1.A.16 The Formate-Nitrite Transporter (FNT) Family
FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea and yeast. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.
With the exception of the yeast protein (627 amino acyl residues), all members of the family are of 256-285 residues in length and exhibit 6-8 putative transmembrane α-helical spanners (TMSs). In one case, that of the E. coli FocA protein, a 6 TMS topology has been established. The yeast protein has a similar apparent topology but has a large C-terminal hydrophilic extension of about 400 residues.
The phylogenetic tree shows clustering according to function and organismal phylogeny. The putative formate efflux transporters (FocA) of bacteria associated with pyruvate-formate lyase (pfl) comprise cluster I; the putative formate uptake permeases (FdhC) of bacteria and archaea associated with formate dehydrogenase comprise cluster II; the nitrite uptake permeases (NirC) of bacteria comprise cluster III, and a yeast protein comprises cluster IV.
The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCO2- and NO2- uptakes are probably coupled to H symport. HCO2- efflux may be driven by the membrane potential by a uniport mechanism or by H antiport. FocA of E. coli catalyzes bidirectional formate transport, has a pentameric quaternary structure and may function by a channel-type mechanism (Falke et al., 2010).
FocA, a representative member of the formate-nitrite transporter family, transports short-chain acids in bacteria, archaea, fungi, algae and certain eukaryotic parasites. Wang et al. (2009) reported the crystal structure of the E. coli FocA at 2.25 A resolution. FocA forms a symmetric pentamer, with each protomer consisting of six TMSs. Despite a lack of sequence homology, the overall structure of the FocA protomer closely resembles that of aquaporin, indicating that FocA is a channel rather than a carrier. Structural analysis identified potentially important channel residues, defined the channel path and revealed two constriction sites. Unlike aquaporin, FocA is impermeable to water but allows the passage of formate.
FocA (2.A.44.1.1) may be able to switch its mode of operation from a passive export channel at high external pH to a secondary active formate/H importer at low pH. The crystal structure of Salmonella typhimurium FocA at pH 4.0 shows that this switch involves a major rearrangement of the amino termini of individual protomers in the pentameric channel (Lü et al., 2011).The amino-terminal helices open or block transport in a concerted, cooperative action that indicates how FocA is gated in a pH-dependent way. Electrophysiological studies show that the protein acts as a specific formate channel at pH 7.0 and that it closes upon a shift of pH to 5.1.
Phylogenetic analysis of prokaryotic FNT sequences revealed eight different subgroups (Mukherjee et al. 2017). Formate, nitrite and hydrosulphide transporters respectively are clustered into two (FocA and FdhC), three (NirC-alpha, NirC-beta and NirC-gamma) and one (HSC) subfamilies plus two FNT subgroups (YfdC-alpha and YfdC-beta) with unassigned function. Structure-based sequence alignments of individual subfamily members revealed that certain positions in the two constriction regions and some residues facing the interior show subfamily-specific conservation (Mukherjee et al. 2017).
The probable transport reactions catalyzed by different members of the FNT family are:
(1) RCO2- or NO2- (out) ⇌ RCO2- or NO2- (in)
(2) HCO2- (in) ⇌ HCO2- (out)
(3) HS- (out) ⇌ HS- (in)