University of Groningen Structural and mechanistic insights into prokaryotic energy-coupling factor transporters

| Energy-coupling factor (ECF) transporters belong to the ATP-binding cassette (ABC)-transporter family and mediate the uptake of essential micronutrients in many prokaryotic species. Two crystal structures of bacterial ECF transporters have recently been obtained and suggest that transport involves an unprecedented re-orientation of a membrane protein in the lipid bilayer during catalysis. In this Progress article, I present the new structural insights, discuss a testable model for the transport mechanism and consider the more general implications of these findings for our understanding of membrane transporters. PROGRESS NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | FEBRUARY 2014 | 79 © 2014 Macmillan Publishers Limited. All rights reserved are predicted to form a dedicated complex. In some cases, two or three components of the complex are fused into a multi-domain protein, resulting in complexes that consist of three or two subunits, rather than four (FIG. 1a). Some organisms encode several group I ECF transporters, and this feature is most pronounced in archaea (for example, Thermofilum pendens contains six transporters) and Actinobacteria6,27. The cellular levels of group I transporters are often regulated according to substrate requirements, such that the transporters are highly expressed when the cytoplasmic concentrations of corresponding substrates are low and their expression is downregulated when the substrate is abundant6. Regulation of ECF transporter expression occurs at the transcriptional and translational levels. In many cases, ribo switches are used to regulate the expression of ECF transporters. Riboswitches are sequence motifs that bind metabolites and are found upstream of the coding region in several mRNAs30. Binding results in alteration of the mRNA structure, which affects transcription or translation. In the case of ECF transporters, the encoding mRNA adopts a conformation that is incompatible with translation when the transported substrate is bound (that is, when substrate levels are high), whereas the substrate-free riboswitch enables translation to proceed6. The S component genes of group II transporters are not located in the same operon as the genes for the ECF module, and multiple different S component genes are usually scattered around the chromosome. These S components, which differ in their substrate specificity, share the same ECF module6,29. Thus, the same ECF module can associate with distinct S components and thereby power the import of chemically diverse substrates; for example, the ECF module of the group II ECF transporter in L. brevis associates with seven different S components that transport seven different substrates (FIG. 1b). As different S components lack a high degree of sequence similarity, the use of the same ECF module by group II transporters raises an intriguing question: how does the same ECF module recognize unrelated S components? The recent crystal structures21,22 provide some clues to explain how this might be possible (see below). The ECF modules of group II transporters are usually constitutively expressed6. By contrast, expression of the different S components is regulated, often by ribo switches in the encoding mRNAs6,10,13 (see above). This enables the cellular pool of S components to increase substantially when the corresponding substrate is lacking5,6,10. As a result, the number of ECF modules in a cell may become limiting, resulting in a surplus of S components that do not have an ECF-module partner. A potential role for these lone S components could be to scavenge scarce micronutrients from the Table 1 | Substrate specificity and distribution of ECF transporters S component Substrate*‡ Group* Prokaryotic distribution* BioY Biotin (vitamin B 7 ) I, II and solitary Actinobacteria; Archaea; Chlamydia spp. ; Cyanobacteria; Deinococcus spp. ; Firmicutes; Fusobacteria; Proteobacteria; Spirochaetes; Thermotogae; Thermus spp. CbiMN Co I Actinobacteria; Archaea§; Bacteroidetes; Cyanobacteria; Firmicutes§; Proteobacteria; Spirochaetes; Thermotogae CblT Dimethylbenzimidazole‡ Mostly II Firmicutes CbrT Cobalamin (vitamin B 12 )‡ I and II Actinobacteria§ ; Archaea; Firmicutes§ FolT Folates (vitamin B 9 ) II Firmicutes§; Themotogae HmpT or PdxU2¶ Hydroxymethylpyrimidine or pyridoxine‡ Mostly II Archaea; Firmicutes§; Thermotogae§ HstT Unknown Mostly I Actinobacteria; Archaea; Firmicutes; Spirochaetes LipT Lipoate‡ II Firmicutes MtaT Methionine precursor‡ I Actinobacteria; Archaea; Firmicutes MtsT S-adenosylmethionine‡ I Archaea; Firmicutes§; Proteobacteria NiaX Niacin (vitamin B 3 ) II Firmicutes NikMN Ni I Actinobacteria; Archaea§; Bacteroidetes; Cyanobacteria; Firmicutes; Proteobacteria§; Spirochaetes PanT Pantothenate (vitamin B 5 ) Mostly II Actinobacteria; Firmicutes§; Themotogae PdxU Pyridoxine (vitamin B 6 )‡ Mostly II Actinobacteria; Archaea§; Firmicutes§;Thermotogae§ QueT Queuosine or precursor‡ Mostly II Actinobacteria; Firmicutes§; Thermotogae QrtT Queuosine or precursor‡ I and II Firmicutes; Thermotogae; Actinobacteria; Proteobacteria RibU Riboflavin (vitamin B 2 ) Mostly II Actinobacteria; Archaea; Firmicutes§; Thermotogae§ ThiT Thiamin (vitamin B 1 ) II Firmicutes ThiW Thiazole‡ I and II Actinobacteria; Archaea; Chloroflexi; Firmicutes TrpP Tryptophan I and II Archaea; Firmicutes YkoE Hydroxymethylpyrimidine‡ I Actinobacteria§; Archaea; Firmicutes§ *Data taken from REFS 6,27,29. ‡ These substrates are only predicted to be transported by the corresponding S component. §The phyla in which the indicated S components are most abundant. ¶This family of S components was originally annotated as HmpT but was later renamed PdxU2 because genome context analysis showed that the proteins might be specific for pyridoxine. P R O G R E S S 80 | FEBRUARY 2014 | VOLUME 12 www.nature. com/reviews/micro © 2014 Macmillan Publishers Limited. All rights reserved Nature Reviews | Microbiology a Group I b Group II c Solitary S components