Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment

Wackett, Lawrence P.

doi:10.1074/jbc.r400014200

Cited by 54 publications

(34 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…These processes, along with biosynthesis, largely govern the carbon cycle, which is dependent on microbial enzymes which use organic compounds as a carbon and energy source (Wackett, 2004).…”

Section: Introductionmentioning

confidence: 99%

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Germano

Cannavan

Mendes

et al. 2012

Pesq. agropec. bras.

View full text Add to dashboard Cite

The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE) and their biochar (BC). Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (α-ARHD bacterial gene) were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF) and agriculture (AG) -, and the biochar (SF_BC and AG_BC, respectively). Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC) in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD) gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture.

show abstract

Section: Introductionmentioning

confidence: 99%

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Germano

Cannavan

Mendes

et al. 2012

Pesq. agropec. bras.

View full text Add to dashboard Cite

show abstract

“…AtzA is the first enzyme of the most thoroughly characterized pathway, the atzABCDEF triazinecatabolic pathway, which was isolated in the early 1990s from Pseudomonas sp. strain ADP (12,32) and is thought to have evolved recently in direct response to the use of chlorinated s-triazine herbicides (44,55,56). The entire catabolic pathway is encoded by the transmissible pADP1 plasmid (33).…”

mentioning

confidence: 99%

Catalytic Improvement and Evolution of Atrazine Chlorohydrolase

Scott

Jackson

Coppin

et al. 2009

Appl Environ Microbiol

View full text Add to dashboard Cite

The atrazine chlorohydrolase AtzA has evolved within the past 50 years to catalyze the hydrolytic dechlorination of the herbicide atrazine. It is of wide research interest for two reasons: first, catalytic improvement of the enzyme would facilitate its application in bioremediation, and second, because of its recent evolution, it presents a rare opportunity to examine the early stages in the acquisition of new catalytic activities. Using a structural model of the AtzA-atrazine complex, a region of the substrate-binding pocket was targeted for combinatorial randomization. Identification of improved variants through this process informed the construction of a variant AtzA enzyme with 20-fold improvement in its k cat /K m value compared with that of the wild-type enzyme. The reduction in K m observed in the AtzA variants has allowed the full kinetic profile for the AtzA-catalyzed dechlorination of atrazine to be determined for the first time, revealing the hitherto-unreported substrate cooperativity in AtzA. Since substrate cooperativity is common among deaminases, which are the closest structural homologs of AtzA, it is possible that this phenomenon is a remnant of the catalytic activity of the evolutionary progenitor of AtzA. A catalytic mechanism that suggests a plausible mechanistic route for the evolution of dechlorinase activity in AtzA from an ancestral deaminase is proposed.

show abstract

“…Microorganisms respond to new chemical inputs in the environment by evolving new enzymes and pathways (30). sTriazine herbicides such as atrazine are anthropogenic chemicals that have recently been observed to be metabolized by soil bacteria (21,26,28,29,31).…”

mentioning

confidence: 99%

Purification and Characterization of Allophanate Hydrolase (AtzF) from Pseudomonas sp. Strain ADP

2005

Self Cite

View full text Add to dashboard Cite

AtzF, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. In the present study, the atzF gene from Pseudomonas sp. strain ADP was cloned and expressed as a His-tagged protein, and the protein was purified and characterized. AtzF had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. and hydroxylamine to generate malonohydroxamate, potentially derived from hydroxylamine capture of an enzyme-tethered acyl group. Three putative catalytically important residues, one lysine and two serines, were altered by site-directed mutagenesis, each with complete loss of enzyme activity. The identity of a putative serine nucleophile was probed using phenyl phosphorodiamidate that was shown to be a time-dependent inhibitor of AtzF. Inhibition was due to phosphoroamidation of Ser189 as shown by liquid chromatography/matrix-assisted laser desorption ionization mass spectrometry. The modified residue corresponds in sequence alignments to the nucleophilic serine previously identified in other members of the amidase signature family. Thus, AtzF affects the cleavage of three carbon-to-nitrogen bonds via a mechanism similar to that of enzymes catalyzing single-amide-bond cleavage reactions. AtzF orthologs appear to be widespread among bacteria.

show abstract

Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment

Cited by 54 publications

References 55 publications

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Catalytic Improvement and Evolution of Atrazine Chlorohydrolase

Purification and Characterization of Allophanate Hydrolase (AtzF) from Pseudomonas sp. Strain ADP

Contact Info

Product

Resources

About