2.A.63 The Monovalent Cation (K+ or Na+):Proton Antiporter-3 (CPA3) Family

The CPA3 family may consist of bacterial multicomponent K+:H+ and Na+:H+ antiporters. The best characterized such systems are the PhaABCDEFG system of Rhizobium meliloti that functions in pH adaptation and as a K+ efflux system, and the MnhABCDEFG system of Staphylococcus aureus that functions as a Na+ efflux Na+:H+ antiporter. A homologous but only partially sequenced system was earlier reported to catalyze Na+:H+ antiport in an alkalophilic Bacillus strain. PhaA and PhaD are respectively homologous to the ND5 and ND4 subunits of the H+-pumping NADH:ubiquinone oxidoreductase (TC #3.D.1). Homologous protein subunits from E. coli NADH:quinone oxidoreductase can functionally replace MrpA and MrpD in Bacillus subtilis (Moparthi et al., 2011). The seven Pha proteins are of the following sizes (in #aas) and exhibit the following putative numbers of transmembrane α-helical spanners (TMSs): A, 725 and 17; B, 257 and 5; C, 115 and 3; D, 547 and 13; E, 161 and 3; F, 92 and 3; G, 120 and 3. Thus, all are predicted to be integral membrane proteins. Corresponding values for the S. aureus Mnh system are: A, 801 and 18; B, 142 and 4; C, 113 and 3; D, 498 and 13; E, 159 and 4; F, 97 and 3; G, 118 and 3. In view of the complexity of the system and the homology with NDH family protein constituents, a complicated energy coupling mechanism, possibly involving a redox reaction, cannot be ruled out.

Homologues of PhaA, B, C and D and Nha1, 2, 3 and 4 of an alkalophilic Bacillus strain are the Yuf(Mrp)T, U, V and D genes of Bacillus subtilis. In this system, YufT is believed to be responsible for Na+:H+ antiporter activity, but it does not have activity in the absence of other constituents of the operon. YufF (MrpF) appears to catalyze cholate efflux, possibly by a Na+ symport mechanism (Ito et. al, 2000). It plays a major role in Na+ extrusion (Kosono et al., 1998; Ito et.al., 1999) and is required for initiation of sporulation (Kosono et al., 2000), Additionally, another component of the operon, MrpF (equivalent to PhaF of R. meliloti) has been implicated in choline and Na+ efflux (Ito et. al., 1999). The MrpA-G proteins of B. subtilis have been shown to be present in a single multicomponent complex (Kajiyama et al., 2007). They provide Na+/H+ antiport activity and function in multiple compound resistance and pH homeostasis.

Na+ or Li+ does, but K+, Ca2+, and Mg2+ do not support significant antiport by the Gram-positive bacterial systems (2.A. and 3) (Swartz et al., 2007). Na+(Li+)/H+ antiporters have alkaline pH optima and apparent Km values for Na+ that are among the lowest reported for bacterial Na+/H+ antiporters. Na+/H+ antiport consumes the pmf and therefore is probably electrogenic (Swartz et al., 2007).

The mrp homolog gene cluster mrpCD1D2EFGAB (Ap-mrp) was found in a halotolerant cyanobacterium, Aphanothece halophytica, amplified, and expressed in Escherichia coli mutant TO114 (Fukaya et al., 2009). Ap-mrp complemented the salt-sensitive phenotype of strain TO114 and exhibited Na+:H+ and Li+:H+ exchange activities (Fukaya et al., 2009).

