, as well as in the producer’s resistance to its own secondary metabolite. In this work, we performed in silico analysis of genes encoding transporters from ramoplanin and other LDP BGCs. We investigated the domain architecture of these transporters, discovered their homologues in BGCs from MIBiG and beyond, generated models of secondary and tertiary structures, and compared the overall LDP BGCs transport genes blueprint. We were able to identify previously uncharacterized gene encoding ABC transporter within ramoplanin BGC – ramo3. Ramo1 and Ramo3 in ramoplanin BGC appear to be paralogues coding for a permease subunit of the ABC transporter. In every other LDP BGCs, except for chersinamycin BGC, we found only one corresponding homologue encoding this type of protein. Similarly, we found that Ramo2 and Ramo23 are also homologous proteins, which appear to be ATP-binding subunits of the ABC transporter; Ramo2 and Ramo23 have only one homologue in each other LDP BGCs. Next, we were able to describe Ramo8 as ATP-binding ABC transporter, containing both ATPase and transmembrane parts, similar to those encoded in GPA BGCs. For Ramo8, we modelled 3D structure as well as quaternary structure for homodimer of this protein. Finally, our in silico analysis revealed Ramo31 to be a proton membrane antiporter, having distant homologue only in chersinamycin BGC; most likely Ramo31 is not connected to ramoplanin biosynthesis.