Nucléotide Text description

NUCLEOTIDE METABOLISM

Purine metabolism

The 54 L. plantarum strains are all highly similar in the metabolic pathways for purine metabolism. Differences between strains are found in only few genes (Figure 14). The first is the 3',5'-cyclic-nucleotide phosphodiesterase (EC: PDE – OG_2189). This gene converts 3',5'-cyclic GMP into GMP.  In strains NIZO2257, NIZO2258, UCMA_3037 and P8 this gene is frameshifted. The genes purM (EC 6.3.3.1) in strain NIZO3894 and guaA (EC 6.3.5.2) in strain NIZO2259 appear to be truncated. Another gene that appears to be a pseudogene in some strains is the adeC gene (EC: 3.5.4.2). It converts adenine into hypoxanthine. In strains 19.1 and NAB1 this gene appears to be frameshifted.

More differences are seen in paralogs of genes found in the purine metabolic pathways. For example, three paralogs are found of the ADP-ribose pyrophosphatase gene in strain WCFS1.

Several newly sequenced strains have paralogs of genes that are not found in one of the known reference strains. The most prominent are genes encoding a ribonucleoside-diphosphate reductase complex. Two of those genes are labeled as a beta-subunit and the other is labeled an alpha-subunit. These genes are found encoded on putative plasmids in 19 new strains: 19.1, NIZO1838, NIZO2256, NIZO2257, NIZO2258, NIZO2262, NIZO2457, NIZO2484, NIZO2485, NIZO2494, NIZO2741, NIZO2753, NIZO2801, NIZO2802, NIZO2806, NIZO2814, NIZO3400, NIZO3892, and NIZO3894.

Other paralogs genes include pseudogenes for DNA-directed RNA polymerase beta subunit (EC2.7.7.6) found in strains NIZO2262, NIZO3892 and NIZO3894, an anaerobic ribonucleoside-triphosphate reductase (EC: 1.17.4.2) in strains 19.1, NIZO1838, NIZO2256, NIZO2753 NIZO2802, NIZO2806 and UCMA_3037 and an adenine deaminase (EC: 3.5.4.2) in strain NIZO3400. Some of these extra genes are on plasmids, as they are also on plasmids of reference strains 16, ST-III and ZJ316.

 

Pyrimidine metabolism

In the pyrimidine metabolic pathways, only a minor difference is found between all strains that is not already described for the purine metabolic pathways (Figure 15), i.e. in strain NAB1 the genes for upp (EC 2.4.2.9) and pyrR1 both appear to be frameshifted. Furthermore, the pyrimidine metabolism pathway contains less paralog genes than the purine pathways. An additional thioredoxin reductase (EC: 1.8.1.9) is found encoded in strain NIZO2801, presumably on a plasmid.