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  • 1
    Language: English
    In: Infection and immunity IAI, 2010, Vol.78(9), pp.3898-3904
    Description: Haemophilus ducreyi must adapt to the environment of the human host to establish and maintain infection in the skin. Bacteria generally utilize stress response systems, such as the CpxRA two-component system, to adapt to hostile environments. CpxRA is the only obvious two-component system contained in the H. ducreyi genome and negatively regulates the lspB-lspA2 operon, which encodes proteins that enable the organism to resist phagocytosis. We constructed an unmarked, in-frame H. ducreyi cpxA deletion mutant, 35000HPΔcpxA. In human inoculation experiments, 35000HPΔcpxA formed papules at a rate and size that were significantly less than its parent and was unable to form pustules compared to the parent. CpxA usually has kinase and phosphatase activities for CpxR, and the deletion of CpxA leads to the accumulation of activated CpxR due to the loss of phosphatase activity and the ability of CpxR to accept phosphate groups from other donors. Using a reporter construct, the lspB-lspA2 promoter was downregulated in 35000HPΔcpxA, confirming that CpxR was activated. Deletion of cpxA downregulated DsrA, the major determinant of serum resistance in the organism, causing the mutant to become serum susceptible. Complementation in trans restored parental phenotypes. 35000HPΔcpxA is the first H. ducreyi mutant that is impaired in its ability to form both papules and pustules in humans. Since a major function of CpxRA is to control the flow of protein traffic across the periplasm, uncontrolled activation of this system likely causes dysregulated expression of multiple virulence determinants and cripples the ability of the organism to adapt to the host. ; Includes references ; p. 3898-3904.
    Keywords: Bacterial Proteins -- Physiology ; Haemophilus Ducreyi -- Pathogenicity ; Protein Kinases -- Physiology;
    ISSN: 0019-9567
    E-ISSN: 10985522
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  • 2
    In: Infection and Immunity, 2007, Vol. 75(1), p.113
    Description: Haemophilus ducreyi is a gram-negative bacterium that is the causative agent of chancroid. Strain 35000HP has been well characterized and is representative of the majority of H. ducreyi strains. Strain 35000HP produces a lipooligosaccharide (LOS) that contains D-glycero-D-manno-heptose in the main oligosaccharide chain extension; the lbgB gene has been shown to encode the DD-heptosyltransferase. The lbgB gene is found in a gene cluster together with the lbgA gene, which encodes for the galactosyltransferase I. These two genes are flanked by two housekeeping genes, rpmE and xthA, encoding the ribosomal protein L31 and the exonuclease III, respectively. Recently, a second group of H. ducreyi strains have been identified. Strain 33921, a representative of the class II strains, produces an LOS that lacks DD-heptose in the oligosaccharide portion of its LOS. To better understand the biosynthesis of the DD-heptose-deficient 33921 LOS, we cloned and sequenced the corresponding lbgAB genomic region from strain 33921. Similar to strain 35000HP, the 33921 genome contains xthA and rpmE. However, between these two genes we identified genes encoding two putative glycosyltransferases that were not highly homologous to the 35000HP lbgAB genes. In this study, we demonstrate that the product of one of these genes encodes a galactosyltransferase. In addition, dot blot hybridization determined that 3 of 35 strains tested had the atypical transferases present, as did 4 strains characterized as class II strains by other criterion. These data indicate that the lbgAB genes can serve as one indicator of the classification of H. ducreyi strains.
    Keywords: Medicine ; Biology;
    ISSN: 0019-9567
    ISSN: 00199567
    E-ISSN: 10985522
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  • 3
    In: Infection and Immunity, 2004, Vol. 72(2), p.1143
    Description: The nucleotide sequence of pNAD1, a plasmid from Haemophilus ducreyi identified on the basis of its ability to confer NAD independence on Actinobacillus pleuropneumoniae and H. influenzae, has been determined. In addition to containing the nadV gene, the plasmid contains homologues of the rstR and rstA genes, genes encoding repressor and replication proteins, respectively, in the Vibrio CTX phi and the Vibrio RS1 element, suggesting a single-stranded bacteriophage origin for pNAD1. Tandem copies of the plasmid are integrated into the H. ducreyi 35000HP genome.
