ArticleApplied and environmental microbiology2006
Transcriptomic assessment of isozymes in the biphenyl pathway of Rhodococcus sp. strain RHA1.
Article in Applied and environmental microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 79 citations in OpenAlex.
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- Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630.Scientific reports · 2018Article
- Insight Into Metabolic Versatility of an Aromatic Compounds-DegradingFrontiers in microbiology · 2018Article
- Expression, purification and kinetic characterization of recombinant benzoate dioxygenase fromMolecular biology research communications · 2016Article
- Characterization of p-hydroxycinnamate catabolism in a soil Actinobacterium.Journal of bacteriology · 2014Article
- Rhodococcus jostii porin A (RjpA) functions in cholate uptake.Applied and environmental microbiology · 2013Article
- Two transporters essential for reassimilation of novel cholate metabolites by Rhodococcus jostii RHA1.Journal of bacteriology · 2012Article
- Gene cluster encoding cholate catabolism in Rhodococcus spp.Journal of bacteriology · 2012Article
- Specific gene responses of Rhodococcus jostii RHA1 during growth in soil.Applied and environmental microbiology · 2012Article
- Proteomic analysis of survival of Rhodococcus jostii RHA1 during carbon starvation.Applied and environmental microbiology · 2012Article
- Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential.Antonie van Leeuwenhoek · 2012Article
- Proteomic profiling of the dioxin-degrading bacterium Sphingomonas wittichii RW1.Journal of biomedicine & biotechnology · 2012Article
- Vanillin catabolism in Rhodococcus jostii RHA1.Applied and environmental microbiology · 2012Article
- Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.PLoS genetics · 2011Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rhodococcus sp. RHA1 grows on a broad range of aromatic compounds and vigorously degrades polychlorinated biphenyls (PCBs). Previous work identified RHA1 genes encoding multiple isozymes for most of the seven steps of the biphenyl (BPH) pathway, provided evidence for coexpression of some of these isozymes, and indicated the involvement of some of these enzymes in the degradation of BPH, ethylbenzene (ETB), and PCBs. To investigate the expression of these isozymes and better understand how they contribute to the robust degradative capacity of RHA1, we comprehensively analyzed the 9.7-Mb genome of RHA1 for BPH pathway genes and characterized the transcriptome of RHA1 growing on benzoate (BEN), BPH, and ETB. Sequence analyses revealed 54 potential BPH pathway genes, including 28 not previously reported. Transcriptomic analysis with a DNA microarray containing 70-mer probes for 8,213 RHA1 genes revealed a suite of 320 genes of diverse functions that were upregulated during growth both on BPH and on ETB, relative to growth on the control substrate, pyruvate. By contrast, only 65 genes were upregulated during growth on BEN. Quantitative PCR assays confirmed microarray results for selected genes and indicated that some of the catabolic genes were upregulated over 10,000-fold. Our analysis suggests that up to 22 enzymes, including 8 newly identified ones, may function in the BPH pathway of RHA1. The relative expression levels of catabolic genes did not differ for BPH and ETB, suggesting a common regulatory mechanism. This study delineated a suite of catabolic enzymes for biphenyl and alkyl-benzenes in RHA1, which is larger than previously recognized and which may serve as a model for catabolism in other environmentally important bacteria having large genomes.
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