Functional characterization of diverse ring‐hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in <i>Sphingobium</i> sp. PNB

Khara, Pratick; Roy, Madhumita; Chakraborty, Joydeep; Ghosal, Debajyoti; Dutta, Tapan K.

doi:10.1016/j.fob.2014.03.001

Cited by 58 publications

(37 citation statements)

References 74 publications

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“…PNB, Sphingobium sp. P2 and S. yanoikuyae strain B1 (Demaneche et al, 2004;Jakoncic et al, 2007;Jouanneau and Meyer, 2006;Khara et al, 2014;Pinyakong et al, 2003a,b;Romine et al, 1999aRomine et al, , 1999bSchuler et al, 2009;Yu et al, 2007). Accordingly, BphA1f is responsible for the capability of S. yanoikuyae B1 to dihydroxylate large aromatic compounds, such as chrysene and benzo[a]pyrene .…”

Section: Catabolically Versatile Enzymes Used In Multiple Pahdegradatmentioning

confidence: 99%

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi

Kang

Goikavi

et al. 2015

International Biodeterioration & Biodegradation

155

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Section: Catabolically Versatile Enzymes Used In Multiple Pahdegradatmentioning

confidence: 99%

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi

Kang

Goikavi

et al. 2015

International Biodeterioration & Biodegradation

155

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“…Two genera mainly represented the group: Novosphingobium sp. and Sphingomonas sp., which are known to degrade various PAHs due to their substrate unspecific dioxygenases 30,31 . Bradyrhizobiaceae had a significant presence in the 10-40 cm interval.…”

Section: Discussionmentioning

confidence: 99%

Mud volcanoes and the presence of PAHs

Remizovschi

Carpa

Forray

et al. 2020

Sci Rep

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A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well -an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by Gc-MS and δ 13 C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative pAH-degrading bacterial otUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.

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“…Metabolically versatile Sphingomonad strains, capable of degrading various aromatic compounds, contained seven pairs of genes coding for α and β subunits of RHOs organized in several clusters, and only one set of genes encoding the electron transport system (Khara et al . ). Similarly, a novel micro‐organism belonging to the Rhodocyclaceae family (strain PG1) had eight sets of genes coding for RHO enzymes (Singleton et al .…”

Section: Discussionmentioning

confidence: 97%

“…The identified metagenomic fragment contained sequences encoding six oxygenase component of RHOs, which were classified as belonging to three different functional classes (Chakraborty et al 2012) and presented potential substrates with various chemical structures . The recent sequencing of the genome of PAH-degrading bacterial strains showed that these micro-organisms often carry multiple genes encoding the oxygenase component of RHOs, distributed throughout their genome (Lai et al 2012;Zhang and Anderson 2012;Cui et al 2013;Khara et al 2014;Singleton et al 2015). In fact, the organization of the genes involved in PAH biodegradation pathways originally described in Pseudomonas strains (two gene clusters encoding the enzymes involved in the upper and lower pathways), is now known to be extremely rare (Suenaga et al 2009).…”

Section: Discussionmentioning

confidence: 99%

“…For instance, Cycloclasticus strains, which are highly specialized in the utilization of aromatic compounds, were found to carry at least 12 RHO a-subunit genes (Lai et al 2012;Cui et al 2013). Metabolically versatile Sphingomonad strains, capable of degrading various aromatic compounds, contained seven pairs of genes coding for a and b subunits of RHOs organized in several clusters, and only one set of genes encoding the electron transport system (Khara et al 2014). Similarly, a novel micro-organism belonging to the Rhodocyclaceae family (strain PG1) had eight sets of genes coding for RHO enzymes (Singleton et al 2015).…”

Section: Discussionmentioning

confidence: 99%

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Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments

et al. 2015

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Aims: To investigate the potential to degrade polycyclic aromatic hydrocarbons (PAHs) of yet-to-be cultured bacterial populations from chronically-polluted intertidal sediments. Methods and Results:A gene variant encoding the alpha subunit of the catalytic component of an aromatic ring-hydroxylating oxygenase (RHO) was abundant in intertidal sediments from chronically-polluted subantarctic and temperate coastal environments, and its abundance increased after PAH amendment. Conversely, this marker gene was not detected in sediments from a non-impacted site, even after a short-term PAH exposure. A metagenomic fragment carrying this gene variant was identified in a fosmid library of subantarctic sediments. This fragment contained five pairs of alpha and beta subunit genes and a lone alpha subunit gene of oxygenases, classified as belonging to three different RHO functional classes. In silico structural analysis suggested that two of these oxygenases contain large substrate-binding pockets, capable of accepting high molecular weight PAHs. Conclusions:The identified uncultured microorganism presents the potential to degrade aromatic hydrocarbons with various chemical structures, and could represent an important member of the PAH-degrading community in these polluted coastal environments. Accepted ArticleThis article is protected by copyright. All rights reserved. Significance and Impact of Study:This work provides valuable information for the design of environmental molecular diagnostic tools and for the biotechnological application of RHO enzymes.

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Functional characterization of diverse ring‐hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB

Cited by 58 publications

References 74 publications

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Mud volcanoes and the presence of PAHs

Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments

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