Genome Analysis of Moraxella catarrhalis Strain RH4, a Human Respiratory Tract Pathogen

Vries, Stefan de; Hijum, Sacha A. F. T. van; Schueler, Wolfgang; Riesbeck, Kristian; Hays, John P.; Hermans, Peter W. M.; Bootsma, Hester J.

doi:10.1128/jb.01831-12

Cited by 11 publications

(31 citation statements)

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“…Gene symbols are gene annotations from M. catarrhalis strain 25239 (GenBank accession number CP007669). Assigned role category and predicted protein location are from de Vries et al (48). Role categories: 1, DNA metabolism; 2, fatty acid and phospholipid metabolism; 3, cell envelope; 4, protein fate; 5, hypothetical proteins; 6, protein synthesis; 7, unknown function; 8, transport and binding proteins; 9, central intermediary metabolism; 10, energy metabolism; 11, purines, pyrimidines, nucleosides, and nucleotides; 12, cellular processes; 13, transcription.…”

Section: Resultsmentioning

confidence: 99%

ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media

et al. 2014

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Moraxella catarrhalis is a significant cause of otitis media and exacerbations of chronic obstructive pulmonary disease. Here, we characterize a phase-variable DNA methyltransferase (ModM), which contains 5'-CAAC-3' repeats in its open reading frame that mediate high-frequency mutation resulting in reversible on/off switching of ModM expression. Three modM alleles have been identified (modM1-3), with modM2 being the most commonly found allele. Using single-molecule, real-time (SMRT) genome sequencing and methylome analysis, we have determined that the ModM2 methylation target is 5'-GAR(m6)AC-3', and 100% of these sites are methylated in the genome of the M. catarrhalis 25239 ModM2 on strain. Proteomic analysis of ModM2 on and off variants revealed that ModM2 regulates expression of multiple genes that have potential roles in colonization, infection, and protection against host defenses. Investigation of the distribution of modM alleles in a panel of M. catarrhalis strains, isolated from the nasopharynx of healthy children or middle ear effusions from patients with otitis media, revealed a statistically significant association of modM3 with otitis media isolates. The modulation of gene expression via the ModM phase-variable regulon (phasevarion), and the significant association of the modM3 allele with otitis media, suggests a key role for ModM phasevarions in the pathogenesis of this organism.

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Section: Resultsmentioning

confidence: 99%

ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media

et al. 2014

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“…Further, we confirmed the role in complement resistance of genes encoding the outer membrane lipoprotein MCR_0117, phosphoserine phosphatase ( serB ), GTP‐dependent nucleic acid‐binding protein ( engD ), 3‐phosphoshikimate 1‐carboxy‐vinyltransferase ( aroA ), and the hypothetical protein MCR_0996. All 11 newly identified complement resistance genes of M. catarrhalis BBH18 are conserved across disease‐associated lineage 1 M. catarrhalis isolates (de Vries et al ., ; Davie et al ., ; Zomer et al ., 2012b), with the exception that olpA (MCR_1761) is not conserved in ATCC 43617, which is a lineage 1 isolate sensitive to NHS (data not shown).…”

Section: Resultsmentioning

confidence: 99%

Deciphering the genetic basis of Moraxella catarrhalis complement resistance: a critical role for the disulphide bond formation system

Vries

Rademakers

Jongh

et al. 2013

Molecular Microbiology

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SummaryThe complement system is an important innate defence mechanism, and the ability to resist complement-mediated killing is considered a key virulence trait of the respiratory tract pathogen M. catarrhalis. We studied the molecular basis of complement resistance by transcriptional profiling and Tn-seq, a genome-wide negative-selection screenings technology. Exposure of M. catarrhalis to human serum resulted in increased expression of 84 genes and reduced expression of 134 genes, among which genes encoding ABC transporter systems and surface proteins UspA1 and McaP. By subjecting a ∼ 15 800 transposon mutant library to serum, mutants of 53 genes were negatively selected, including the key complement-resistance factor uspA2H. Validation with directed mutants confirmed Tn-seq phenotypes of uspA2H and 11 newly identified genes, with mutants of MCR_0424, olpA, MCR_1483, and dsbB most severely attenuated. Detailed analysis showed that both components of the disulphide bond formation (DSB) system, DsbB and DsbA, were required for complement-resistance in multiple isolates, and fulfil a critical role in evasion of IgG-dependent classical pathway-mediated killing. Lipooligosaccharide (LOS) structure and membrane stability were severely affected in ΔdsbA strains, suggesting a pivotal role for the DSB system in LOS structure safeguarding and membrane stability maintenance.

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“…Prophage [33], Me Tri virus [28], novel human coronaviruses NL63 and HKU1 [34], novel bat coronaviruses [35], bat coronaviruses 1A, 1B and HKU8 [36], novel human coronavirus [37] Protein-coding gene recognition a x, y, z, S ZCURVE_V [14], ZCURVE_CoV [15] SARS_CoV Various strains of SARS_CoV [38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53] Archaea Methanosarcina mazei [69], Halobacterium species NRC-1 [63], Methanocaldococcus jannaschii [68], Sulfolobus acidocaldarius [72], Haloferax volcanii [73], Desulfurococcus kamchatkensis [74], Thermococcus sibiricus [75], Sulfolobus islandicus [76] Bacteria Moraxella catarrhalis [79], Sorangium cellulosum [80], Microcystis aeruginosa [80], Cyanothece [81], Cupriavidus metallidurans [82], Azolla filiculoides [83], Variovorax paradoxus [18], Corynebacterium pseudotuberculosis [84], [85], Orientia tsutsugamushi [86], Propionibacterium freudenreichii [87], Laribacter hongkongensis…”

Section: Life Domains or Virus Speciesmentioning

confidence: 99%

“…Ori-Finder, an integrated in silico method to predict oriC regions of bacterial genomes, has been developed, based on the Z-curve method, along with distributions of DnaA box patterns, indicator genes, and phylogenetic relationships [78]. Ori-finder has become a commonly used annotation tool for identifying oriCs in newly sequenced archaeal and bacterial genomes, e.g., those of Moraxella catarrhalis [79], Sorangium cellulosum [80], Microcystis aeruginosa [80], Cyanothece [81], Cupriavidus metallidurans [82], Azolla filiculoides [83], Variovorax paradoxus [18], Corynebacterium pseudotuberculosis [84,85], Orientia tsutsugamushi [86], Propionibacterium freudenreichii [87], Laribacter hongkongensis [88], Legionella pneumophila [89], and Ehrlichia canis [90] ( Table 3).…”

Section: Prediction Of Replication Origins In Bacterial Genomesmentioning

confidence: 99%

A Brief Review: The Z-curve Theory and its Application in Genome Analysis

Zhang

2014

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In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.

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Genome Analysis of Moraxella catarrhalis Strain RH4, a Human Respiratory Tract Pathogen

Cited by 11 publications

References 0 publications

ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media

ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media

Deciphering the genetic basis of Moraxella catarrhalis complement resistance: a critical role for the disulphide bond formation system

A Brief Review: The Z-curve Theory and its Application in Genome Analysis

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