Ekaterina Darii

Genome Mining for Innovative Biocatalysts: New Dihydroxyacetone Aldolases for the Chemist’s Toolbox

Stereoselective carboligating enzymes were discovered by a genome mining approach to extend the biocatalysis toolbox. Seven hundred enzymes were selected by sequence comparison from diverse prokaryotic species as representatives of the aldolase (FSA) family diversity. The aldol reaction tested involved dihydroxyacetone (DHA) and glyceraldehyde‐3‐phosphate. The hexose‐6‐phosphate formation was monitored by mass spectrometry. Eighteen enzymes annotated either as transaldolases or aldolases were found to exhibit a DHA aldolase activity. Remarkably, six of them proven as aldolases, and not transaldolases, shared very limited similarities with those currently described. Multiple sequence alignment performed on all enzymes revealed a Tyr in the new DHA aldolases as found in FSAcoli instead of a Phe usually found in transaldolases. Four of these DHA aldolases were biochemically characterised in comparison with FSAcoli. In particular, an aldolase from Listeria monocytogenes exhibited interesting catalytic properties.

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.

Expanding the reaction space of aldolases using hydroxypyruvate as a nucleophilic substrate

Aldolases are key biocatalysts for stereoselective C–C bond formation allowing access to polyoxygenated chiral units through direct, efficient, and sustainable synthetic processes. The aldol reaction involving unprotected hydroxypyruvate and an aldehyde offers access to valuable polyhydroxy-α-keto acids. However, this undescribed aldolisation is highly challenging, especially regarding stereoselectivity. This reaction was explored using, as biocatalysts, a collection of aldolases selected from biodiversity. Several enzymes that belong to the same pyruvate aldolase Pfam family (PF03328) were found to produce the desired hexulosonic acids from hydroxypyruvate and D-glyceraldehyde with complementary stereoselectivities. One of them was selected for the proof of concept as a biocatalytic tool to prepare five (3S,4S) aldol adducts through an eco-friendly process.

Asymmetric reductive amination by a wild-type amine dehydrogenase from the thermophilic bacteria Petrotoga mobilis

The biocatalytic reductive amination of ketone to chiral amine is one of the most challenging reactions. Using a genome-mining approach, we found proteins catalyzing the reductive amination of ketones without a carboxylic function in the α or β position. The synthesis of (4S)-4-aminopentanoic acid (ee ≥99.5%) was achieved with the thermoactive amine dehydrogenase (AmDH) AmDH4 from Petrotoga mobilis in 88% yield. The high stability and substrate tolerance make AmDH4 a very good starting point for further discovery of reductive amination biocatalysts with an enlarged substrate range. This is the first report of wild-type enzymes with related genes having proper NAD(P)H–AmDH activity.

Synthesis of Branched-Chain Sugars with a DHAP-Dependent Aldolase: Ketones are Electrophile Substrates of Rhamnulose-1-phosphate Aldolases

Dihydroxyacetone phosphate (DHAP)-dependent rhamnulose aldolases display an unprecedented versatility for ketones as electrophile substrates. We selected and characterized a rhamnulose aldolase from Bacteroides thetaiotaomicron (RhuABthet) to provide a proof of concept. DHAP was added as a nucleophile to several α-hydroxylated ketones used as electrophiles. This aldol addition was stereoselective and produced branched-chain monosaccharide adducts with a tertiary alcohol moiety. Several aldols were readily obtained in good to excellent yields (from 76 to 95 %). These results contradict the general view that aldehydes are the only electrophile substrates for DHAP-dependent aldolases and provide a new C-C bond-forming enzyme for stereoselective synthesis of tertiary alcohols.

