Identification of Genes Encoding the Folate- and Thiamine-Binding Membrane Proteins in Firmicutes

Eudes, Aymerick; Erkens, Guus B.; Slotboom, Dirk Jan; Rodionov, Dmitry A.; Naponelli, Valeria; Hanson, Andrew D.

doi:10.1128/jb.01070-08

Cited by 53 publications

(68 citation statements)

References 29 publications

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“…ThiW transporters belong to either the group I transporters that are accompanied by the dedicated AT module (in some members of the Archaea and Chloroflexi) (Fig. 2) (7). The folT genes in several Mycoplasma genomes and in Streptococcus suis cluster on the chromosome with the folC gene, encoding the bifunctional enzyme dihydrofolate synthase/folylpolyglutamate synthase, which can add a polyglutamyl tail to folate molecules.…”

Section: Resultsmentioning

confidence: 99%

A Novel Class of Modular Transporters for Vitamins in Prokaryotes

et al. 2009

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The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have yet to be identified, including the vitamin transporters in various human pathogens, whose growth depends strictly on vitamin uptake. Comparative analysis of the ever-growing collection of microbial genomes coupled with experimental validation enables the discovery of such transporters. Here, we used this approach to discover an abundant class of vitamin transporters in prokaryotes with an unprecedented architecture. These transporters have energy-coupling modules comprised of a conserved transmembrane protein and two nucleotide binding proteins similar to those of ATP binding cassette (ABC) transporters, but unlike ABC transporters, they use small integral membrane proteins to capture specific substrates. We identified 21 families of these substrate capture proteins, each with a different specificity predicted by genome context analyses. Roughly half of the substrate capture proteins (335 cases) have a dedicated energizing module, but in 459 cases distributed among almost 100 gram-positive bacteria, including numerous human pathogens, different and unrelated substrate capture proteins share the same energy-coupling module. The shared use of energy-coupling modules was experimentally confirmed for folate, thiamine, and riboflavin transporters. We propose the name energycoupling factor transporters for the new class of membrane transporters.Transport proteins residing in the cytoplasmic membrane allow the selective uptake and efflux of solutes and are essential for cellular growth and metabolism (20). Reflecting the importance of transporters, between 3% and 16% of the genes in prokaryote genomes are predicted to encode transporter proteins (26). These transporters form numerous families that are diverse in structure, energy-coupling mechanisms, and substrate specificities (25). As only a small fraction of predicted transporter proteins have known substrates, the functional prediction and annotation of the specificities of transporter proteins in the rapidly growing number of sequenced genomes represent a substantial challenge (25, 36). For example, the uptake of many cofactors and their precursors is essential for the growth of various pathogenic bacteria whose genomes are sequenced, but the transport proteins involved have not yet been identified. The use of computational comparative genomic techniques including gene colocalization, cooccurrence, and coregulation analyses combined with experimental assays is a powerful approach to identify novel transporters and to uncover their cellular role (for a recent review, see reference 11).The starting point for the present analysis was our recent discovery of multicomponent transport systems for the vitamin biotin (BioYNM) and the transition metals nickel (NikMNQO) and cobalt (CbiMNQO) (14,30). These transporters all have substrate-specific components (S components), which...

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Section: Resultsmentioning

confidence: 99%

A Novel Class of Modular Transporters for Vitamins in Prokaryotes

et al. 2009

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“…In addition, some of the free energy that is released by the hydrolysis of ATP could be used to lower the affinity of the S component for the substrate when the toppled state is reached, thereby enabling the release of the substrate. In complete ECF complexes, substrate affinity seems to be much lower than in solitary S components 9,11,24,26 , probably as a result of rearrangements in the substrate-binding site upon toppling 21 . A reduction in substrate affinity is likely to be important as it would enable the substrate to diffuse into the cytoplasm.…”

Section: Coupling Of Transport To Atp Hydrolysismentioning

confidence: 95%

“…This early work also showed that the energy for transport was supplied by the hydrolysis of ATP 2 . These observations date from the pre-genomics era and, although some of the binding proteins were purified and their amino acid compositions determined 3,4 , the molecular identity of the transport systems remained elusive until the 2000s [6][7][8][9][10][11][12][13][14] .…”

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Structural and mechanistic insights into prokaryotic energy-coupling factor transporters

Slotboom

2013

Nat Rev Microbiol

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117

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“…Based on the in vitro data, a 1:1:1:1 (A1/A2/T/S) quaternary structure for subclass II systems has been proposed (22). Various S units (e.g., the riboflavin-specific RibU, the folate-specific FolT, and the thiamine-specific ThiT) have been analyzed in detail and were found to bind their substrates in vitro with affinity constants in the nanomolar or subnanomolar range (3,6,7). Coinciding results from different laboratories demonstrated that transport activity of subclass II S units strictly depends on the energy-coupling factor (5,13,16,22,25).…”

Section: Discussionmentioning

confidence: 99%