Functional and structural characterization of an ECF-type ABC transporter for vitamin B12

Santos, Joana A; Rempel, S.; Mous, S.; Pereira, Cristiane Tambascia; Beek, Josy ter; Gier, Jan‐Willem de; Guskov, Albert; Slotboom, Dirk Jan

doi:10.7554/elife.35828

Cited by 40 publications

(62 citation statements)

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“…The former structures show what seems to be the pre-translocation state, after the S-component binds its substrate and before associating with the ECF module. The latter reveals a post-translocation state with the substrate-free S-component in the toppled orientation with the empty binding site facing the cytoplasm [6][7][8]14,15 .…”

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confidence: 99%

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

et al. 2020

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Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist of an integral membrane unit, the S-component, and a tripartite ECF module. It has been proposed that the S-component mediates the substrate transport by toppling over in the membrane when docking onto an ECF module. Here, we present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter. Simulations reveal a strong bending of the membrane around the ECF module that provides a driving force for toppling of the S-component. The stability of the toppled state depends on the presence of non-bilayer forming lipids, as confirmed by folate transport activity measurements. Together, our data provide evidence for a lipid-dependent toppling-based mechanism for the folate-specific ECF transporter, a mechanism that might apply to other ECF transporters.

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Membrane mediated toppling mechanism of the folate energy coupling factor transporter

et al. 2020

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“…PEP‐PTS transporter was related to the majority of sugars including sucrose, fructose, glucose (Liu et al., ; Oberholzer et al., ). ABC transporter mainly could make ATP hydrolysis energy with substrate transfer into or out of cells (Roos et al., ; Santos et al., ). Carbohydrate transporter WHH1689 encodes 15 genes involved in phosphoenolpyruvate synthase and 13 genes for protein phosphotransferase.…”

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confidence: 99%

Genomic analysis of Lactobacillus reuteri WHH1689 reveals its probiotic properties and stress resistance

Chen

et al. 2019

Food Science & Nutrition

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Lactobacillus reuteri (L. reuteri) WHH1689, which was isolated from Chinese traditional highland barley wine, exhibited high survival period at room temperature in drinkable probiotic yogurt. This article aimed to indicate the genes involved in probiotic function of WHH1689 and reveal potential stress resistance based on genomic analysis. Analysis of comparative genome with closely related L. reuteri strains identified special stress adaptation. MUMmer and ACT softwares were applied for collinear analysis, and OrthoMCL program was used for sequence alignment involved in distribution of protein cluster. We identified genes coding for carbohydrate transport and enzymes, carbon metabolism pathway, gastrointestinal tract resistance, adhesive ability, and folic acid biosynthesis, etc. Genome sequence and comparative genome analysis of L. reuteri WHH1689 demonstrated specific genes for genetic adaptation and stress resistance. Tolerance, adhesion, and folate test indicated the strain had multiple probiotics. L. reuteri WHH1689 has the potential to be a probiotic candidate in dairy foods.

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“…It therefore appears that cobamide remodeling mechanisms have independently evolved multiple times. Together with the multiple pathways that exist for cobamide biosynthesis, transport, and precursor salvaging (31,33,35,(93)(94)(95)(96)(97)(98)(99), the addition of CbiR to the growing list of enzymes involved in cobamide metabolism highlights the importance of cobamide physiology in the evolution of bacteria.…”

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Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacteriumAkkermansia muciniphila

Mok

Sokolovskaya

Nicolas

et al. 2020

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The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand, though the specific cobamides it can use have not been examined. We found that growth of A. muciniphila strain MucT was nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that have been studied. Unexpectedly, this promiscuity is due to cobamide remodeling – the removal and replacement of the lower ligand – despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share homology with other cobamide remodeling enzymes or B12-binding domains, and instead is a member of the AP endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides they otherwise cannot use in order to grow under a cobamide-requiring condition; this function was confirmed by heterologous expression of cbiR in E. coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment.ImportanceCobamides, the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. Here, we discover that the beneficial human gut bacterium Akkermansia muciniphila can use a diverse range of cobamides due to its ability to change the cobamide structure via “cobamide remodeling”. We identify and characterize the novel enzyme CbiR that is necessary for initiating the cobamide remodeling process. The discovery of this enzyme has implications not only for understanding the ecological role of A. muciniphila in the gut, but for other bacteria that carry this enzyme as well.

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Functional and structural characterization of an ECF-type ABC transporter for vitamin B12

Cited by 40 publications

References 50 publications

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

Genomic analysis of Lactobacillus reuteri WHH1689 reveals its probiotic properties and stress resistance

Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacteriumAkkermansia muciniphila

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