word count: (abstract/importance: 235/145) 14 Text word count: 4911 15 32 Abstract 33 34 Peptidase-containing ABC transporters (PCATs) are a widely distributed family of 35 transporters which secrete double-glycine (GG) peptides. In the opportunistic pathogen 36 Streptococcus pneumoniae (pneumococcus), the PCATs ComAB and BlpAB have been 37 shown to secrete quorum-sensing pheromones and bacteriocins related to the 38 competence and pneumocin pathways. Here, we describe another pneumococcal 39 PCAT, RtgAB, encoded by the rtg locus and found intact in 17% of strains. The 40 Rgg/SHP-like quorum sensing system RtgR/S, which uses a peptide pheromone with a 41 distinctive Trp-X-Trp motif, regulates expression of the rtg locus and provides a 42 competitive fitness advantage in a mouse model of nasopharyngeal colonization. RtgAB 43 secretes a set of co-regulated rtg GG peptides. ComAB and BlpAB, which share a 44 substrate pool with each other, do not secrete the rtg GG peptides. Similarly, RtgAB 45 does not efficiently secrete ComAB/BlpAB substrates. We examined the molecular 46 determinants of substrate selectivity between ComAB, BlpAB, and RtgAB and found 47 that the GG peptide signal sequences contain all the information necessary to direct 48 secretion through specific transporters. Secretion through ComAB and BlpAB depends 49 largely on the identity of four conserved hydrophobic signal sequence residues 50 previously implicated in substrate recognition by PCATs. In contrast, a motif situated at 51 the N-terminal end of the signal sequence, found only in rtg GG peptides, directs 52 secretion through RtgAB. These findings illustrate the complexity in predicting 53 substrate-PCAT pairings by demonstrating specificity that is not dictated solely by signal 54 sequence residues previously implicated in substrate recognition. 55 56 Importance 57 58The export of peptides from the cell is a fundamental process carried out by all 59 bacteria. One method of bacterial peptide export relies on a family of transporters called 60 peptidase-containing ABC transporters (PCATs). PCATs export so-called GG peptides 61 which carry out diverse functions, including cell-to-cell communication and inter-62 bacterial competition. In this work, we describe a PCAT-encoding genetic locus, rtg, in 63 the pathogen Streptococcus pneumoniae (pneumococcus). The rtg locus is linked to 64 increased competitive fitness advantage in a mouse model of nasopharyngeal 65 colonization. We also describe how the rtg PCAT preferentially secretes a set of co-66 regulated GG peptides but not GG peptides secreted by other pneumococcal PCATs. 67These findings illuminate a relatively understudied part of PCAT biology: how these 68 transporters discriminate between different subsets of GG peptides.