Folate-producing bifidobacteria: metabolism, genetics, and relevance

Abstract

Folate (the general term for all bioactive forms of vitamin B₉) plays a crucial role in the evolutionary highly conserved one-carbon (1C) metabolism, a network including central reactions such as DNA and protein synthesis and methylation of macromolecules. Folate delivers 1C units, such as methyl and formyl, between reactants. Plants, algae, fungi, and many bacteria can naturally produce folate, whereas animals, including humans, must obtain folate from external sources. For humans, folate deficiency is, however, a widespread problem. Bifidobacteria constitute an important component of human and many animal microbiomes, providing various health advantages to the host, such as producing folate. This review focuses on bifidobacteria and folate metabolism and the current knowledge of the distribution of genes needed for complete folate biosynthesis across different bifidobacterial species. Biotechnologies based on folate-trophic probiotics aim to create fermented products enriched with folate or design probiotic supplements that can synthesize folate in the colon, improving overall health. Therefore, bifidobacteria (alone or in association with other microorganisms) may, in the future, contribute to reducing widespread folate deficiencies prevalent among vulnerable human population groups, such as older people, women at child-birth age, and people in low-income countries.

Keywords: Bifidobacteria; folate biofortification; folate metabolism; gut microbiota.

Figure 1

The chemical structure of folic acid (mono-glutamate derivate). PABA: Para-aminobenzoic acid.

Figure 2

Shikimate and folate biosynthesis pathway and relevant enzymes and genes involved. Metabolites: I: D-erythrose 4-phosphate; II: phosphoenolpyruvate; III: 7-phosphate-2-dehydro-3-deoxy-D-arabinoheptonate; IV: 3-dehydroquinate; V: 3-dehydroshikimate; VI: shikimate; VII: shikimate 3-phosphate; VIII: 5-O-(1-carboxyvinyl)-3-phosphoshikimate. Enzymes: EC 2.15.1.54: 3-deoxy-7-phosphoheptulonate synthase; EC 4.2.3.4: 3-dehydroquinate synthase; EC 4.2.1.10: 3-dehydroquinate dehydratase I; EC 1.1.1.25: shikimate dehydrogenase; EC 2.7.1.71: shikimate kinase; EC 2.5.1.19: 3-phosphoshikimate 1-carboxyvinyltransferase; EC 4.2.3.5: chorismate synthase; EC 2.6.1.85: aminodeoxychorismate synthase; EC 4.1.3.38: aminodeoxychorismate lyase; EC 3.5.4.16: guanosine triphosphate (GTP) cyclohydrolase; EC 3.6.1.67: dihydroneopterin triphosphate diphosphatase; EC 4.1.2.25: dihydroneopterin aldolase; EC 2.7.6.3: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase; EC 2.5.1.15: dihydropteroate synthase; EC 6.3.2.12: dihydrofolate synthase; EC 6.3.2.17: tetrahydrofolate synthase; EC 1.5.1.3: dihydrofolate reductase. In circles, genes are involved in folate biosynthesis. ^*Enzymes common to mammals.

Figure 3

Folate-mediated one-carbon metabolism. There are two interrelated cycles in folate metabolism that compete for folate cofactors, namely DNA biosynthesis (represented by blue) and methylation (represented by green). In addition, the trans-sulfuration pathway (depicted in pink) breaks down homocysteine. 5,10-methenylTHF: 5,10-methenyltetrahydrofolate; 5,10-methyleneTHF: 5,10-methylenetetrahydrofolate; 5-methylTHF: 5-methyltetrahydrofolate; 10-formylTHF: 10-formyltetrahydrofolate; AHCY: S-adenosylhomocysteine hydrolase; B₂: riboflavin; B₆: vitamin B₆ (pyridoxine); B₁₂: vitamin B₁₂; BHMT: betaine-homocysteine methyltransferase; CBS: cystathionine β-synthase; CTH: cystathionase, DHF: dihydrofolate; DHFR: dihydrofolate reductase; MAT: methionine adenosyltransferase; MTHFD1: methylenetetrahydrofolate dehydrogenase 1/methenyltetrahydrofolate cyclohydrolase/formyltetrahydrofolate synthetase; MTHFR: methylenetetrahydrofolate reductase; MTR: methionine synthase; R: methyl acceptors, such as DNA or histones; SAH: S-adenosylhomocysteine; SAM: S-adenosylmethionine; SHMT1: serine hydroxymethyltransferase 1; THF: tetrahydrofolate; TYMS: thymidylate synthetase.

Figure 4

Presence of genes for the biosynthesis of chorismate, pABA, DHPPP, and THF-polyglutamate pathways and prediction of folate synthesis from the sequenced genomes of type strains of bifidobacterial species so far described. Chorismate pathway comprises aroG 2.5.1.54, aroBK 4.2.3.4, aroQ 4.2.1.10, aroE 1.1.1.25, aroBK 2.7.1.71, aroA 2.5.1.19 and aroC 4.2.3.5; ^bpABA pathway comprise pabA 2.6.1.85 and pabC 4.1.3.38; ^cDHPP pathway comprises folE 3.5.4.16, 3.1.3.1, 3.6.1.-, folBK 4.1.2.25, folBK 2.7.63; ^dTHF-polyglud pathway comprises folP 2.5.1.15, folC 6.3.2.12/17, dfrA 1.5.1.3. Rectangels in green: all genes of the pathway are present; rectangels in red: at least one gene of the pathway is absent. In the right you will find the folate production prediction based on th epresence of pathwas genes: in blue: predicted folate production; in yellow: pABA needed for predicted folate production; in brown, no predicted folate production; ^eall the genes for the biosynthesis of DHPPP are present, with the exception of alkaline phosphatase (EC 3.1.3.1). The dephosphorylation of dihydroneopterin triphosphate into the monophosphate can occur through an alternative route using pyrophosphohydrolase number EC 3.6.1.-. which is present (Rossi 2011).

Figure 5

Phylogenomic tree of Bifidobacterium genus describing the origin and the ability of the type strains of species to produce folate.