Unknown,Transcriptomics,Genomics,Proteomics

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Comparative genomic hybridization of seven strains of the human pathogenic acetic acid bacterium Granulibacter bethesdensis

ABSTRACT: Chronic granulomatous disease (CGD) is a rare genetic defect in neutrophil superoxide formation in which patients develop recurrent life-threatening infections with Staphylococcus aureus, Serratia marcescens, Burkholderia cepacia, Nocardia and Aspergillus species. We recently described a novel member of the Acetobacteraceae, Granulibacter bethesdensis, in several CGD patients who presented with fever and lymphadenitis. In order to more fully understand the infectivity of this novel human pathogen we sequenced the genome of Granulibacter bethesdensis to its entirety and identified a single, circular chromosome consisting of 2,708,355 base pairs with a G+C content of 59.07%. We identified 2,437 predicted protein-encoding open reading frames (ORFS) of which, 75.17% have a biological functional annotation. Comparison of G. bethesdensis to another member of the Acetobacteraceae, Gluconobacter oxydans, indicates functional conservation between the two genomes, but also the presence of ORFS unique to G. bethesdensis consistent with virulence, adherence, DNA uptake and methanol utilization. In addition, comparative genome analysis of G. bethesdensis to known CGD pathogens demonstrated broad conservation of putative virulence factors. Finally, G. bethesdensis isolate DNAs were hybridized to a high density custom array, towards characterizing plasticity zones, which occur in regions with genes related to DNA uptake systems, transcriptional regulators and those of unknown function. Together these results provide insight into a novel human pathogen, which is geographically dispersed, is undergoing gain or loss of important DNA elements and which infects patients with CGD.

ORGANISM(S): Granulibacter bethesdensis

SUBMITTER: Dan Sturdevant

PROVIDER: E-TABM-148 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The genome-wide transcriptional responses of the strictly aerobic -proteobacterium Gluconobacter oxydans 621H to oxygen limitation, to the absence of the cytochrome bc1 complex, and to low pH were studied using DNA microarray analyses. Oxygen limitation caused expression changes of 486 genes, representing 20% of the chromosomal genes. Genes with an increased mRNA level included those for terminal oxidases, the cytochrome bc1 complex, transhydrogenase, two alcohol dehydrogenases, heme biosynthesis, PTS proteins, proteins involved in cyclic diGMP synthesis and degradation, two sigma factors, flagella and chemotaxis proteins, several stress proteins, and a putative exporter protein. The downregulated genes comprised those for respiratory dehydrogenases, enzymes of central metabolism, PQQ biosynthesis, outer membrane receptors, Sec proteins, and proteins involved in transcription and translation. A M-NM-^TqrcABC mutant of G. oxydans showed a growth defect during cultivation on mannitol at pH 4 under oxygen saturation. Comparison of the transcriptomes of this mutant versus the wild type under these conditions revealed 51 differentially expressed genes. Interestingly, almost all of the 45 genes with increased expression in the M-NM-^TqrcABC mutant at pH 4 were also upregulated in the wild type grown at pH 6 under oxygen limitation. These results support an active role of the cytochrome bc1 complex in G. oxydans respiration. The transcriptome comparison of G. oxydans wild type at pH 4 versus pH 6 in mannitol medium under oxygen-saturated conditions uncovered only 72 differentially expressed genes. The 35 upregulated genes included those for cytochrome bd oxidase, major polyol dehydrogenase, iron storage and oxidative stress proteins. Among the 37 downregulated genes were some encoding enzymes dealing with carbon dioxide, such as biotin carboxylase, biotin carboxyl carrier protein, and carboanhydrase. These results give first insights into global transcriptional responses of G. oxydans. DNA microarray experiments were repeated independently three times for G. oxydans M-NM-^TqrcABC versus wild type and G. oxydans grown at pH 4 versus pH 6 and four times for G. oxydans grown at oxygen limitation versus pH oxygen saturation in biological replicates.

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Comparative genomic hybridization of seven strains of the human pathogenic acetic acid bacterium Granulibacter bethesdensis

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