9.A.18 The Peptide Uptake Permease (PUP) Family

Two proteins, the SbmA protein (406 aas) of E. coli and the BacA protein (420 aas) of Rhizobium meliloti comprise the PUP family. SbmA has been reported to be the permease for uptake of thiazole ring-containing peptide antibiotics such as Microcin B17 and Microcin J25 as well as the non-peptide antibiotic, bleomycin, across the cytoplasmic membrane (Salomón and Farías, 1995), and BacA is a nodulation protein essential for bacterial development when Rhizobium is in symbiosis with a leguminous plant such as alfalfa (Glazebrook et al., 1993). These two proteins exhibit 64% identity and are functionally interchangeable in both E. coli and R. meliloti (Ichige et al., 1997).

R. meliloti bacA null mutants show increased resistance to bleomycin and certain aminoglycosides as well as increased sensitivity to ethanol and detergents. The latter properties are not characteristic of E. coli sbmA mutants. It has been hypothesized that BacA may take up peptide substances required for developmental progression towards bacteroid formation. BacA (but not SbmA) may also play a role in the maintenance of membrane integrity (see below).

PUP family proteins are homologous to, but show a low degree of sequence similarity to, a few putative ABC-type transporters in Gram-negative and Gram-positive bacteria which, unlike SbmA and BacA, possess ATP-binding cassette (ABC)-containing domains. SbmA and BacA also differ from these putative ABC proteins in possessing 7 rather than 6 putative transmembrane α-helical spanners. It is possible that ABC-protein constituents of the PUP family will be found, but the mechanism of energy coupling to PUP family permeases is not currently known. A BacA homologue in Mycobacterium tuberculosis with an ATP hydrolyzing domain takes up antimicrobial peptides and bleomycin, (Q50614; TC#3.A.1.203.4; Domenech et al. 2009). It is possible that all BacA homologues will prove to belong to the ABC superfamily, but the cytoplasmic ATPase domains of the Rhizobial and Escherichia homologues have not been identifited.

Ferguson et al., 2004 reported (1) that BacA of Sinhorizobium and Brucella shows sequence similarity to the long-chain fatty acid transporter ABCD1 (ALD, the adrenoleukodystrophy protein; TC #3.A.1.203.3), (2) that bacA mutants show increased sensitivity to detergents and other cell disrupting agents, and (3) that BacA affects the very long-chain fatty acid (27-hydroxy-C28:0 and 29-hydroxy-C30:0 fatty acids) content of the lipid A constituent of lipopolysaccharides. This led to the postulate that BacA is an export permease for activated long-chain fatty acids, required for the synthesis of lipid A (Ferguson et al., 2004). Direct transport and mode of energy coupling have yet to be demonstrated. However, Ardissone et al. (2011) showed that BacA of a Rhizobium species is a peptide uniporter essential for bacteroid differentiation.

The generalized reactions currently proposed for proteins of the PUP family are:

(1) Peptide antibiotic (periplasm) →  Peptide antibiotic (cytoplasm)

(2) Activated long-chain fatty acid (cytoplasm)  →  Activated long-chain fatty acid (periplasm)



Ardissone, S., H. Kobayashi, K. Kambara, C. Rummel, K.D. Noel, G.C. Walker, W.J. Broughton, and W.J. Deakin. (2011). Role of BacA in lipopolysaccharide synthesis, peptide transport, and nodulation by Rhizobium sp. strain NGR234. J. Bacteriol. 193: 2218-2228.

Domenech, P., H. Kobayashi, K. LeVier, G.C. Walker, and C.E. Barry, 3rd. (2009). BacA, an ABC transporter involved in maintenance of chronic murine infections with Mycobacterium tuberculosis. J. Bacteriol. 191: 477-485.

Ferguson, G.P., A. Datta, J. Baumgartner, R.M. Roop, 2nd, R.W. Carlson, and G.C. Walker. (2004). Similarity to peroxisomal-membrane protein family reveals that Sinorhizobium and Brucella BacA affect lipid-A fatty acids. Proc. Natl. Acad. Sci. USA 101: 5012-5017.

Glazebrook, J., A. Ichige, and G.C. Walker. (1993). A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development. Genes Dev. 7: 1485-1497.

