Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen

Abstract

Moraxella catarrhalis is an emerging human-restricted respiratory tract pathogen that is a common cause of childhood otitis media and exacerbations of chronic obstructive pulmonary disease in adults. Here, we report the first completely assembled and annotated genome sequence of an isolate of M. catarrhalis, strain RH4, which originally was isolated from blood of an infected patient. The RH4 genome consists of 1,863,286 nucleotides that form 1,886 protein-encoding genes. Comparison of the RH4 genome to the ATCC 43617 contigs demonstrated that the gene content of both strains is highly conserved. In silico phylogenetic analyses based on both 16S rRNA and multilocus sequence typing revealed that RH4 belongs to the seroresistant lineage. We were able to identify almost the entire repertoire of known M. catarrhalis virulence factors and mapped the members of the biosynthetic pathways for lipooligosaccharide, peptidoglycan, and type IV pili. Reconstruction of the central metabolic pathways suggested that RH4 relies on fatty acid and acetate metabolism, as the genes encoding the enzymes required for the glyoxylate pathway, the tricarboxylic acid cycle, the gluconeogenic pathway, the nonoxidative branch of the pentose phosphate pathway, the beta-oxidation pathway of fatty acids, and acetate metabolism were present. Moreover, pathways important for survival under challenging in vivo conditions, such as the iron-acquisition pathways, nitrogen metabolism, and oxidative stress responses, were identified. Finally, we showed by microarray expression profiling that approximately 88% of the predicted coding sequences are transcribed under in vitro conditions. Overall, these results provide a foundation for future research into the mechanisms of M. catarrhalis pathogenesis and vaccine development.

FIG. 1.

Diagram of the M. catarrhalis RH4 genome. Gene coordinates are indicated. From the inside to the outside, the circles show the GC skew, the G+C content, the genes on the forward strand, and the genes on the reverse strand. The colors in the two outermost rings indicate the functional classes of the genes and correspond to the colors in Table S1 in the supplemental material. The diagram was generated using CGview (28).

FIG. 2.

Modular arrangement and functional domains of UspA1 (A) and UspA2H (B) of RH4. Both proteins are drawn to scale. The various sequence cassettes and the known functional domains are indicated. The VEEG repeats of UspA2H are indicated by asterisks because they only partially match the repeat motif. Abbreviations: CTER1, C-terminal region 1; CTER2, C-terminal region 2.

FIG. 3.

Predicted central metabolism of M. catarrhalis RH4. The glycolysis pathway is incomplete and lacks the key enzymes phosphofructokinase and pyruvate kinase. The enzymes of glycolysis are expected to be involved in the gluconeogenic pathway, all enzymes of which were found to be present. Fatty acid degradation and acetate assimilation are probably very important, as they supply the tricarboxylic acid (TCA) cycle with acetyl-CoA. The complete glyoxylate pathway is present and allows bypass of the TCA cycle, which lacks both subunits of succinyl-CoA synthetase.

FIG. 4.

Expression profiles of chromosomal CRISPR regions I (CRISPR1) and II (CRISPR2). The exponential-growth-phase log₂ probe signal intensities of both strands (open circles, reverse-strand probes; filled circles, forward-strand probes) demonstrate that there is reverse-strand expression of both CRISPR1 and CRISPR2. The localization of CRISPR1 and CRISPR2 is indicated below the graph. Comparable results were obtained during the lag and stationary growth phases (data not shown).