An estimate of the overall similarity between Pedobacter heparinus
and P. saltans
] was generated with the GGDC-Genome-to-Genome Distance Calculator [49
]. This system calculates the distances by comparing the genomes to obtain high-scoring segment pairs (HSPs) and interfering distances from a set of three formulae (1, HSP length / total length; 2, identities / HSP length; 3, identities / total length). The comparison of P. heparinus
and P. saltans
revealed that an average of only 4.7% of the two genomes are covered with HSPs. The identity within these HSPs was 82.3%, whereas the identity over the whole genome was 3.8%.
The fraction of shared genes in the genomes of P. heparinus
, P. saltans
and Novosphingobium aromaticivorans
] is shown in a Venn diagram (). The phyogentically distant reference genome of N. aromaticivorans
was selected based on its similar genome size and due to a lack of complete reference type strain genomes from the Sphingobacteriaceae.
The numbers of pairwise shared genes were calculated with the phylogenetic profiler function of the IMG ER platform [48
]. The homologous genes within the genomes were detected with a maximum E-value of 10-5
and a minimum identity of 30%. Only about one quarter of all genes (954 genes) are shared by all three genomes, whereas the two Pedobacter
species share 2,732 genes, corresponding to 63.7% (P. heparinus
) and 70.9% (P. saltans
) of their genes. The pairwise comparison of N. aromaticivorans
with the two Pedobacter
species revealed only 154 (P. heparinus
) and 65 (N. aromaticivorans
) homologous genes ().
Venn diagram depicting the intersections of protein sets (total number of derived protein sequences in parentheses) of P. heparinus, P. saltans and N. aromaticivorans.
Among those genes that are shared by the three genomes, are those which might be responsible for the yellow color of the organisms. These genes encode enzymes that are involved in the synthesis of carotenoids. Biosynthesis of carotenoids starts with geranylgeranyl pyrophosphate synthases combining farnesyl pyrophosphate with C5
isoprenoid units to C20
-molecules, geranylgeranyl pyrophosphate. The phytoene synthase catalyzes the condensation of two geranylgeranyl pyrophosphate molecules followed by the removal of diphosphate and a proton shift leading to the formation of phytoene. Sequential desaturation steps are catalyzed by phytoene desaturase followed by cyclization of the ends of the molecules catalyzed by the lycopene cyclase [52
]. Genes encoding lycopene cyclases (Phep_2088, Pedsa_2222, Saro_1817) and phytoene synthases (Phep_2092, Pedsa_2218, Saro_1814) were identified in the genomes. In the two Pedobacter
species, genes coding for phytoene desaturases (Phep_2093, Pedsa_2217) were also identified. A carotene hydroxylase gene (Saro_1168) was only identified in the genome of N. aromaticivorans
As the two Pedobacter species are known for their ability to degrade heparin, it is not surprising that the genomes encode several heparinase encoding genes: seven (P. saltans) and five (P. heparinus) heparinases, were identified, whereas N. aromaticivorans encodes only one heparinase.
Fucoidan degradation was not determined experimentally, but is assumed as both P. saltans
and P. heparinus
have genes for eleven and ten α-fucosidases respectively. In addition, 12 (P. saltans
) and 18 (P. heparinus
) α-sulfatases genes were identified, whereas N. aromaticivorans
contains only five α-sulfatases and no α-fucosidase genes. Experimental evidence for the fucoidan hydrolysis in Pedobacter
has not been found, but for Mucilaginibacter paludis
and M. gracilis,
which are also members of the family Sphingobacteriaceae,
have been experimentally confirmed to exhibit fucoidan degradation [53
]. Moreover, Sakai et al
] reported the existence of intracellular α-L-fucosidases and sulfatases, which enable ‘F. fucoidanolyticus’
to degrade fucoidan.