Fig 1.
Circular representation of A. Schaalii DSM15541T genome (27 scaffolds).
Features from the outer circle to the center are: genes on the forward strand (color by COG categories), genes on the reverse strand (color by COG cataegories), RNA genes (tRNA green, rRNA red, other RNAs black), % G+C content, GC skew (purple/olive) and codon adaptation index. The figure was obtained using OmicCircos [36].
Table 1.
General genome characteristics of Actinotignum schaalii DSM 15541T.
Fig 2.
Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences.
The tree showing the phylogenetic position of A. schaalii DSM 15441T, the type strains of other species of the genus Actinotignum and other related members of the genera of the family Actinomycetaceae. Jonesia denitrificans was used as outgroup. Bootstrap values (>70%), expressed as a percentage of 1000 replication, are indicated at the nodes. Bar, 0.1% substitution per nucleotide position.
Fig 3.
Semiphosphorylative Entner-Duodoroff pathway as it operates in A. schaalii.
This pathway involves either oxidation of glucose by the membrane-bound glucose dehydrogenase (gdh) to form glucono-1,5-lactone which is then converted to gluconate by gluconolactonase or gluconate is taken up by the cell via a putative gluconate permease (GntP). Gluconate is then converted to 2-keto-3-deoxygluconate (KDG) by a specific gluconate dehydratase (ILVD_EDD). Further metabolism of KDG involves its phosphorylation by KDG kinase to form KDPG, followed by cleavage by EDA to pyruvate and glyceraldehyde-3-phosphate. Glyceraldehyde-3-phosphate is further converted to form another pyruvate molecule via common reaction of the EM pathway. A similar modified ED pathway has been shown to occur in several Clostridium species e.g. Clostridium aceticum [49] and halophilic archaea, e.g. Halobacterium saccharovorum [50]. Abbreviations: gdh, glucose-1-dehydrogenase; gnl, gluconolactonase; ilvD/EDD, dihydroxyacid dehydratase; KDGK, 2-dehydro-3-deoxygluconokinase; EDA, 2-dehydro-3-deoxyphosphogluconate aldolase; GAP, glyceraldehyde 3-phosphate dehydrogenase; PGM, phosphoglycerate mutase; ENO, enolase; PYK, pyruvate kinase.
Fig 4.
Scheme showing predicted pyruvate fermentation pathway in A. schaalii.
The genes found in A. schaalii suggest that pyruvate is either oxidatively decarboxylated to acetyl-CoA via pyruvate dehydrogenase (pdh) or it may be reduced to lactate by the action of lactate dehydrogenase or it may be converted to acetyl-CoA and formate by pyruvate-formate lyase. Acetyl-CoA may be converted into ethanol, during which 2 NADH are oxidized via a fused acetaldehyde/alcohol dehydrogenase encoded by adhE, ot it may be converted to acetate through an acetyl phosphate intermediate using phosphotransacetylase (pta) and acetate kinase (ack) with the concomitant production of ATP. Abbreviations: LDH, L-lactate dehydrogenase; PTA, phosphotransacetylase; AK, acetate kinase.
Table 2.
Toxin-antitoxin systems of Actinotignum schaalii.
Fig 5.
Comparison of the amino acid sequences of the QRDRs of both GyrA and ParC in A. schaalii with the equivalent region of E. coli.
Hotspots for mutation giving rise to fluoroquinolone resistance are at serine 83 and aspartate 87 of the GyrA and at serine 80 and aspartate 84 of ParC (according to E. coli numbering).