In accordance with the known ability of L. methylohalidivorans DSM 14336T to selleck inhibitor grow by oxidation of methyl halides , the genome analysis revealed the genes for the proposed pathway of methyl chloride metabolism as described by McDonald et al. 2002 . Using the JGI-IMG BLASTp tool [51,52], the gene for first methyltransferase I (cmuA) indeed yielded a hit to the gene cmuA (��predicted cobalamin binding protein��, Meth_2531) in the genome of L. methylohalidivorans DSM 14336T, with a sequence similarity of 31%. Searching for the second enzyme methyltransferase II (cmuB) yielded a hit to the enzyme adjacent to the predicted cobalamin binding protein (��methionine synthase I (cobalamin-dependent), methyltransferase domain��, Meth_2528).
For the next enzymes in the methyl-chloride metabolism, we compared the genes metF, folD, purU and FDH and found the following results: 39% similarity to a 5,10-methylenetetrahydrofolate reductase (Meth_1763), for metF; 56% to a 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl-tetrahydrofolate cyclohydrolase (Meth_4077, Meth_3180) for folD; 36% to a phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent (Meth_2536) for purU; and 79% to a formate dehydrogenase (Meth_4011) for FDH. An estimate of the DNA-DNA hybridization (DDH) similarity between L. methylohalidivorans DSM 14336T and the draft genomes of L. aquimarina DSM 24565T, L. nanhaiensis DSM 24252T, P. arcticus DSM 23566T, P. caeruleus DSM 24564T, P. daeponensis DSM 23529T, P. gallaeciensis CIP 105210T and P.
inhibens DSM 16374T was generated with the GGDC Genome-to-Genome Distance Calculator version 2.0 [53-55]. This system calculates the distances by comparing the genomes to obtain HSPs (high-scoring segment pairs) and interfering distances from three formulae (1, HSP length / total length; 2, identities / HSP length; 3, identities / total length) . Table 7 shows the results of the pairwise comparisons between L. methylohalidivorans DSM 14336T and the other seven genomes. As the results of the 16S rRNA analysis (Figure 1) revealed, the two Leisingera species L. methylohalidivorans and L. aquimarina show a close relationship, whereas L. nanhaiensis does not cluster together with the other two Leisingera species. The DDH similarities calculated in silico yielded similar results, indicating that the classification of L.
nanhaiensis might need to be reconsidered. Furthermore, the DDH similarities of L. methylohalidivorans to Phaeobacter species are not significantly smaller, especially in the case Entinostat of P. caeruleus and P. daeponensis, than to L. aquimarina and as already described to L. nanhaiensis. Table 7 DDH similarities between L. methylohalidivorans DSM 14336T and the other Leisingera and Phaeobacter species (with genome-sequenced type strains) calculated in silico with the GGDC server version 2.0 .