Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

Abstract

The availability of thousands of sequenced genomes has revealed the diversity of biochemical solutions to similar chemical problems. Even for molecules at the heart of metabolism, such as cofactors, the pathway enzymes first discovered in model organisms like Escherichia coli or Saccharomyces cerevisiae are often not universally conserved. Tetrahydrofolate (THF) (or its close relative tetrahydromethanopterin) is a universal and essential C1-carrier that most microbes and plants synthesize de novo. The THF biosynthesis pathway and enzymes are, however, not universal and alternate solutions are found for most steps, making this pathway a challenge to annotate automatically in many genomes. Comparing THF pathway reconstructions and functional annotations of a chosen set of folate synthesis genes in specific prokaryotes revealed the strengths and weaknesses of different microbial annotation platforms. This analysis revealed that most current platforms fail in metabolic reconstruction of variant pathways. However, all the pieces are in place to quickly correct these deficiencies if the different databases were built on each other's strengths.

Systems biology of host–microbe metabolomics

“…Additionally, gene annotations are lacking or unspecific and/or the associated pathways are not accounted for by the automated reconstruction pipelines, resulting in a less predictive draft reconstruction. Moreover, even universal pathways vary in the enzymes carrying out individual steps . As a result, annotation platforms often fail to correctly reconstruct these variant pathways .…”

“…Moreover, even universal pathways vary in the enzymes carrying out individual steps . As a result, annotation platforms often fail to correctly reconstruct these variant pathways . Several recent comparative genomics studies have resulted in the improvement of genome annotations in gut microbial genomes .…”

“…158 As a result, annotation platforms often fail to correctly reconstruct these variant pathways. 158 Several recent comparative genomics studies have resulted in the improvement of genome annotations in gut microbial genomes. [159][160][161] Such efforts will ultimately result in an improved predictive potential of automated reconstructions derived from the genome sequence.…”

Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties

“…Therefore, it is expected that these strains are not auxotrophic for folates or DHP but can produce folate in the presence of PABA supplementation.The presence/absence of the components of the folate biosynthesis pathway is reported based on KEGG pathway analysis. Previous studies have revealed that B. subtilis genome harbor all the pathways components and have been engineered for folate production[63,65,66].…”

The uridylyltransferase GlnD and tRNA modification GTPase MnmE allosterically control Escherichia coli folylpoly-γ-glutamate synthase FolC

“…2.A.88) (4) or a member of the folate-biopterin transporter (FBT) family present in protists, cyanobacteria, and plants (TC no. 2.A.71) (5)(6)(7)(8)(9). Once inside the cell, folate is reduced via DHF reductase (FolA) to DHF and then to THF (Fig.…”