Evolution of Catabolic Pathways: Genomic Insights into Microbial
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            -Triazine Metabolism

Shapir, Nir; Mongodin, Emmanuel F.; Sadowsky, Michael J.; Daugherty, Sean C.; Nelson, Karen E.; Wackett, Lawrence P.

doi:10.1128/jb.01257-06

Cited by 99 publications

(103 citation statements)

References 79 publications

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“…A range of growth rates, scored on an arbitrary scale from 1 to 5, were observed when the clones were restreaked on selection medium (examples are shown in Supplementary Data Figure S2). The fastest-growing clones formed colonies in less than 30 h. Sequencing showed that eight unique variants had been selected, one of which, purF (1)(2)(3)(4), dominated the pool with 22 occurrences (Table 1). We also sequenced a variant, 1-Neg, that was not able to complement the tryptophan auxotrophy of E. coli JMB9ΔtrpF cells (Table 1).…”

Section: Selection Of Improved Variantsmentioning

confidence: 99%

A Study in Molecular Contingency: Glutamine Phosphoribosylpyrophosphate Amidotransferase is a Promiscuous and Evolvable Phosphoribosylanthranilate Isomerase

Patrick

Matsumura

2008

Journal of Molecular Biology

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SummaryThe prevalence of paralogous enzymes implies that novel catalytic functions can evolve on preexisting protein scaffolds. The weak secondary activities of proteins, which reflect catalytic promiscuity and substrate ambiguity, are plausible starting points for this evolutionary process. In this study, we observed the emergence of a new enzyme from the ASKA collection of Escherichia coli open reading frames (ORFs). The over-expression of (His) 6 -tagged glutamine phosphoribosylpyrophosphate amidotransferase (PurF) unexpectedly rescued a ΔtrpF E. coli strain from starvation on minimal media. The wild-type PurF and TrpF enzymes are unrelated in sequence, tertiary structure or catalytic mechanism. The promiscuous phosphoribosylanthranilate isomerase (PRAI) activity of the ASKA PurF variant apparently stems from a pre-existing affinity for phosphoribosylated substrates. The relative fitness of the (His) 6 -PurF/ΔtrpF strain was improved 4.8-fold to nearly wild-type levels by random mutagenesis of purF and genetic selection. The evolved and ancestral PurF proteins were purified and reacted with phosphoribosylanthranilate in vitro. The best evolvant (k cat /K M = 0.3 s −1 .M −1 ) was ~25-fold more efficient than its ancestor, but >10 7 -fold less efficient than the wild-type PRAI. These observations demonstrate in quantitative terms that the weak secondary activities of promiscuous enzymes can dramatically improve the fitness of contemporary organisms.

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Section: Selection Of Improved Variantsmentioning

confidence: 99%

A Study in Molecular Contingency: Glutamine Phosphoribosylpyrophosphate Amidotransferase is a Promiscuous and Evolvable Phosphoribosylanthranilate Isomerase

Patrick

Matsumura

2008

Journal of Molecular Biology

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“…Usually they were dealkylated forms, however now hydroxylated forms of atrazine reported. Such observations are also seen in new metabolic pathways of atrazine biodegradation which suggests that atrazine metabolism has evolved in the last three decades (Shapir et al, 2007). Various research studies have pointed out that several s-triazine degradation pathways usually converge to cyanuric acid, subsequently by hydrolytic ring cleavage (Eaton and Karns, 1991a;Eaton and Karns, 1991b).…”

Section: Biodegradation Of Atrazinementioning

confidence: 86%

“…As initially atrazine was considered to be recalcitrant, but few microorganisms reported for degradation till mid-1990. However, now various microorganisms capable of degrading atrazine were reported across the globe due to extensive substrate ranges discovered in bacteria (Shapir et al, 2007;Vaishampayan et al, 2007). Not only had this but the reports of intermediate metabolites of atrazine degradation also increased.…”

Section: Biodegradation Of Atrazinementioning

confidence: 96%

“…For herbicide-contaminated soils, land farming has been one of the most important bioremediation sites which involve biostimulation (Felsot et al, 2003). In bioremediation of groundwater study, atrazine is readily biodegraded under controlled conditions (Shapir et al, 2007). It was found that biodegrading capacity is inhibited in the presence of external nitrogen and carbon sources (Govantes et al, 2009).…”

Section: Biological Methodsmentioning

confidence: 99%

“…AtrA gene in Rhodococcus strain TE1 involved in N-dealkylation of atrazine and forms DIA and DEA (Shao et al, 1995). AtzB (hydroxyatrazine ethylaminohydrolase) catalyzes hydroxyatrazine and form Nisopropylammelide which further catalyzed by AtzC (N-isopropylammelide isopropylamino hydrolase), forming a cyanuric acid (Martinez et al, 2001;Shapir et al, 2007). converts cyanuric acid into biurate.…”

Section: Genetic Basis Of Atrazine Biodegradationmentioning

confidence: 99%

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Untitled

2017

RJLBPCS

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ABSTRACT:Increasing human population is putting enormous pressure on food supply and agriculture. To increase crop production, pesticides are used intensively. Atrazine (herbicide) which has proved economical in case of maize and sorghum for yield increase and price reduction for farmers. However, extensive use of atrazine in agriculture resulted in pollution and adverse effects on the environment.There is need to tackle atrazine contamination. This review explores the way for atrazine remediation.

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Bioremediation

Prince

2009

Kirk-Othmer Encyclopedia of Chemical Technology

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Bioremediation is the process of judiciously exploiting biological processes to minimize an unwanted environmental impact; usually the aim is the removal of a contaminant from the biosphere. Like most definitions in biology, that of bioremediation is the subject of some debate. A narrow definition might focus on the conversion of contaminating organic molecules to CO 2 , water, and inorganic ions, and the oxidation or reduction of contaminating inorganic ions such as nitrate or ammonia to harmless forms, in this case nitrogen gas. A broader definition would include biological processes for ameliorating extremes of pH, concentrating contaminants so that they can be more easily removed by physical techniques, converting toxic species to less toxic or less bioavailable forms that pose less of a threat to the environment, and restoring functional ecosystems to contaminated or disturbed sites when the contaminants or disturbance cannot be removed.

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Evolution of Catabolic Pathways: Genomic Insights into Microbial s -Triazine Metabolism

Cited by 99 publications

References 79 publications

A Study in Molecular Contingency: Glutamine Phosphoribosylpyrophosphate Amidotransferase is a Promiscuous and Evolvable Phosphoribosylanthranilate Isomerase

A Study in Molecular Contingency: Glutamine Phosphoribosylpyrophosphate Amidotransferase is a Promiscuous and Evolvable Phosphoribosylanthranilate Isomerase

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Bioremediation

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