Abstract
The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.
Highlights
The genus Actinotignum was introduced by [1] to accommodate bacterial strains which are associated with human infections and previously classified in the genus Actinobaculum
Following steps were performed for assembly: (1) filtered Illumina reads were assembled using Velvet [21], (2) 1–3 kb simulated paired end reads were created from Velvet contigs using wgsim [22], (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG [23]
In general the predicted physiological capabilities are in good agreement with reported experimental observations
Summary
The genus Actinotignum was introduced by [1] to accommodate bacterial strains which are associated with human infections and previously classified in the genus Actinobaculum. A. schaalii resides as a commensal in the human genital and urinary tract [2]. It is an opportunistic pathogen associated with urinary tract infections (UTI), bloodstream infections, endocarditis, abscess formation, Fournier’s gangrene and vertebral osteomyelitis, predominantly in elderly patients [3, 4, 5, 6]. A. schaalii has the typical morphological, physiological and chemotaxonomic characteristics observed in other members of the genus Actinotignum. A. schaalii ferments glucose, L-arabinose, maltose, D-ribose, sucrose and xylose. The organism is positive for α-glucosidase and leucine arylamidase activities and negative for the other enzyme activities tested by the API ZYM (bioMerieux) panel. The diagnostic whole-cell sugars include glucose, rhamnose and 6-deoxytalose. The DNA G+C content initially reported with 57 mol% [7], was much lower than the 62.2% inferred from the genome sequence
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