Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates

Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, USA.
BMC Genomics (Impact Factor: 3.99). 01/2011; 12(1):70. DOI: 10.1186/1471-2164-12-70
Source: PubMed


M. catarrhalis is a gram-negative, gamma-proteobacterium and an opportunistic human pathogen associated with otitis media (OM) and exacerbations of chronic obstructive pulmonary disease (COPD). With direct and indirect costs for treating these conditions annually exceeding $33 billion in the United States alone, and nearly ubiquitous resistance to beta-lactam antibiotics among M. catarrhalis clinical isolates, a greater understanding of this pathogen's genome and its variability among isolates is needed.
The genomic sequences of ten geographically and phenotypically diverse clinical isolates of M. catarrhalis were determined and analyzed together with two publicly available genomes. These twelve genomes were subjected to detailed comparative and predictive analyses aimed at characterizing the supragenome and understanding the metabolic and pathogenic potential of this species. A total of 2383 gene clusters were identified, of which 1755 are core with the remaining 628 clusters unevenly distributed among the twelve isolates. These findings are consistent with the distributed genome hypothesis (DGH), which posits that the species genome possesses a far greater number of genes than any single isolate. Multiple and pair-wise whole genome alignments highlight limited chromosomal re-arrangement.
M. catarrhalis gene content and chromosomal organization data, although supportive of the DGH, show modest overall genic diversity. These findings are in stark contrast with the reported heterogeneity of the species as a whole, as wells as to other bacterial pathogens mediating OM and COPD, providing important insight into M. catarrhalis pathogenesis that will aid in the development of novel therapeutic regimens.

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Available from: John P Hays, Oct 09, 2015
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    • "The other transposon insertions which reduced growth under iron-limiting conditions were in the rnd gene (MCR_0843, ribonuclease D) and the MCR_0457 gene encoding a hypothetical protein. All of the identified genes were found to be highly conserved across M. catarrhalis clinical isolates (de Vries et al., 2010; Davie et al., 2011), with levels of identity ranging from 99% to 100% (data not shown). "
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    ABSTRACT: Iron sequestration by the human host is a first line defence against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron starvation during colonization. We determined the genetic requirements for M. catarrhalis BBH18 growth during iron starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). By subjecting a large random transposon mutant library to growth under iron-limiting conditions, mutants of the MCR_0996-rhlB-yggW operon, rnd, and MCR_0457 were negatively selected. Growth experiments using directed mutants confirmed the GAF phenotypes with ΔyggW (putative haem-shuttling protein) and ΔMCR_0457 (hypothetical protein) most severely attenuated during iron starvation, phenotypes which were restored upon genetic complementation of the deleted genes. Deletion of yggW resulted in similar attenuated phenotypes in three additional strains. Transcriptional profiles of ΔyggW and ΔMCR_0457 were highly altered with 393 and 192 differentially expressed genes respectively. In all five mutants, expression of nitrate reductase genes was increased and of nitrite reductase decreased, suggesting an impaired aerobic respiration. Alteration of iron metabolism may affect nasopharyngeal colonization as adherence of all mutants to respiratory tract epithelial cells was attenuated. In conclusion, we elucidated the genetic requirements for M. catarrhalis growth during iron starvation and characterized the roles of the identified genes in bacterial growth and host interaction.
    Molecular Microbiology 11/2012; 87(1). DOI:10.1111/mmi.12081 · 4.42 Impact Factor
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    • "In support of quorum signaling as a mechanism for these effects on M. catarrhalis, there was no significant benefit in terms of antibiotic resistance or persistence in vivo in parallel experiments using an isogenic NTHi luxS mutant strain. Notably, no AI-2 quorum signal production was detected for any M. catarrhalis strain, and recent data analyzing a number of sequenced M. catarrhalis genomes show that none have a homologue for the luxS genetic determinant of this quorum signal (Davie et al., 2011). Moreover, M. catarrhalis bacteria had the capacity to take up purified DPD from culture supernatants, and addition of purified DPD to M. catarrhalis bacteria also promoted biofilm density and antibiotic resistance in vivo (Armbruster et al., 2010). "
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    ABSTRACT: Quorum signals are diffusible factors produced by bacteria that coordinate communal responses. For nontypeable Haemophilus influenzae (NTHi), a series of recent papers indicate that production and sensing of quorum signals are determinants of biofilm formation/maturation and persistence in vivo. In this mini-review I will summarize the current knowledge about quorum signaling/sensing by this organism, and identify specific topics for additional study.
    Frontiers in Cellular and Infection Microbiology 07/2012; 2:100. DOI:10.3389/fcimb.2012.00100 · 3.72 Impact Factor
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    • "(c) Alignment of the C-terminal sequences of GatAs from these strains and 12 new genome sequences from geographically and phenotypically diverse clinical isolates of M. catarrhalis. There are three identical GatA(479–492) BRO-2 sequences, eight identical GatA(479–492) BRO-1 sequences and two identical GatA(479–491) wt sequences (de Vries et al., 2010; Davie et al., 2011). Amino acids in lower-case type are not conserved in the three sequences. "
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    ABSTRACT: Only about half of bacterial species use an asparaginyl-tRNA synthetase (AsnRS) to attach Asn to its cognate tRNA(Asn). Other bacteria, including the human pathogen Moraxella catarrhalis, a causative agent of otitis media, lack a gene encoding AsnRS, and form Asn-tRNA(Asn) by an indirect pathway catalysed by two enzymes: first, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) catalyses the formation of aspartyl-tRNA(Asn) (Asp-tRNA(Asn)); then, a tRNA-dependent amidotransferase (GatCAB) transamidates this 'incorrect' product into Asn-tRNA(Asn). As M. catarrhalis has a Gln-tRNA synthetase, its GatCAB functions as an Asp-tRNA(Asn) amidotransferase. This pathogen rapidly evolved to about 90 % ampicillin resistance worldwide by insertion of a bro-1 β-lactamase gene within the gatCAB operon. Comparison of the GatCAB subunits from bro-1 β-lactamase-positive and bro-negative strains showed that the laterally transferred bro-1 gene, inserted into the gatCAB operon, affected the C-terminal sequence of GatA. The identity between the C-terminal sequences of GatA(wt) (residues 479-491) and of GatA(BRO-1) (residues 479-492) was about 36 %, whereas the rest of the GatA sequence was relatively conserved. The characterization of these two distinct GatCABs as well as the hybrid GatCAB containing GatA(1-478)(wt)(479-492)(BRO-1) and truncated GatCAB enzymes of M. catarrhalis showed that the substitution in GatA(wt) of residues 479-492 of GatA(BRO-1) causes increased specificity for glutamine, and decreased specificity for Asp-tRNA(Asn) in the transamidation reaction. We conclude that the bro gene insertion has altered the kinetic parameters of Asp-tRNA(Asn) amidotransferase, and we propose a model for gatA evolution after the insertion of bro-1 at the carboxyl end of gatA.
    Microbiology 06/2012; 158(Pt 9):2363-71. DOI:10.1099/mic.0.060095-0 · 2.56 Impact Factor
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