MATERIALS AND METHODS
Bacterial strain and growth conditions.
Sequencing of the M. catarrhalis RH4 genome.
In silico phylogenetic typing.
Microarray expression profiling.
Nucleotide sequence and microarray data accession numbers.
RESULTS AND DISCUSSION
General genome features and comparative genomics.
Biosynthesis of cell wall structures.
Protein localization prediction.
Central metabolic pathways.
|Genome size (nt)||1,863,286|
|G+C content (%)||41.7|
|No. of genes||1,964|
|No. of protein-encoding ORFs||1,886|
|Avg ORF size (bp)||850|
|Coding density (%)||86.1|
|No. of rRNA genes||12|
|No. of tRNA genes||50|
|Functional class||No. of proteins||% of total|
|Amino acid biosynthesis||77||4.0|
|Purines, pyrimidines, nucleosides, and nucleotides||36||1.9|
|Fatty acid and phospholipid metabolism||40||2.1|
|Biosynthesis of cofactors, prosthetic groups, and carriers||90||4.7|
|Central intermediary metabolism||33||1.7|
|Transport and binding proteins||148||7.8|
|Mobile and extrachromosomal element functions||21||1.1|
|Disrupted reading frame||16||0.8|
|% RH4 CDSs in alignment||% of mismatches allowed in alignment||No. of CDSs||% of total|
|RH4 locus||Gene||Common name and general function of protein||Characteristics||Level of expression in growth phases in BHI mediumb|
|MCR_1198||uspA1||Ubiquitous surface protein A1; functions in adhesion to epithelial cells and ECM components, inhibition of NF-κB proinflammatory response via CEACAM binding, serum resistance, binding of complement regulatory proteins, and biofilm formation||9 poly(G) repeats upstream of the ORF, reported to correlate with a low level of expressionc||+++||+++||+++|
|MCR_0329||uspA2H||Ubiquitous surface protein A2H; functions in adhesion to epithelial cells, serum resistance, and biofilm formation||+++||+++||+++|
|MCR_0617||mid/hag||Immunoglobulin D binding protein/hemagglutinin; functions in adhesion to epithelial cells and IgD binding||3 triplets of G residues at 5′ end within the ORF, reported to correlate with a high level of expressiond||+++||++||+++|
|MCR_0419||mcaP||M. catarrhalis adherence protein; functions in adhesion to epithelial cells||+++||+++||+++|
|MCR_1698||ompCD||Outer membrane protein CD; functions in adhesion to epithelial cells and middle ear mucin||RFLP pattern 1 (∼200- and 100-nt BseJI restriction fragments), which is almost exclusively found in 16S type 1 isolatese||+++||+++||+++|
|MCR_0492||copB||Outer membrane protein CopB; involved in serum resistance and important for in vivo survival||RFLP type II (332- and 187-nt NsaI restriction fragments), which is found almost exclusively in 16S rRNA type I isolatese||+++||+++||++|
|MCR_0858||ompE||Outer membrane protein E; involved in serum resistance||Putative homolog of long-chain fatty acid transporter FadL||+++||+++||+++|
|MCR_1591||bro-2||Beta-lactamase family protein BRO-2||++||++||++|
|Subcellular localizationa||No. of proteins||% of total|
|Cytoplasm (possibly secreted via nonclassical pathways), intracellular or secreted||35||1.9|
|Inner membrane, multitransmembrane||257||13.6|
|Inner membrane, multitransmembrane (lipid-modified N terminus)||4||0.2|
|Inner membrane, C terminally anchored (with CS)||1||0.1|
|Inner membrane (periplasm), N terminally anchored (no CS)||124||6.6|
|Inner membrane (periplasm), N terminally anchored (with CS)||14||0.7|
|Inner membrane (periplasm), lipid anchored||12||0.6|
|Periplasm, secreted (with CS)||22||1.2|
|Outer membrane, lipid anchored||53||2.9|
|Outer membrane, β-barrel protein (no CS)||19||1.0|
|Outer membrane, β-barrel protein (with CS)||23||1.2|
|Outer membrane (no clear SP found but have β-barrel), intracellular or β-barrel||20||1.1|
|Extracellular, secreted (with CS)||18||1.0|
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