Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase

2016 ◽  
Vol 13 (2) ◽  
pp. 226-234 ◽  
Author(s):  
Ridao Chen ◽  
Bingquan Gao ◽  
Xiao Liu ◽  
Feiying Ruan ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Enzyme Promiscuity

Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects

2020 ◽  
Vol 27 (5) ◽  
pp. 400-410
Author(s):  
Valentina De Luca ◽  
Luigi Mandrich
Keyword(s):  
Gene Evolution ◽  
Sequence Divergence ◽  
High Specificity ◽  
Industrial Applications ◽  
Point Of View ◽  
Enzyme Promiscuity ◽  
Primary Activity ◽  
Starting Point ◽  
Main Activity

: Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.

scholarly journals Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides

2021 ◽  
Vol 12 ◽  
Author(s):  
Harshit Malhotra ◽  
Sukhjeet Kaur ◽  
Prashant S. Phale
Keyword(s):  
Environmental Fate ◽  
Health Sector ◽  
Enzyme Promiscuity ◽  
Adaptive Laboratory Evolution ◽  
Evolutionary Mechanisms ◽  
Ecological Disturbance ◽  
C1 Metabolism ◽  
Carbamate Pesticides ◽  
The Past ◽  
Biochemical Analyses

Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.

scholarly journals Enzyme promiscuity drives branched-chain fatty acid synthesis in adipose tissues

2018 ◽  
Vol 14 (11) ◽  
pp. 1021-1031 ◽  
Author(s):  
Martina Wallace ◽  
Courtney R. Green ◽  
Lindsay S. Roberts ◽  
Yujung Michelle Lee ◽  
Justin L. McCarville ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Synthesis ◽  
Acid Synthesis ◽  
Chain Fatty Acid ◽  
Enzyme Promiscuity ◽  
Adipose Tissues ◽  
Branched Chain

Evolutionary dynamics of natural product biosynthesis in bacteria

2020 ◽  
Vol 37 (4) ◽  
pp. 566-599 ◽  
Author(s):  
Marc G. Chevrette ◽  
Karina Gutiérrez-García ◽  
Nelly Selem-Mojica ◽  
César Aguilar-Martínez ◽  
Alan Yañez-Olvera ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Evolutionary Dynamics ◽  
Chemical Diversity ◽  
Enzyme Promiscuity ◽  
Evolutionary Mechanisms ◽  
Natural Product Biosynthesis ◽  
Metabolic Traits

We review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial natural products biosynthesis, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits.

scholarly journals Enzyme promiscuity and evolution in light of cellular metabolism

FEBS Journal ◽  
2020 ◽  
Vol 287 (7) ◽  
pp. 1260-1261 ◽  
Author(s):  
Dan S. Tawfik
Keyword(s):  
Cellular Metabolism ◽  
Enzyme Promiscuity

scholarly journals MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
James G Jeffryes ◽  
Ricardo L Colastani ◽  
Mona Elbadawi-Sidhu ◽  
Tobias Kind ◽  
Thomas D Niehaus ◽  
...  
Keyword(s):  
Open Access ◽  
Untargeted Metabolomics ◽  
Enzyme Promiscuity

Ostensible Enzyme Promiscuity: Alkene Cleavage by Peroxidases

2010 ◽  
Vol 16 (47) ◽  
pp. 14142-14148 ◽  
Author(s):  
Francesco G. Mutti ◽  
Miguel Lara ◽  
Markus Kroutil ◽  
Wolfgang Kroutil
Keyword(s):  
Enzyme Promiscuity

scholarly journals Discovery and reduction of nonspecific activities of the major herbicide-resistance gene BAR

2017 ◽  
Author(s):  
Bastien Christ ◽  
Ramon Hochstrasser ◽  
Luzia Guyer ◽  
Rita Francisco ◽  
Sylvain Aubry ◽  
...  
Keyword(s):  
Amino Acids ◽  
Herbicide Resistance ◽  
Catalytic Mechanism ◽  
Genetically Engineered ◽  
Structural Basis ◽  
Enzyme Promiscuity ◽  
Transgenic Expression ◽  
Phosphinothricin Acetyltransferase

Herbicide resistance is a major trait of genetically modified (GM) crops. Currently, resistance to phosphinothricin (also known as glufosinate) is the second most widespread genetically engineered herbicide-resistance trait in crops after glyphosate resistance1,2. Resistance to phosphinothricin in plants is achieved by transgenic expression of the bialaphos resistance (BAR) or phosphinothricin acetyltransferase (PAT) genes, which were initially isolated from the natural herbicide bialaphos-producing soil bacteria Streptomyces hygroscopicus and S. viridochromogenes, respectively3,4. Mechanistically, BAR and PAT encode phosphinothricin acetyltransferase, which transfers an acetyl group from acetyl coenzyme A (acetyl-CoA) to the α-NH2 group of phosphinothricin, resulting in herbicide inactivation1. Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids1, whether transgenic expression of BAR and PAT affects plant endogenous metabolism in vivo was not known. Combining metabolomics, plant genetics, and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species examined. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced nonspecific activities compared to its wild-type counterpart. Our results demonstrate that transgenic expression of enzymes as a common strategy in modern biotechnology may render unintended metabolic consequences arisen from enzyme promiscuity. Understanding of such phenomena at the mechanistic level will facilitate better design of maximally insulated systems featuring heterologously expressed enzymes.

