Fig 1.
Glycerol assimilation through the fermentative pathway, showing the oxidative and reductive pathways.
In the oxidative route, glycerol is converted in dihydroxyacetone (DHA) and dihydroxyacetone phosphate (DHA-P) by the products of dhaD and dhaMKL genes. In the reductive branch, glycerol is reduced to 1,3-PD by the successive action of glycerol dehydratase (GDHt) (encoded by three dhaB genes) and 1,3 propanediol oxidoreductase (encoded by dhaT gene). The genes refer to those found in K. pneumoniae.
Fig 2.
Distribution of dha genes in completely sequenced Bacteria and Archaea genomes.
On top, the genomic arrangement of dha genes present in Klebsiella pneumoniae is depicted; arrows indicate the direction of transcription. In parenthesis by the side of each taxonomic group, the number of total genomes analyzed within each group is given. Taxonomic groups in which dha genes were identified are depicted by rectangular boxes; the numbers inside indicate the number of genomes with “the complete pathway /at least one gene”, either reductive (A) or oxidative (B).
Fig 3.
Genomic organization of the reductive pathway.
(A) Orthologous dha genes (in grey) are represented by block arrows showing their position and orientation (out of scale). Gene arrangement is conserved in the seven organisms shown. Mesorhizobium, Mycobacterium and Hyphomicrobium have fused dhaB1 and dhaB2 genes. (B) Fusobacterium I. polytropus contains two dha regulons: genes coding for GDHt B12-dependent and its reactivation factor (grey arrows) are found in the plasmid or in the genome; and those coding for B12-independent (red arrows) are present in the genome. (C) Partial sequence alignment of the B12-independent glycerol dehydratase large subunit showing a highly conserved region corresponding to a glycyl radical domain.
Table 1.
Genes identified for the reductive and oxidative pathway in the anaerobic metabolism of glycerol.
Comparison of genes from Klebsiella pneumoniae to B.intermedia, D. alkenivorans, H. jeotgali, Hyphomicrobium sp., I. polytropus, M. loti and M. opportunistum.
Fig 4.
Evolutionary history of dha genes.
Maximum-likelihood phylogenetic tree of concatenated dhaB1, dhaB2, dhaB3, dhaF and dhaG genes. Numbers at the nodes indicate the percentage of bootstrap support (upper values for the ML tree and lower values for the NJ tree; only number above 50% are shown). Nodes with less than 50% bootstrap support are condensed. Colors depict different taxonomic groups: Proteobacteria (blue), Firmicutes (red), Spirochaetes (purple), Fusobacteria (green), Actinobacteria (orange), Synergistetes (brown).