    Keywords: Haemophilus Ducreyi ; Vibrio ; Haemophilus Ducreyi ; Vibrio ; Genomes ; Nucleotide Sequence ; Plasmids ; Phages ; Genomes ; Nucleotide Sequence ; Plasmids ; Phages ; Nadv Gene ; Rstr Gene ; Rsta Gene ; Nadv Gene ; Rstr Gene ; Rsta Gene ; Plasmids ; Structure & Sequence ; Nad ; Rs1 Element ; Nad ; Rs1 Element ; Nad ; Rs1 Element ; Nadv Gene ; Rsta Gene ; Rstr Gene;
    ISSN: 0019-9567
    ISSN: 00199567
    E-ISSN: 10985522
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  • 4
    In: Infection and Immunity, 2004, Vol. 72(5), p.3002
    Description: In 1995, The Institute for Genomic Research completed the genomic sequence of a rough derivative of Haemophilus influenzae serotype d, strain KW20. This sequence, though extremely useful in understanding the basic biology of H. influenzae, has yet to provide significant insight into our understanding of disease caused by nontypeable H. influenzae (NTHI), because serotype d strains are not generally pathogens. In contrast, NTHI strains are frequently mucosal pathogens and are the primary pathogens of chronic otitis media as well as a significant cause of acute otitis media in children. Thus, it is of great importance to further understand their biology. We used a DNA-based microarray approach to identify genes present in a clinical isolate of NTHI that were absent from strain Rd. We also sequenced the genome of a second NTHI isolate from a child with chronic otitis media to threefold coverage and then used an array of bioinformatics tools to identify genes present in this NTHI strain but absent from strain Rd. These methods were complementary in approach and results. We identified, in both strains, homologues of H. influenzae lav, an autotransported protein of unknown function; tnaA, which encodes tryptophanase; as well as a homologue of Pasteurella multocida tsaA, which encodes an alkyl peroxidase that may play a role in protection against reactive oxygen species. We also identified a number of putative restriction-modification systems, bacteriophage genes and transposon-related genes. These data provide new insight that complements and extends our ongoing analysis of NTHI virulence determinants.
    Keywords: Medicine ; Biology;
    ISSN: 0019-9567
    ISSN: 00199567
    E-ISSN: 10985522
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  • 5
    Language: English
    In: PLoS ONE, August 26, 2014, Vol.9(8)
    Description: Nontypeable Haemophilus influenzae (NTHi) are Gram-negative commensal bacteria that reside in the nasopharynx. NTHi can also cause multiple upper and lower respiratory tract diseases that include sinusitis, conjunctivitis, bronchitis, and otitis media. In numerous bacterial species the ferric uptake regulator (Fur) acts as a global regulator of iron homeostasis by negatively regulating the expression of iron uptake systems. However in NTHi strain 86-028NP and numerous other bacterial species there are multiple instances where Fur positively affects gene expression. It is known that many instances of positive regulation by Fur occur indirectly through a small RNA intermediate. However, no examples of small RNAs have been described in NTHi. Therefore we used RNA-Seq analysis to analyze the transcriptome of NTHi strain 86-028NPrpsL and an isogenic 86-028NPrpsL[DELTA]fur strain to identify Fur-regulated intergenic transcripts. From this analysis we identified HrrF, the first small RNA described in any Haemophilus species. Orthologues of this small RNA exist only among other Pasteurellaceae. Our analysis showed that HrrF is maximally expressed when iron levels are low. Additionally, Fur was shown to bind upstream of the hrrF promoter. RNA-Seq analysis was used to identify targets of HrrF which include genes whose products are involved in molybdate uptake, deoxyribonucleotide synthesis, and amino acid biosynthesis. The stability of HrrF is not dependent on the RNA chaperone Hfq. This study is the first step in an effort to investigate the role small RNAs play in altering gene expression in response to iron limitation in NTHi.
    Keywords: Hemophilus Infections -- Analysis ; Bacteria -- Analysis ; Rna -- Analysis ; Gene Expression -- Analysis
    ISSN: 1932-6203
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  • 6
    Language: English
    In: PLoS ONE, March 19, 2013, Vol.8(3), p.e59388
    Description: Type VI secretion systems (T6SS) are a class of macromolecular secretion machines that are utilized by a number of bacteria for inter-bacterial competition or to elicit responses in eukaryotic cells. Acinetobacter baumannii is an opportunistic pathogen that causes severe infections in humans. These infections, including pneumonia and bacteremia, are important, as they are often associated with hospitals and medical-settings where they disproportionally affect critically ill patients like those residing in intensive care units. While it is known that A. baumannii genomes carry genes whose predicted products have homology with T6SS-associated gene products from other bacteria, and secretion of a major T6SS structural protein Hcp has been demonstrated, no additional work on an A. baumannii T6SS has been reported. Herein, we demonstrated that A. baumannii strain M2 secretes Hcp and this secretion was dependent upon TssB, an ortholog of a bacteriophage contractile sheath protein, confirming that strain M2 produces a functional T6SS. Additionally, we demonstrated that the ability of strain M2 to out-compete Escherichia coli was reliant upon the products of tssB and hcp. Collectively, our data have provided the first evidence demonstrating function in inter-bacterial competition, for a T6SS produced by A. baumannii.
