Aerobic Degradation of Aromatic Hydrocarbons

Pérez‐Pantoja, Danilo; González, Bernardo; Pieper, Dietmar H.

doi:10.1007/978-3-319-39782-5_10-1

Cited by 12 publications

(4 citation statements)

References 187 publications

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“…Anoxia in the natural environment of SRP precludes O 2 -dependent oxygenase-catalysed reactions for the activation of hydrocarbons as long known from aerobic bacteria (Pérez-Pantoja, González, & Pieper, 2010). Evidence for SRP to be capable of anaerobic degradation of hydrocarbons was provided from isolation and investigation of respective novel strains.…”

Section: Saturated and Aromatic Hydrocarbonsmentioning

confidence: 98%

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Rabus

Venceslau

Wöhlbrand

et al. 2015

Advances in Microbial Physiology

265

286

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Section: Saturated and Aromatic Hydrocarbonsmentioning

confidence: 98%

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Rabus

Venceslau

Wöhlbrand

et al. 2015

Advances in Microbial Physiology

265

286

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“…Pre-existing enzymes have to acquire new substrate specificities, and the shape and kinetics of the enzymes involved fit to each other to avoid the escape of intermediates [84,92]. In addition, the flow of the resulting products has to be wired to the extant biochemical network in order to generate a growth advantage that allows its selection.…”

Section: Ros Enters a Feedback Loop Into The CDmentioning

confidence: 99%

From the selfish gene to selfish metabolism: Revisiting the central dogma

Lorenzo

2014

BioEssays

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The standard representation of the Central Dogma (CD) of Molecular Biology conspicuously ignores metabolism. However, both the metabolites and the biochemical fluxes behind any biological phenomenon are encrypted in the DNA sequence. Metabolism constrains and even changes the information flow when the DNA-encoded instructions conflict with the homeostasis of the biochemical network. Inspection of adaptive virulence programs and emergence of xenobiotic-biodegradation pathways in environmental bacteria suggest that their main evolutionary drive is the expansion of their metabolic networks towards new chemical landscapes rather than perpetuation and spreading of their DNA sequences. Faulty enzymatic reactions on suboptimal substrates often produce reactive oxygen species (ROS), a process that fosters DNA diversification and ultimately couples catabolism of the new chemicals to growth. All this calls for a revision of the CD in which metabolism (rather than DNA) has the leading role.

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“…To do so, aerobic bacteria rely on the addition of either one or two atoms of molecular oxygen by mono or dioxygenases. They transform aromatic compounds into central intermediates of aromatics degradation such as catechol, protocatechuate and gentisate [ 10 ]. Then, ring-cleaving dioxygenases catalyze ring fission via the ortho - or meta -cleavage pathway.…”

Section: Introductionmentioning

confidence: 99%

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

et al. 2021

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Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.

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Aerobic Degradation of Aromatic Hydrocarbons

Cited by 12 publications

References 187 publications

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

From the selfish gene to selfish metabolism: Revisiting the central dogma

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

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