The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome

Suenaga, Hikaru; Mizuta, Shiori; Miyazaki, Kentaro

doi:10.1111/j.1574-6941.2009.00719.x

Cited by 20 publications

(7 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…strain 1YdBTEX2) could be isolated only from a site with high concentrations of the same compounds, which is in accordance with a high turnover number and a low affinity for catechol. This suggests that in response to pollutant concentrations, the enzymes were positively selected in the environment [44, 45]. …”

Section: Resultsmentioning

confidence: 99%

Strategy of Pseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate

et al. 2017

View full text Add to dashboard Cite

Phenol- and naphthalene-degrading indigenous Pseudomonas pseudoalcaligenes strain C70 has great potential for the bioremediation of polluted areas. It harbours two chromosomally located catechol meta pathways, one of which is structurally and phylogenetically very similar to the Pseudomonas sp. CF600 dmp operon and the other to the P. stutzeri AN10 nah lower operon. The key enzymes of the catechol meta pathway, catechol 2,3-dioxygenase (C23O) from strain C70, PheB and NahH, have an amino acid identity of 85%. The metabolic and regulatory phenotypes of the wild-type and the mutant strain C70ΔpheB lacking pheB were evaluated. qRT-PCR data showed that in C70, the expression of pheB- and nahH-encoded C23O was induced by phenol and salicylate, respectively. We demonstrate that strain C70 is more effective in the degradation of phenol and salicylate, especially at higher substrate concentrations, when these compounds are present as a mixture; i.e., when both pathways are expressed. Moreover, NahH is able to substitute for the deleted PheB in phenol degradation when salicylate is also present in the growth medium. The appearance of a yellow intermediate 2-hydroxymuconic semialdehyde was followed by the accumulation of catechol in salicylate-containing growth medium, and lower expression levels and specific activities of the C23O of the sal operon were detected. However, the excretion of the toxic intermediate catechol to the growth medium was avoided when the growth medium was supplemented with phenol, seemingly due to the contribution of the second meta pathway encoded by the phe genes.

show abstract

Section: Resultsmentioning

confidence: 99%

Strategy of Pseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate

et al. 2017

View full text Add to dashboard Cite

show abstract

“…JF8 (Hatta et al ., 2003) (Fig. 2), which, however, preferred catechol over 2,3‐dihydroxybiphenyl as a substrate (Suenaga et al ., 2009a). In addition, the library contained clones with extradiol dioxygenases having homology to BphC 2,3‐dihydroxybiphenyl dioxygenase of Terrabacter sp.…”

Section: Function‐based Screening For Novel Activitiesmentioning

confidence: 99%

Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

Vílchez-Vargas

Junca

Pieper

2010

Environmental Microbiology

View full text Add to dashboard Cite

SummaryMicrobial degradation is the main mechanism responsible for the recovery of contaminated sites, where a huge body of investigations is available in which most concentrate on single isolates from soils capable of mineralizing pollutants. The rapid development of molecular techniques in recent years allows immense insights into the processes in situ, including identification of organisms active in target sites, community member interactions and catabolic gene structures. Only a detailed understanding of the functioning and interactions within microbial communities will allow their rational manipulation for the purpose of optimizing bioremediation efforts. We will present the status of the current capabilities to assess and predict catabolic potential of environmental sites by applying gene fingerprinting, catabolome arrays, metagenomics and complementary 'omics' technologies. Collectively, this will allow tracking regulation and evolution within microbial communities ultimately aiming to understand the mechanisms taking place in large scale bioremediation treatments for aromatic decontamination.

show abstract

“…The advent of metagenomic approaches has revealed an even higher degree of diversity [11–15]. We have previously targeted extradiol dioxygenases, which convert colorless catecholic compounds to yellowish ring-opened products, to screen degradation pathways and identify novel enzymes belonging to new subfamilies [11], as well as novel arrangements in the degradation pathway genes [16,17]. …”

Section: Introductionmentioning

confidence: 99%

Metagenomic Screening for Aromatic Compound-Responsive Transcriptional Regulators

Uchiyama

Miyazaki

2013

PLoS ONE

Self Cite

View full text Add to dashboard Cite

We applied a metagenomics approach to screen for transcriptional regulators that sense aromatic compounds. The library was constructed by cloning environmental DNA fragments into a promoter-less vector containing green fluorescence protein. Fluorescence-based screening was then performed in the presence of various aromatic compounds. A total of 12 clones were isolated that fluoresced in response to salicylate, 3-methyl catechol, 4-chlorocatechol and chlorohydroquinone. Sequence analysis revealed at least 1 putative transcriptional regulator, excluding 1 clone (CHLO8F). Deletion analysis identified compound-specific transcriptional regulators; namely, 8 LysR-types, 2 two-component-types and 1 AraC-type. Of these, 9 representative clones were selected and their reaction specificities to 18 aromatic compounds were investigated. Overall, our transcriptional regulators were functionally diverse in terms of both specificity and induction rates. LysR- and AraC- type regulators had relatively narrow specificities with high induction rates (5-50 fold), whereas two-component-types had wide specificities with low induction rates (3 fold). Numerous transcriptional regulators have been deposited in sequence databases, but their functions remain largely unknown. Thus, our results add valuable information regarding the sequence–function relationship of transcriptional regulators.

show abstract

The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome

Cited by 20 publications

References 38 publications

Strategy of Pseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate

Strategy of Pseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate

Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

Metagenomic Screening for Aromatic Compound-Responsive Transcriptional Regulators

Contact Info

Product

Resources

About