Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp.

Brežná, Barbara; Khan, Ashraf A.; Cerniglia, Carl E.

doi:10.1016/s0378-1097(03)00328-8

Cited by 91 publications

(56 citation statements)

References 45 publications

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“…In order to test this, we introduced sigK or sigK-rskA homologues into M. tuberculosis ⌬sigK (with polar effect on rskA) from the most distantly related mycobacterium for which a genome sequence has been determined and a sigK homologue is present. For this, we used M. gilvum (95% identity in 16S rRNA), best known for its capacity to degrade polycyclic aromatic hydrocarbons (5).…”

Section: Resultsmentioning

confidence: 99%

Evolution of the Mycobacterial SigK Regulon

2008

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Previous studies have established that members of the Mycobacterium tuberculosis complex exhibit variable production of the antigenic proteins MPT70 and MPT83 due to mutations in their positive regulator, SigK (sigma factor K), and their negative regulator, RskA (regulator of sigma K). To further understand this highly specific SigK-controlled regulon, we have undertaken evolutionary studies to determine the presence of homologues of SigK-regulated genes in other organisms and to predict its transcriptional network. Evolutionary analysis indicates that the positive and negative regulators are conserved across many organisms, but that the genes under their control are variable. Moreover, the addition, loss, and movement of various genes in the mpt70/83 locus suggest that these genes are unlikely to be cotranscribed. To test predictions from sequence analysis, we have used promoter luciferase fusions and Northern blots to show that the majority of genes in this locus have their own promoters, of which a subset are SigK regulated (mpt83, dipZ, mpt70, and Rv0449c). Next, we have shown that the intracellular inducibility of mpt70 and mpt83 is a conserved property, shared between M. tuberculosis and Mycobacterium marinum. In addition, we have shown that SigK and RskA from an environmental mycobacterium isolate (M. gilvum PYR-GCK) complemented the regulatory activity of M. tuberculosis ⌬sigK rskA. Together, our data indicate that the regulatory system SigK/RskA is conserved across the Mycobacterium genus, whereas the regulon under its control varies considerably across species.Mycobacterium tuberculosis is an extremely successful pathogen of humans, infecting an estimated one-third of the world's population. This capacity to persist in the host, despite the dynamic alterations effected by the host immune response, testifies to an evolved capacity of the organism to regulate its genetic expression to the conditions encountered during infection. Indeed, a number of studies have demonstrated that disruption of M. tuberculosis regulatory elements, such as sigma factors, results in reduced virulence in experimental models (21,28,30).The determination of genomic sequences for a number of nonpathogenic mycobacteria has revealed that homologues of many genes, including regulatory elements, are often present in organisms that are not virulent to humans. For instance, comparative analysis has demonstrated conservation of biochemical pathways and a secretory system important for full virulence of M. tuberculosis (7,10). This indicates that genetic elements and the proteins they encode that exist in other mycobacteria either serve an important function in M. tuberculosis pathogenicity or have evolved a specific role in M. tuberculosis complex organisms. As a number of predicted regulatory elements are also conserved between environmental mycobacteria and M. tuberculosis, it follows that an evolutionary analysis may guide predictions about the origins of such elements, the transcriptional networks they control, and the stimuli that...

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Section: Resultsmentioning

confidence: 99%

Evolution of the Mycobacterial SigK Regulon

2008

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“…Cells were scraped from the plates into 1 ml H 2 O and pelleted by centrifugation for 10 min at 5900 g. Genomic DNA was isolated according to the protocol for Gram-positive bacteria with the Qiagen DNeasy Kit. Additional strains (Table 1) were cultivated on mineral basal salt (MBS) medium supplemented with sorbitol and phenanthrene as described previously (Brezna et al, 2003).…”

Section: Methodsmentioning

confidence: 99%

“…To screen bacterial strains for phtAa, total genomic DNA was embedded in agarose plugs, digested by XbaI and separated by pulsed field gel electrophoresis (PFGE) as described previously (Brezna et al, 2003). Restriction fragments were separated at 14 uC in a 1 % agarose gel in 0?56 TBE buffer using a contour-clamped homogeneous electric field (CHEF) apparatus (CHEF-DR II, Bio-Rad).…”

Section: Methodsmentioning

confidence: 99%

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Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1

et al. 2004

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Mycobacterium vanbaalenii PYR-1 is capable of degrading polycyclic aromatic hydrocarbons (PAHs) to ring cleavage metabolites. This study identified and characterized a putative phthalate degradation operon in the M. vanbaalenii PYR-1 genome. A putative regulatory protein ( phtR) was encoded divergently with five tandem genes: phthalate dioxygenase large subunit ( phtAa), small subunit ( phtAb), phthalate dihydrodiol dehydrogenase ( phtB), phthalate dioxygenase ferredoxin subunit ( phtAc) and phthalate dioxygenase ferredoxin reductase ( phtAd ). A 6?7 kb EcoRI fragment containing these genes was cloned into Escherichia coli and converted phthalate to 3,4-dihydroxyphthalate. Homologues to the operon region were detected in a number of PAH-degrading Mycobacterium spp. isolated from various geographical locations. The operon differs from those of other Gram-positive bacteria in both the placement and orientation of the regulatory gene. In addition, the M. vanbaalenii PYR-1 pht operon contains no decarboxylase gene and none was identified within a 37 kb region containing the operon. This study is the first report of a phthalate degradation operon in Mycobacterium spp.

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“…The biochemical pathways of pyrene degradation by Mycobacterium have also been identified Kim et al, 2007). The genes encoding the a and b subunits of dioxygenases have been sequenced in many strains (Brezna et al, 2003;Sho et al, 2004;Kim et al, 2007). Lake sediment studies showed that copy numbers of nidA gene were positively related to pyrene mineralization and nidA gene can serve as a biomarker for pyrene degradation (DeBruyn et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

Peng

Cai

Qiao

et al. 2010

Environmental Pollution

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This study investigates the dynamics of pyrene degradation rates, microbial communities, and functional gene copy numbers during the incubation of pyrene-spiked soils. Spiking pyrene to the soil was found to have negligible effects on the bacterial community present. Our results demonstrated that there was a significant difference in nidA gene copy numbers between sampling dates in QZ soil. Mycobacterium 16S rDNA clone libraries showed that more than 90% mycobacteria detected were closely related to fastgrowing PAH-degrading Mycobacterium in pyrene-spiked soil, while other sequences related to slowgrowing Mycobacterium were only detected in the control soil. It is suggested that nidA gene copy number and fast-growing PAH-degrading Mycobacterium could be used as indicators to predict pyrene contamination and its degradation activity in soils.

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Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp.

Cited by 91 publications

References 45 publications

Evolution of the Mycobacterial SigK Regulon

Evolution of the Mycobacterial SigK Regulon

Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

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