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  • 1
    Language: English
    In: Journal of bacteriology, December 2014, Vol.196(23), pp.4012-25
    Description: Haemophilus ducreyi causes the sexually transmitted disease chancroid and a chronic limb ulceration syndrome in children. In humans, H. ducreyi is found in an abscess and overcomes a hostile environment to establish infection. To sense and respond to membrane stress, bacteria utilize two-component systems (TCSs) and extracytoplasmic function (ECF) sigma factors. We previously showed that activation of CpxRA, the only intact TCS in H. ducreyi, does not regulate homologues of envelope protein folding factors but does downregulate genes encoding envelope-localized proteins, including many virulence determinants. H. ducreyi also harbors a homologue of RpoE, which is the only ECF sigma factor in the organism. To potentially understand how H. ducreyi responds to membrane stress, here we defined RpoE-dependent genes using transcriptome sequencing (RNA-Seq). We identified 180 RpoE-dependent genes, of which 98% were upregulated; a major set of these genes encodes homologues of envelope maintenance and repair factors. We also identified and validated a putative RpoE promoter consensus sequence, which was enriched in the majority of RpoE-dependent targets. Comparison of RpoE-dependent genes to those controlled by CpxR showed that each transcription factor regulated a distinct set of genes. Given that RpoE activated a large number of genes encoding envelope maintenance and repair factors and that CpxRA represses genes encoding envelope-localized proteins, these data suggest that RpoE and CpxRA appear to play distinct yet complementary roles in regulating envelope homeostasis in H. ducreyi.
    Keywords: Gene Expression Regulation, Bacterial ; Stress, Physiological ; Bacterial Proteins -- Metabolism ; Cell Membrane -- Physiology ; Haemophilus Ducreyi -- Physiology ; Protein Kinases -- Metabolism ; Sigma Factor -- Metabolism
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 2
    Language: English
    In: Int. J. of Computational Biology and Drug Design, 2014, Vol 7 Issue 2/3, pp 195 - 213
    Description: High throughput bacterial RNA-Seq experiments can generate extremely high and imbalanced sequencing coverage. Over- or under-estimation of gene expression levels will hinder accurate gene differential expression analysis. Here we evaluated strategies to identify expression differences of genes with high coverage in bacterial transcriptome data using either raw sequence reads or unique reads with duplicate fragments removed. In addition, we proposed a generalised linear model (GLM) based approach to identify imbalance in read coverage based on sequence compositions. Our results show that analysis using raw reads identifies more differentially expressed genes with more accurate fold change than using unique reads. We also demonstrate the presence of sequence composition related biases that are independent of gene expression levels and experimental conditions. Finally, genes that still show strong coverage imbalance after correction were tagged using statistical approach.
    Keywords: bacterial transcriptome sequencing; RNA-Seq; gene differential expression; coverage imbalance; tri-nucleotides; GLM; generalised linear modelling; computational biology; RNA sequences; gene expression levels.
    ISSN: 1756-0756
    ISSN: 17560756
    ISSN: 1756-0764
    ISSN: 17560764
    E-ISSN: 1756-0764
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  • 3
    In: Journal of Bacteriology, Feb, 1996, Vol.178(3-4), p.808(9)
    Description: A study was conducted to determine the role of the pili expressed by Haemophilus ducreyi in the pathogenesis of the genital ulcer disease chancroid. A gene encoding the 24K protein of fine, tangled pili, termed ftpA, was isolated and examined by molecular techniques. The results showed that the FtpA protein lacked homology with other pilins, but shared homoloy with proteins that polymerize ordered rings in Escherichia coli and Treponema pallidum.
    Keywords: Hemophilus Infections -- Genetic Aspects
    ISSN: 0021-9193
    E-ISSN: 10985530
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  • 4
    Language: English
    In: Microbiology (Reading, England), April 2008, Vol.154(Pt 4), pp.1152-60
    Description: To identify Haemophilus ducreyi transcripts that are expressed during human infection, we used selective capture of transcribed sequences (SCOTS) with RNA isolated from pustules obtained from three volunteers infected with H. ducreyi, and with RNA isolated from broth-grown bacteria used to infect volunteers. With SCOTS, competitive hybridization of tissue-derived and broth-derived sequences identifies genes that may be preferentially expressed in vivo. Among the three tissue specimens, we identified 531 genes expressed in vivo. Southern blot analysis of 60 genes from each tissue showed that 87 % of the identified genes hybridized better with cDNA derived from tissue specimens than with cDNA derived from broth-grown bacteria. RT-PCR on nine additional pustules confirmed in vivo expression of 10 of 11 selected genes in other volunteers. Of the 531 genes, 139 were identified in at least two volunteers. These 139 genes fell into several functional categories, including biosynthesis and metabolism, regulation, and cellular processes, such as transcription, translation, cell division, DNA replication and repair, and transport. Detection of genes involved in anaerobic and aerobic respiration indicated that H. ducreyi likely encounters both microenvironments within the pustule. Other genes detected suggest an increase in DNA damage and stress in vivo. Genes involved in virulence in other bacterial pathogens and 32 genes encoding hypothetical proteins were identified, and may represent novel virulence factors. We identified three genes, lspA1, lspA2 and tadA, known to be required for virulence in humans. This is the first study to broadly define transcripts expressed by H. ducreyi in humans.
    Keywords: Genes, Bacterial ; Haemophilus Ducreyi -- Genetics ; Skin Diseases, Bacterial -- Microbiology
    ISSN: 1350-0872
    E-ISSN: 14652080
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