Anne Zaparucha

Revealing the hidden functional diversity of an enzyme family

Millions of protein database entries are not assigned reliable functions, preventing the full understanding of chemical diversity in living organisms. Here, we describe an integrated strategy for the discovery of various enzymatic activities catalyzed within protein families of unknown or little known function. This approach relies on the definition of a generic reaction conserved within the family, high-throughput enzymatic screening on representatives, structural and modeling investigations and analysis of genomic and metabolic context. As a proof of principle, we investigated the DUF849 Pfam family and unearthed 14 potential new enzymatic activities, leading to the designation of these proteins as β-keto acid cleavage enzymes. We propose an in vivo role for four enzymatic activities and suggest key residues for guiding further functional annotation. Our results show that the functional diversity within a family may be largely underestimated. The extension of this strategy to other families will improve our knowledge of the enzymatic landscape.

A Conserved Gene Cluster Rules Anaerobic Oxidative Degradation of l-Ornithine

For the ornithine fermentation pathway, described more than 70 years ago, genetic and biochemical information are still incomplete. We present here the experimental identification of the last four missing genes of this metabolic pathway. They encode L-ornithine racemase, (2R,4S)-2,4-diaminopentanoate dehydrogenase, and the two subunits of 2-amino-4-ketopentanoate thiolase. While described only for the Clostridiaceae to date, this pathway is shown to be more widespread.

Agelasines J, K, and L from the Solomon Islands Marine Sponge Agelas cf. mauritiana

Three new diterpene alkaloids, agelasine J (3), agelasine K (4), and agelasine L (5), were isolated from the marine sponge Agelas cf. mauritiana collected in the Solomon Islands. The structures of these compounds were elucidated by physical data analyses. They displayed in vitro antimalarial activity against Plasmodium falciparum.

Asymmetric Michael reaction under PTC conditions without solvent Importance of π interactions for the enantioselectivity

Abstract Michael addition of diethyl acetylaminomalonate to chalcone under Asymmetric Phase Transfer Catalysis without solvent has been successfully carried out in the presence of ephedrinium salts. Substituent effects on the benzyl moiety of the ammonium part of the catalyst revealed the importance of π-π attractive interactions between the catalyst and the electrophile on enantioselectivity. The best result (82% ee) was obtained with easy accessible (S) binaphthyl compound.

Biomimetically inspired short access to the 2-aminoimidazole-fused tetracyclic core of (+/-)-dibromoagelaspongin.

A six-step synthesis of the tetracyclic core of the natural compound (+/-)-dibromoagelaspongin, isolated from Agelas sp. Sponge, was achieved from the commercially available 5-aminopentan-1-ol, 2-trichloroacetylpyrrole, and 2-aminopyrimidine. Following a biomimetic inspired approach, successive oxidative reactions including the final DMDO biomimetic oxidation gave the interesting triaminomethane-fused core.

3-Keto-5-aminohexanoate Cleavage Enzyme A COMMON FOLD FOR AN UNCOMMON CLAISEN-TYPE CONDENSATION

The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn2+ cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the “domain of unknown function” DUF849.

Synthesis of Mono‐ and Dihydroxylated Amino Acids with New α‐Ketoglutarate‐Dependent Dioxygenases: Biocatalytic Oxidation of CH Bonds

Iron(II)/α‐ketoacid‐dependent oxygenases (αKAOs) are enzymes that mainly catalyse hydroxylation reaction. By using a genomic approach combining sequence comparison and protein‐domain sharing, a set of 131 αKAO enzymes was prepared. The screening of various substrates revealed five new αKAOs. Four αKAOs were found to be active towards L‐lysine, L‐ornithine and L‐arginine with total regio‐ and stereoselectivities and yielding the corresponding 3‐ or 4‐hydroxyamino acids. The enzymatic cascade reaction with two stereoselective regiodivergent αKAOs enabled the synthesis of 3,4‐dihydroxy‐L‐lysine.

A novel acyl-CoA beta-transaminase characterized from a metagenome.

Background Bacteria are key components in all ecosystems. However, our knowledge of bacterial metabolism is based solely on the study of cultivated organisms which represent just a tiny fraction of microbial diversity. To access new enzymatic reactions and new or alternative pathways, we investigated bacterial metabolism through analyses of uncultivated bacterial consortia. Methodology/Principal Findings We applied the gene context approach to assembled sequences of the metagenome of the anaerobic digester of a municipal wastewater treatment plant, and identified a new gene which may participate in an alternative pathway of lysine fermentation. Conclusions We characterized a novel, unique aminotransferase that acts exclusively on Coenzyme A (CoA) esters, and proposed a variant route for lysine fermentation. Results suggest that most of the lysine fermenting organisms use this new pathway in the digester. Its presence in organisms representative of two distinct bacterial divisions indicate that it may also be present in other organisms.

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.

A Partial Synthesis of the Skeleton of Deoxypumiloside, a Putative Intermediate in Camptothecin Biosynthesis

Ajmalicine (3) was used as the starting material for the synthesis of a camptothecin-like skeleton. After C-21 activation through allylic conjugation, regiospecific tertiary amine oxidation was achieved with mercury salts. Subsequent biomimetic oxidation of the indole nucleus then gave quinolone lactam 14. A two-step process finally afforded 4, a close analogue of deoxypumiloside (5), one of the putative intermediates in the biosynthesis of camptothecin.