Ap-MrpB is 220 amino acyl residue long and has 6 putative TMSs. TC-BLAST searchers reveal that it shows significant (e-7) similarity with protein PF1428 of Pyrococcus furiosus (TC# 3.D.1.4.1 and PhaB of Sinorhizobium meliloti (2.A.63.1.1)). The CPA3 family is characterized as being multi component K+ or Na+:H+ antiporters having seven different constituents, some resembling components of NADH dehydrogenase complexes. It is probable that this gene cluster belongs to the CPA3 family. However, the evidence presented by Fukaya et al. (2009) suggests that this subunit alone, rather than the entire complex, is sufficient for catalysis of Na+:H+ antiport. If this is the case, then the other subunits of the complex may be auxiliary subunits serving regulatory, catalytic or dissimilar functions. Several of these subunits in the presumed Mrp complex of Aphanothece halophytica are demonstrably homologous to corresponding subunits in the other CPA3 family members.

The generalized reaction believed to be catalyzed by CPA3 family members is:

[K+ or Na+] (in) + H+ (out) ⇌ [K+ or Na+] (out) + H+ (in)

This family belongs to the Na+ Transporting Mrp Superfamily.



Fukaya, F., W. Promden, T. Hibino, Y. Tanaka, T. Nakamura, and T. Takabe. (2009). An Mrp-like cluster in the halotolerant cyanobacterium Aphanothece halophytica functions as a Na+/H+ antiporter. Appl. Environ. Microbiol. 75: 6626-6629.

Hamamoto, T., M. Hashimoto, M. Hino, M. Kitada, Y. Seto, T. Kudo, and K. Horikoshi. (1994). Characterization of a gene responsible for the Na+/H+ antiporter system of alkalophilic Bacillus species strain C-125. Mol. Microbiol. 14: 939-946.

Hiramatsu, T., K. Kodama, T. Kuroda, T. Mizushima, and T. Tsuchiya. (1998). A putative multisubunit Na+/H+ antiporter from Staphylococcus aureus. J. Bacteriol. 180: 6642-6648.

Ito, M., A.A. Guffanti, B. Oudega, and T.A. Krulwich. (1999). Mrp, a multigene, multifunctional locus in Bacillus subtilis with roles in resistance to cholate and to Na+ and in pH homeostasis. J. Bacteriol. 181: 2394-2402.

Ito, M., A.A. Guffanti, W. Wang and T.A. Krulwich (2000). Results of non-polar mutations in each of the seven Bacillus subtilis mrp genes suggest complex interactions among the gene products in support of Na+- and Alkali- but not cholate-resistance. J. Bacteriol. 182: 5663-5670.

Kajiyama Y., Otagiri M., Sekiguchi J., Kudo T. and Kosono S. (2009). The MrpA, MrpB and MrpD subunits of the Mrp antiporter complex in Bacillus subtilis contain membrane-embedded and essential acidic residues. Microbiology. 155(Pt 7):2137-47.

Kajiyama, Y., M. Otagiri, J. Sekiguchi, S. Kosono, and T. Kudo. (2007). Complex formation by the mrpABCDEFG gene products, which constitute a principal Na+/H+ antiporter in Bacillus subtilis. J. Bacteriol. 189: 7511-7514.

Kosono, S., S. Morotomi, M. Kitada, and T. Kudo. (1999). Analyses of a Bacillus subtilis homologue of the Na+/H+ antiporter gene which is important for pH homeostasis of alkaliphilic Bacillus sp. C-125. Biochim. Biophys. Acta. 1409: 171-175.

Kosono, S., Y. Ohashi, F. Kawamura, M. Kitada, and T. Kudo. (2000). Function of a principal Na+/H(+) antiporter, ShaA, is required for initiation of sporulation in Bacillus subtilis. J. Bacteriol. 182: 898-904.

Moparthi, V.K., B. Kumar, C. Mathiesen, and C. Hägerhäll. (2011). Homologous protein subunits from Escherichia coli NADH:quinone oxidoreductase can functionally replace MrpA and MrpD in Bacillus subtilis. Biochim. Biophys. Acta. 1807: 427-436.

Morino, M., S. Natsui, T. Ono, T.H. Swartz, T.A. Krulwich, and M. Ito. (2010). Single site mutations in the hetero-oligomeric Mrp antiporter from alkaliphilic Bacillus pseudofirmus OF4 that affect Na+/H+ antiport activity, sodium exclusion, individual Mrp protein levels, or Mrp complex formation. J. Biol. Chem. 285: 30942-30950.

