Fig 1.
Phylogenetic relationships between Steroidobacter cummioxidans sp. nov., strain 35Y and members of the family Sinobacteraceae on the basis of 16S rRNA gene sequences.
The phylogenetic tree was constructed by using the maximum likelihood method, and the 16S rRNA gene sequence of Nitrosomonas aestuarii Nm69 was used as the outgroup. Numbers at nodes indicate levels of bootstrap support (%) based on a maximum likelihood analysis of 1000 resampled datasets; values of less than 50 % are not shown. Bar, 0.02 nucleotide substitutions per site. Solid lines represent the lengths of branches; dotted lines are used to align the tip labels for better visualization; circle represents the node.
Table 1.
Characteristics of Steroidobacter cummioxidans strain 35Y (35Y), Steroidobacter flavus CPCC 100154 (CPCC 100154), Steroidobacter agariperforans KA5-B (KA5-B), Steroidobacter denitrificansis DSM 18526 (DSM 18526).
Table 2.
Basic genome features of Steroidobacter cummioxidans strain 35Y.
Fig 2.
Predicted natural rubber degradation pathway of Steroidobacter cummioxidans strain 35Y.
The pathway comprises of five steps: (1) biosynthesis of rubber oxygenases and extracellular oxidative cleavage of polyisoprene chains, (2) import of oligoisoprenes, (3) β-oxidation, (4) acetyl-CoA and propionyl-CoA metabolism, and (5) anaplerotic reactions and gluconeogenesis. RoxA: Rubber oxygenase A, RoxB: Rubber oxygenase B, ODTD: 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al, Mce: Mammalian cell entry protein, Mla: An ABC transport system that maintains lipid asymmetry, TBDRs: TonB-dependent outer membrane receptors, FACS: fatty acyl coenzyme A (CoA) synthetase: FadL: It encodes outer membrane proteins/ transporters involved in long-chain fatty acid, TCA: Tricarboxylic acid cycle, PEP: Phosphoenolpyruvate.
Table 3.
Distribution and loci of mammalian cell entry cluster related putative genes in the draft genome of Steroidobacter cummioxidans strain 35Y.
Fig 3.
Putative gene cluster of maintenance of outer membrane lipid asymmetry pathway in the draft genome of Steroidobacter cummioxidans strain 35Y.
STC_01552 and STC_01553 are intervening genes in this Mla gene cluster (shown in red). Mla: An ABC transport system that maintains lipid asymmetry. For functional description of mla genes, refer to Table D in S1 Text.