    Keywords: Genomes -- Health Aspects ; Bacteria -- Health Aspects ; Escherichia Coli -- Health Aspects ; Genomics -- Health Aspects
    ISSN: 1932-6203
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  • 7
    Language: English
    In: PLoS ONE, Oct 5, 2011, Vol.6(10), p.e25923
    Description: Strains of nontypeable Haemophilus influenzae show enormous genetic heterogeneity and display differential virulence potential in different clinical settings. The igaB gene, which encodes a newly identified IgA protease, is more likely to be present in the genome of COPD strains of H. influenzae than in otitis media strains. Analysis of igaB and surrounding sequences in the present study showed that H. influenzae likely acquired igaB from Neisseria meningitidis and that the acquisition was accompanied by a ~20 kb genomic inversion that is present only in strains that have igaB. As part of a long running prospective study of COPD, molecular typing of H. influenzae strains identified a clonally related group of strains, a surprising observation given the genetic heterogeneity that characterizes strains of nontypeable H. influenzae. Analysis of strains by 5 independent methods (polyacrylamide gel electrophoresis, multilocus sequence typing, igaB gene sequences, P2 gene sequences, pulsed field gel electrophoresis) established the clonal relationship among the strains. Analysis of 134 independent strains collected prospectively from a cohort of adults with COPD demonstrated that ~10% belonged to the clonal group. We conclude that a clonally related group of strains of nontypeable H. influenzae that has two IgA1 protease genes (iga and igaB) is adapted for colonization and infection in COPD. This observation has important implications in understanding population dynamics of H. influenzae in human infection and in understanding virulence mechanisms specifically in the setting of COPD.
    Keywords: Genomes -- Analysis ; Genomes -- Health Aspects ; Proteases -- Analysis ; Proteases -- Health Aspects ; Chronic Obstructive Lung Disease -- Analysis ; Chronic Obstructive Lung Disease -- Health Aspects ; Immunoglobulin A -- Analysis ; Immunoglobulin A -- Health Aspects ; Virulence (Microbiology) -- Analysis ; Virulence (Microbiology) -- Health Aspects ; Hemophilus Infections -- Analysis ; Hemophilus Infections -- Health Aspects ; Genes -- Analysis ; Genes -- Health Aspects ; Genomics -- Analysis ; Genomics -- Health Aspects
    ISSN: 1932-6203
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  • 8
    In: Bioinformatics, 2001, Vol.17(12), pp.1105-1112
    Description: Motivation: The process of determining the functional sequencecontent of an organism is confounded by several factors. Large protein coding sequences are relatively easy to find by statistical methods. Smaller proteins however may escape detection due to their size falling below some arbitrary researcher-defined minimum cutoff, or the inability to precisely define a promoter, or translational start (Delcher et al. , Nucleic Acids Res. , 27 , 46364641, 1999). Promoter and regulatory sequences themselves are difficult to define due to a significant amount of allowable sequence variation, as well as a probable lack of any completely accurate whole-organismal gene catalogs to date. Finally, certain genes coding functional RNAs may have insufficient structural or sequence constraints to be detectable by normal sequence structure/pattern searching methods (Eddy and Rivas, Bioinformatics , 16 , 583605, 2000). In those cases where there are multiple closely related organisms that have been sequenced, there is additional information that may be used in the investigation of sequence contentthat being the possible conserved nature of functional sequences between the organisms. We present a method for the utilization of this conserved information to detect genes and other potentially functional sequences that may be missed by standard ORF-calling, RNA finding, and pattern matching software. The tricross programs produce a multi-way cross comparison of three sets of sequences, determine which are conserved in all three sets, and produce a graphical (Virtual Reality Modelling LanguageVRML; (ISO/IEC 14772-1: 1997, VDC), 1997) representation as well as alignments of all sequence triples found. The software can also be applied to a pair of sequence sets, though the noise in the results increases. Results: Tricross has been used to examine the intergenic-sequence content of the three archaeal Pyrococcus genomes to determine the most highly related sequences remaining between the annotated protein and RNA coding sequences. Set to relatively stringent similarity requirements for the search, tricross found 101 intergenic sequences conserved among the three organisms. Interestingly, 29 of these appear to contain members of a family of small RNA molecules (Kiss-Laszlo et al. , EMBO J. , 17 , 797807, 1998) only recently discovered in the Archaea (Armbruster, OSU, Diss., 1988; Omer et al. , Science , 288 , 517522, 2000; Gaspin et al. , J. Mol. Biol. , 297 , 895906, 2000). While some of the remaining 72 appear to be individual highly conserved promoter sequences, others have no currently known biological significance. Although originally developed to facilitate the examination of intergenic sequences, none of the tricross logic is inherently specific to intergenic sequences. The software can also be applied to gene sequences, and has been used to produce inter-genomic gene order dot-plots for Haemophilus influenzae (Fleischmann et al. , Science , 269 , 496512, 1995) versus H.ducreyi (unpublished data), and Neisseria meningiditis Z2491 (serogroup A) (Parkhill et al. , Nature , 404 , 502506, 2000) versus Neisseria meningiditis Z58 (serogroup B) (Tettelin et al. , Science , 287 , 18091815, 2000) versus Neisseria gonorrhoeae (Lewis et al. , http://micro-gen.ouhsc.edu/, 2000). Availability: The tricross software package is available from http://www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html. Contact: ray@biosci.ohio-state.edu; daniels.7@osu.edu; munsonr@pediatrics.ohio-state.edu Supplementary information: Additional data from the cross-genomic comparisons examined in the discussion section are linked from http://www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html.
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 13674811
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