Haag, A.F., M.F. Arnold, K.K. Myka, B. Kerscher, S. Dall''Angelo, M. Zanda, P. Mergaert, and G.P. Ferguson. (2013). Molecular insights into bacteroid development during Rhizobium-legume symbiosis. FEMS Microbiol. Rev. 37: 364-383.

Ichige, A. and G.C. Walker. (1997). Genetic analysis of the Rhizobium meliloti bacA gene: functional interchangeability with the Escherichia coli sbmA gene and phenotypes of mutants. J. Bacteriol. 179: 209-216.

Marlow, V.L., A.F. Haag, H. Kobayashi, V. Fletcher, M. Scocchi, G.C. Walker, and G.P. Ferguson. (2009). Essential role for the BacA protein in the uptake of a truncated eukaryotic peptide in Sinorhizobium meliloti. J. Bacteriol. 191: 1519-1527.

Maruya, J. and K. Saeki. (2010). The bacA gene homolog, mlr7400, in Mesorhizobium loti MAFF303099 is dispensable for symbiosis with Lotus japonicus but partially capable of supporting the symbiotic function of bacA in Sinorhizobium meliloti. Plant Cell Physiol. 51: 1443-1452.

Salomón, R.A. and R.N. Farías. (1995). The peptide antibiotic Microcin 25 is imported through the TonB pathway and the SbmA protein. J. Bacteriol. 177: 3323-3325.

Travin, D.Y., R. Jouan, A. Vigouroux, S. Inaba-Inoue, J. Lachat, F. Haq, T. Timchenko, D. Sutormin, S. Dubiley, K. Beis, S. Moréra, K. Severinov, and P. Mergaert. (2023). Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria. mBio e0021723. [Epub: Ahead of Print]

Usui, M., Y. Yoshii, S. Thiriet-Rupert, J.M. Ghigo, and C. Beloin. (2023). Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance. Commun Biol 6: 275.


TC#NameOrganismal TypeExample

Microcin uptake permease, SbmA, of 406 aas and 7 or 8 TMSs. It may function as a peptide uptake porter. The biofilm environment favors rapid evolution of resistance and provides new insights into the dynamic evolution of antibiotic resistance (Usui et al. 2023). For example, mutations in sbmA occur with high frequency in biofilms, but not in the planktonic state.

Gram-negative bacteria

SbmA of E. coli (P0AFY6)


Bacteroid development protein, BacA; probably a peptide/bleomycin uptake transporter (Ardissone et al., 2011; Marlow et al., 2009). The bacterial BacA protein is essential for bacteroid differentiation in legumes producing nodule-specific cysteine-rich peptides (NCRs), which induce the terminal differentiation of the bacteria into bacteroids (Haag et al. 2013). This protein and others in this family are homologous to the membrane constituents of 3.A.1.203 family in the ABC superfamily in TCDB. Takes up phazolicin (PHZ), a peptide antibiotic (Travin et al. 2023). The frequency of spontaneous PHZ-resistant mutants in Sinorhizobium meliloti is below the detection limit because PHZ can enter S. meliloti cells through two promiscuous peptide transporters,, BacA (TC# 9.A.18.1.2) and YejABEF (TC# 3.A.1.5.49), which belong to the SLiPT (SbmA-like peptide transporter) and ABC (ATP-binding cassette) transporter families, respectively. The dual-uptake mode explains the lack of observed resistance acquisition because the simultaneous inactivation of both transporters is necessary for resistance to PHZ. Since both BacA and YejABEF are essential for the development of functional symbiosis of S. meliloti with leguminous plants, the unlikely acquisition of PHZ resistance via the inactivation of these transporters is further disfavored. A whole-genome transposon sequencing screen did not reveal additional genes that can provide strong PHZ resistance when inactivated. However, it was found that the capsular polysaccharide KPS, a novel putative envelope polysaccharide PPP (PHZ-protecting polysaccharide), as well as the peptidoglycan layer jointly contribute to the sensitivity of S. meliloti to PHZ, most likely serving as barriers that reduce the amount of PHZ transported inside the cell (Travin et al. 2023).

Gram-negative bacteria

BacA of Rhizobium meliloti (Q08120)


SmbA/BacA-like transporter, SBT


SBT of Cryptosporidium muris (B6AF79)


BacA peptide/bleomycin uptake porter (Marlow et al., 2009).


BacA of Brucella abortus (Q9KI15)


Bacteroides development protein, BacA (Maruya and Saeki, 2010).


BacA of Mesorhizobium loti (Q986E2)