scholarly journals Glucosamine-6P and glucosamine-1P, respectively an activator and a substrate of rhodococcal ADP-glucose pyrophosphorylases, show a hint to ascertain (actino)bacterial glucosamine metabolism

2020 ◽  
Author(s):  
AE Cereijo ◽  
HM Alvarez ◽  
AA Iglesias ◽  
MD Asencion Diez
Keyword(s):  
Carbon Storage ◽  
Nitrogen Availability ◽  
Carbon Sources ◽  
Catalytic Performance ◽  
Biofuel Production ◽  
Enzyme Promiscuity ◽  
Evolutionary Mechanisms ◽  
Intermediary Metabolite ◽  
Main Regulator ◽  
Temporary Carbon Storage

AbstractRhodococcus spp. are important microorganisms for biotechnological purposes, such as bioremediation and biofuel production. The latter, founded on the oleaginous characteristic (high lipid accumulation) exhibited by many Rhodococcus species when grown in certain carbon sources under low nitrogen availability. These bacteria accumulate glycogen during exponential growth, and the glucan plays a role as an intermediary metabolite for temporary carbon storage related to lipid metabolism. The kinetic and regulatory properties of the ADP-glucose pyrophosphorylase (ADP-GlcPPase) from Rhodococcus jostii supports this hypothesis. The enzyme was found able to use glucosamine-1P as an alternative substrate. Curiously, the activity with glucosamine-1P was sensitive to glucose-6P, the main activator of actinobacterial ADP-GlcPPases. Herein, we report the study of glucosamine-1P related to the activity and regulation of ADP-GlcPPases from R. jostii and R. fascians, with the finding that glucosamine-6P is also a significant activator. Glucosamine-6P, belonging to a node between carbon and nitrogen metabolism, was identified as a main regulator in Actinobacteria. Thus, its effect on rhodococcal ADP-GlcPPases reinforces the function proposed for glycogen as temporary carbon storage. Results indicate that the activity of the studied enzymes using glucosamine-1P as a substrate responds to the activation by several metabolites that improve their catalytic performance, which strongly suggest metabolic feasibility. Then, studying the allosteric regulation exerted on an alternative activity would open two scenarios for consideration: (i) the existence of new molecules/metabolites yet undescribed, and (ii) evolutionary mechanisms underlying enzyme promiscuity that give rise new metabolic features in bacteria.

scholarly journals Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

2018 ◽  
Author(s):  
Po-Hsiang Wang ◽  
Kevin Correia ◽  
Han-Chen Ho ◽  
Naveen Venayak ◽  
Kayla Nemr ◽  
...  
Keyword(s):  
Amino Acid ◽  
Microbial Communities ◽  
Driving Forces ◽  
Expression Patterns ◽  
Amino Acid Supplementation ◽  
Amino Acid Exchange ◽  
Enzyme Promiscuity ◽  
Nadph Regeneration ◽  
Balance Analysis ◽  
Acid Exchange

AbstractMost microorganisms in the biosphere live in communities and develop coordinated metabolisms via trading metabolites. In this study, we sought to deconstruct the metabolic interdependency in organohalide-respiring microbial communities enriched withDehalobacter restrictus(Dhb), using a complementary approach of computational metabolic modeling and experimental validation.Dhbpossesses a complete set of genes for amino acid biosynthesis yet requires amino acid supplementation. We reconciled this discrepancy using Flux Balance Analysis with consideration for cofactor availability, enzyme promiscuity, and shared protein expression patterns of severalDhbstrains. Experimentally,13C incorporation assays, growth assays, and metabolite analysis of strain PER-K23 cultures were performed to validate the model predictions. The model resolved thatDhb’s amino acid dependency results from restricted NADPH regeneration and diagnosed that malate supplementation can replenish intracellular NADPH using malic enzyme. Interestingly, we observed unexpected export of glutamate and pyruvate in parallel to malate consumption in the strain PER-K23 cultures. Further experiments onDhb-enriched consortium ACT-3 suggested an interspecies malate-pyruvate shuttle betweenDhband a glutamate-auxotrophicBacteroidessp., reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study reveals that redox constraints and metabolic complementarity are important driving forces for amino acid exchange in anaerobic microbial communities.

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