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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. Members of the Cation/Proton Antiporter (CPA) superfamily, the Ion Transport (IT) superfamily, and the Na+-translocating Mrp transporter superfamily can catalyze Na+/H+ antiiport (Patiño-Ruiz et al. 2022). Transport mechanisms for Na+/H+ exchangers that explain their highly pH-regulated activity profiles have been considered (Patiño-Ruiz et al. 2022).

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, 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.63.1.2 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 aas 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.

Mrp antiporters are broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA-G, are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus, which are reported to sustain Na+/H+ antiport activity with the MrpA subunit alone (Ito et al. 2017). Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti, bile salt tolerance in Bacillus subtilis and Vibrio cholerae, arsenic oxidation in Agrobacterium tumefaciens, pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus, and the conversion of energy involved in metabolism and hydrogen production in archaea (Ito et al. 2017). In addition, some Mrp antiporters transport K+ and Ca2+ instead of Na+, depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their coupling cations.

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

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

References associated with 2.A.63 family:

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. 19700555
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. 7715455
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. 9852009
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. 10198001
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. 11004162
Ito, M., M. Morino, and T.A. Krulwich. (2017). Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea. Front Microbiol 8: 2325. 29218041
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. 19389778
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. 17693497
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. 9878723
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. 10648512
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. 21236240
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. 20624916
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. 18408029
Patiño-Ruiz, M., C. Ganea, and O. Călinescu. (2022). Prokaryotic Na/H Exchangers-Transport Mechanism and Essential Residues. Int J Mol Sci 23:. 36012428
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. 9680201
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. 17293423
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. 19460820