Morino, M., S. Natsui, T.H. Swartz, T.A. Krulwich, and M. Ito. (2008). Single Gene Deletions of mrpA to mrpG and mrpE Point Mutations Affect Activity of the Mrp Na+/H+ Antiporter of Alkaliphilic Bacillus and Formation of Hetero-Oligomeric Mrp Complexes. J. Bacteriol. 190: 4162-4172.

Putnoky, P., A. Kereszt, T. Nakamura, G. Endre, E. Grosskopf, P. Kiss, and A. Kondorosi. (1998). The pha gene cluster of Rhizobium meliloti involved in pH adaptation and symbiosis encodes a novel type of K+ efflux system. Mol. Microbiol. 28: 1091-1101.

Swartz, T.H., M. Ito, T. Ohira, S. Natsui, D.B. Hicks, and T.A. Krulwich. (2007). Catalytic properties of Staphylococcus aureus and Bacillus members of the secondary cation/proton antiporter-3 (Mrp) family are revealed by an optimized assay in an Escherichia coli host. J. Bacteriol. 189: 3081-3090.

Yamaguchi, T., F. Tsutsumi, P. Putnoky, M. Fukuhara, and T. Nakamura. (2009). pH-dependent regulation of the multi-subunit cation/proton antiporter Pha1 system from Sinorhizobium meliloti. Microbiology 155: 2750-2756.


TC#NameOrganismal TypeExample

Multicomponent K+:H+ antiporter, PhaABCDEFG. Can also transport Na+ (Yamaguchi et al., 2009).


PhaABCDEFG of Sinorhizobium meliloti


Multicomponent Na+:H+ antiporter, NhaA-G. Nha1,2,3,(4)


NhaA-G of Bacillus halodurans (strain C-125)
NhaA (804 aas)(Q7AJV8)
NhaB (146 aas)(Q7AJV9)
NhaC (112 aas)(Q7AJW0)
NhaD (493 aas)(Q9KD98)
NhaE (158 aas)(Q9KD99)
NhaF (95 aas)(Q9KDA0)
NhaG (117 aas)(Q9KDA1) 

2.A.63.1.3Multicomponent Na+:H+ antiporter, MnhABCDEFG Bacteria MnhABCDEFG of Staphylococcus aureus

Multicomponent Na+:H+ antiporter, MrpA-G (ShaA-G) (all components comprise a multi-component complex) (Kajiyama et al., 2007; Morino et al., 2008). The MrpA, MrpB, and MrpD subunits contain membrane-embedded and essential acidic residues (Kajiyama et al. 2009). Several residues important for Na+/H+ antiport activity, sodium exclusion, individual Mrp protein levels, or Mrp complex formation have been identified (Morino et al., 2010).

Gram-positive bacteria

MrpA-G of Bacillus subtilis
MrpA (801 aas; Q9K2S2)
MrpB (143 aas; O05259)
MrpC (113 aas; O05260)
MrpD (493 aas; O05229)
MrpE (158 aas; Q7WY60)
MrpF (94 aas; O05228)
MrpG (124 aas; O05227)



Putative membrane protein of Streptomyces coelicolor


TC#NameOrganismal TypeExample

The Na+:H+ antiporter, MrpA-G complex. Catalyzes Na+:H+ and Li+:H+ antiport. The MrpB subunit may have this transport activity by itself (Fukaya et al., 2009).

Halotolerant cyanobacteria

MrpA-G of Aphanothece halophytica
MrpA (C7G3J5)
MrpB (C7G3J6)
MrpC (C7G3I9)
MrpD1 (C7G3J0)
MrpD2 (C7G3J1)
MrpE (C7G3J2)
MrpF (C7G3J3)
MrpG (C7G3J4)


TC#NameOrganismal TypeExample