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Central Metabolism
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The differences in presence/absence of genes belonging to central metabolism across the 54 L. plantarum strain are listed in Table 5.
The glycolysis pathway of the 54 Lactobacillus plantarum strains is highly similar (Figure 1). Most of the differences are found in the number of paralogs of genes. For example, there are 11 copies of the 6-phospho-beta-glucosidase found in strain WCFS1, but in strains NIZO2257 and NIZO2258 only 4 copies of this gene are found. There are some strains that appear to have missing or split genes in central metabolism (Table 5). Strains 19.1, ER, NAB1 and NAB2 have a split glucose-6-phosphate isomerase pgi gene (EC: 5.3.1.9). This gene catalyses the isomerization of phosphorylated glucose and fructose. Strain JDM1 has the pck gene (EC: 4.1.1.49) truncated, meaning that this strain cannot use citrate as a carbon source. After the glycolysis all strains can use the formed pyruvate in two ways. The first is converting it to lactate by lactate dehydrogenase (EC 1.1.1.27) and the other is to convert it to acetyl-CoA by the pyruvate dehydrogenase complex (EC: 1.2.4.1, 2.3.1.12, 1.8.1.4). The 4 genes necessary for the last conversion are found adjacent to each other on the genome.
Few differences are found in pyruvate metabolism among the 54 L. plantarum strains. As for the glycolysis pathway, the only differences are found in the number of paralogs for certain enzymes (Figure 2). In strains NIZO1840, NIZO2259, NIZO2802 and NIZO3893 a plasmid-encoded D-lactate dehydrogenase (EC: 1.1.2.5) is found (Table 5). This gene converts D-lactate into pyruvate and is not found in other strains. However, all strains have a chromosomal D-lactate dehydrogenase gene (EC: 1.1.1.28) (OG_1669) (Tables 1, 2).
In the pentose phosphate metabolic pathway more differences are observed than in the other two pathways (Figure 3). In 21 strains, a glucose-1-dehydrogenase gene (EC: 1.1.1.47) is present. This gene catalyses the conversion of β-D-glucose into D-glucono-1,5-lactone. In strains 19.1, ER, NAB1, NAB2, NIZO2484, NIZO2757, NIZO2766 and IPLA88 the gluconokinase gntK gene (EC: 2.7.1.12) is a pseudogene (Table 5). Some strains have 3 paralogous transaldolase genes (EC: 2.2.1.2), but in strains NIZO1840, NIZO2776, NIZO2801 and NIZO3894 neither gene is present. These genes are generally part of a sugar utilization cassette, which are highly variable in L. plantarum strains (1) (2). The same can be said for the paralogs of ribulose-phosphate 3-epimerase (EC: 5.1.3.1). All strains have one fully conserved gene (OG_1910), while two paralogs (OG_5223, OG_3263) are variable and linked to specific sugar utilization cassettes. OG_5223 is found only in NIZO2029 strain, while OG_3263 is fond in 11 strains (Table 1). |
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