Elucidation of the trigonelline degradation pathway reveals previously undescribed enzymes and metabolites

Significance The experimental dissection of novel metabolic pathways, from genes and enzymes to metabolites, is a key issue for improving our knowledge of the enzymatic capabilities of the microbial world and providing accurate functional annotation of genomes. We used an integrative methodology combining the phenotyping of a complete genome-scale mutant collection of Acinetobacter baylyi ADP1 with an untargeted liquid chromatography/MS-based approach to uncover the degradation pathway of trigonelline (TG), a widespread osmolyte. We provide extensive information about this unusual N-heterocyclic aromatic degradation route that expands the metabolite repertoire. The occurrence of conserved gene clusters for TG dissimilation in soil, plant-associated, and marine bacteria underlines its environmental abundance. Trigonelline (TG; N-methylnicotinate) is a ubiquitous osmolyte. Although it is known that it can be degraded, the enzymes and metabolites have not been described so far. In this work, we challenged the laboratory model soil-borne, gram-negative bacterium Acinetobacter baylyi ADP1 (ADP1) for its ability to grow on TG and we identified a cluster of catabolic, transporter, and regulatory genes. We dissected the pathway to the level of enzymes and metabolites, and proceeded to in vitro reconstruction of the complete pathway by six purified proteins. The four enzymatic steps that lead from TG to methylamine and succinate are described, and the structures of previously undescribed metabolites are provided. Unlike many aromatic compounds that undergo hydroxylation prior to ring cleavage, the first step of TG catabolism proceeds through direct cleavage of the C5–C6 bound, catalyzed by a flavin-dependent, two-component oxygenase, which yields (Z)-2-((N-methylformamido)methylene)-5-hydroxy-butyrolactone (MFMB). MFMB is then oxidized into (E)-2-((N-methylformamido) methylene) succinate (MFMS), which is split up by a hydrolase into carbon dioxide, methylamine, formic acid, and succinate semialdehyde (SSA). SSA eventually fuels up the TCA by means of an SSA dehydrogenase, assisted by a Conserved Hypothetical Protein. The cluster is conserved across marine, soil, and plant-associated bacteria. This emphasizes the role of TG as a ubiquitous nutrient for which an efficient microbial catabolic toolbox is available.

Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

Meaning and consequence of the coexistence of competitive hydrogen bond/salt forms on the dissociation orientation of non-covalent complexes

Non-covalent complexes (NCC) between hexose monophosphates (HexP) and arginine (R) were analyzed using ESI MS and MS/MS in negative mode under different (hard, HC and soft, SC) desolvation conditions. High resolution mass spectrometry (HRMS) revealed the presence of different ionic species, namely, homo- and heteromultimers of R and HexP. Deprotonated heterodimers and corresponding sodiated species were enhanced under HC likely due to a decrease in available charge number associated with the reduction of H+/Na+ exchange. The quantum calculations showed that the formation of covalent systems is very little exothermic, therefore, such systems are disfavored. Desolvation dependent CID spectra of deprotonated [(HexP+R)‒H]- complexes demonstrated that they can exist within the hydrogen bond (HB) and salt bridge (SB) forms, yielding either NCC separation or covalent bond cleavages, respectively. Although HB forms are the main species, they cannot survive under HC; therefore, the minor SB forms became detectable. Energy-resolved mass spectrometry (ERMS) experiments revealed diagnostic fragment ions from both SB and HB forms, providing evidence that these isomeric forms are inconvertible. SB formation should result from the ionic interactions of highly acidic group of HexP with strongly basic guanidine group of arginine and thus requires an arginine zwitterion (ZW) form. This was confirmed by quantum calculations. Ion-ion interactions are significantly affected by the presence of sodium cation as demonstrated by the fragmentation patterns of sodiated complex species. Regarding CID data, only SB between protonated amino group of R and deprotonated phosphate group of HexP could be suggested, but the primary amine is not enough basic then, the SB must be fleeting. Nevertheless, the observation of the covalent bond cleavages suggests the presence of structures with a free negative charge able to induce fragmentations. Indeed, according to quantum calculations, solvated salt (SS) systems involving Na+/COO- salt solvated by neutral phosphate and negative charge on sugar ring are preferentially formed.