Cofactor selectivity in methylmalonyl-CoA mutase, a model cobamide-dependent enzyme

Sokolovskaya, Olga M.; Mok, Kenny C.; Park, Jong Duk; Tran, Jennifer L.; Quanstrom, Kathryn; Taga, Michiko E.

doi:10.1101/637140

Cited by 5 publications

(6 citation statements)

References 137 publications

(251 reference statements)

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“…The colon houses the greatest abundance of bacteria and archaea in humans, with cobalamin and non-cobalamin analogs themselves modulating the bacterial growth; hence, large oral doses of B 12 will alter the gut microbial composition. Colonic bacteria produce structural analogs of vitamin B 12 (Allen and Stabler, 2008;Sokolovskaya et al, 2020) that have been reported to inhibit the two B 12dependent enzymes in rodents (Stabler et al, 1991) and humans (Bito et al, 2020;Sokolovskaya et al, 2021Sokolovskaya et al, , 2019. These B 12 analogs traverse the gut epithelium and their presence in blood has, in a few cases, been correlated with severe neurological impairment (Carmel et al, 1988).…”

Section: Hydroxocobalaminmentioning

confidence: 99%

Versatile enzymology and heterogeneous phenotypes in cobalamin complementation type C disease

et al. 2022

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Section: Hydroxocobalaminmentioning

confidence: 99%

Versatile enzymology and heterogeneous phenotypes in cobalamin complementation type C disease

et al. 2022

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“…MUT assay -MUT activity was measure in hepatic extracts using a thiokinase-coupled, spectrophotometric assay (46,47). Total protein lysates were isolated from frozen samples with NP-40 cell lysis buffer (Thermo Fisher Scientific, Waltham, MA) containing protease inhibitor using a Polytron PT2100 homogenizer (Kinematica).…”

Section: Measurement Of Cbl and Cobaltmentioning

confidence: 99%

Dioxin-elicited decrease in cobalamin redirects hepatic propionyl-CoA metabolism to the β–oxidation-like pathway resulting in acrylyl-CoA conjugate accumulation

Orlowska

Fling

Nault

et al. 2021

Preprint

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2,3,7,8 –Tetrachlorodibenzo –p –dioxin (TCDD) is a persistent environmental contaminant and the prototypical ligand for the aryl hydrocarbon receptor (AhR). AhR mediates the effects of TCDD and related compounds, including the reprograming of intermediate metabolism. Untargeted metabolomics analysis of hepatic extracts prepared from mice orally gavaged with TCDD every 4 days for 28 days identified the dose –dependent induction of acrylyl –CoA, a highly reactive toxic intermediate produced during the metabolism of propionyl –CoA in the cobalamin (Cbl) –independent β –oxidation –like pathway. Acrylyl –CoA is a biomarker of inborn errors of metabolism associated with propionic and methylmalonic acidemia associated with Cbl deficiency, transport and/or defects in Cbl –dependent methylmalonyl –CoA mutase (MUT). Although TCDD repressed gene expression for both the canonical Cbl –dependent carboxylase and the alternate Cbl –independent β –oxidation –like pathways, inhibition occurred only at 30 μg/kg TCDD while acrylyl –CoA levels increased at ~3 μg/kg. In contrast, TCDD decreased serum Cbl and hepatic cobalt levels at ~3 μg/kg TCDD consistent with the dose –dependent increase in acrylyl –CoA levels. TCDD elicited negligible effects on the expression of genes associated with Cbl absorption, transport, trafficking and derivatization to 5 –deoxy –adenosylcobalamin (AdoCbl), the required MUT cofactor. In addition, TCDD induced the decarboxylation of cis –aconitate to itaconate by Acod1. Itaconate can then be activated to itaconyl –CoA, a MUT suicide inactivator that forms an adduct with AdoCbl, blocking MUT activity and reducing Cbl levels. Collectively, these results suggest MUT activity was impaired due to Cbl depletion by TCDD causing propionyl –CoA metabolism to be redirected to the alternate Cbl –independent β –oxidation –like pathway resulting in hepatic acrylyl –CoA accumulation.

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“…All other cyanylated cobamides used in the study were purified from bacterial cultures and cobamides were adenosylated and purified as previously described (50,108). Cyanylated and adenosylated cobamides were quantified as previously described (50). MeCbl was quantified using an extinction coefficient of ε519 = 8.7 mM -1 cm -1 (109).…”

Section: Cobamide Synthesis Adenosylation and Quantificationmentioning

confidence: 99%

“…A study of 20 human subjects showed that the human gut is dominated by the purinyl class of cobamides, with benzimidazolyl and phenolyl cobamides and Cbi also present (42). The structural diversity in cobamides impacts growth and metabolism, as most organisms studied to date are selective in their cobamide use (39,(46)(47)(48)(49)(50)(51)(52)(53)(54). For example, the human gut bacterium B. thetaiotaomicron can use benzimidazolyl and purinyl, but not phenolyl, cobamides (37); Dehalococcoides mccartyi and most eukaryotic algae are selective for particular benzimidazolyl cobamides (55)(56)(57); and Sporomusa ovata requires phenolyl cobamides (58).…”

Section: Introductionmentioning

confidence: 99%

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

Mok

Sokolovskaya

Nicolas

et al. 2020

Preprint

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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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Cofactor selectivity in methylmalonyl-CoA mutase, a model cobamide-dependent enzyme

Cited by 5 publications

References 137 publications

Versatile enzymology and heterogeneous phenotypes in cobalamin complementation type C disease

Versatile enzymology and heterogeneous phenotypes in cobalamin complementation type C disease

Dioxin-elicited decrease in cobalamin redirects hepatic propionyl-CoA metabolism to the β–oxidation-like pathway resulting in acrylyl-CoA conjugate accumulation

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

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