In vivo directed enzyme evolution in nanoliter reactors with antimetabolite selection.

Scoring changes in enzyme or pathway performance by their effect on growth behavior is a widely applied strategy for identifying improved biocatalysts. While in directed evolution this strategy is powerful in removing non-functional catalysts in selections, measuring subtle differences in growth behavior remains difficult at high throughput, as it is difficult to focus metabolic control on only one or a few enzymatic steps over the entire process of growth-based discrimination. Here, we demonstrate successful miniaturization of a growth-based directed enzyme evolution process. For cultivation of library clones we employed optically clear gel-like microcarriers of nanoliter volume (NLRs) as reaction vessels and used fluorescence-assisted particle sorting to estimate the growth behavior of each of the gel-embedded clones in a highly parallelized fashion. We demonstrate that the growth behavior correlates with the desired improvements in enzyme performance and that we can fine-tune selection stringency by including an antimetabolite in the assay. As a model enzyme reaction, we improve the racemization of ornithine, a possible starting block for the large-scale synthesis of sulphostin, by a broad-spectrum amino acid racemase and confirm the discriminatory power by showing that even moderately improved enzyme variants can be readily identified.

Semi-rational engineering of an amino acid racemase that is stabilized in aqueous/organic solvent mixtures.

Enzymes are industrially applied under increasingly diverse environmental conditions that are dictated by the efforts to optimize overall process efficiency. Engineering the operational stability of biocatalysts to enhance their half-lives under the desired process conditions is a widely applied strategy to reduce costs. Here, we present a simple method to enhance enzyme stability in the presence of monophasic aqueous/organic solvent mixtures based on the concept of strengthening the enzyme's surface hydrogen-bond network by exchanging surface-located amino acid residues for arginine. Suitable residues are identified from sequence comparisons with homologous enzymes from thermophilic organisms and combined using a shuffling approach to obtain an enzyme variant with increased stability in monophasic aqueous/organic solvent mixtures. With this approach, we increase the stability of the broad-spectrum amino acid racemase of Pseudomonas putida DSM 3263 eightfold in mixtures with 40% methanol and sixfold in mixtures with 30% acetonitrile.

Exploiting racemases.

Chiral resolutions of racemic mixtures are limited to a theoretical yield of 50 %. This yield can be doubled by integration of a step-wise or continuous racemization of the non-desired enantiomer. Many of the different routes along which the racemization step can be conducted require harsh treatments and are therefore often incompatible with the highly functionalized state of many compounds relevant for the life science industries. Employing enzymatic catalysis for racemization can therefore be highly beneficial. Racemases allow racemization in one reaction step. Most representatives from this group are found in the domain of amino acid or amino acid derivative racemization, with few other examples, notably the racemization of mandelic acid. Corresponding to the importance of enantiospecific conversion of amino acid precursor racemates for the production of enantiopure amino acids, the most important biotechnological use for racemases is the racemization of such precursors. However, alternative uses, in particular for mandelate and amino acid racemases, are emerging. Here, we summarize the natural roles of racemases and their occurrence, the applications, and the biochemistry and engineering of this promising class of biocatalysts.

Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins.

BACKGROUND: Glucose inhibition of gluconeogenic growth suppressor 2 protein (Gis2p) and zinc-finger protein 9 (ZNF9) are conserved yeast and human zinc-finger proteins. The function of yeast Gis2p is unknown, but human ZNF9 has been reported to bind nucleic acids, and mutations in the ZNF9 gene cause the neuromuscular disease myotonic dystrophy type 2. To explore the impact of these proteins on RNA regulation, we undertook a systematic analysis of the RNA targets and of the global implications for gene expression. RESULTS: Hundreds of mRNAs were associated with Gis2p, mainly coding for RNA processing factors, chromatin modifiers and GTPases. Target mRNAs contained stretches of G(A/U)(A/U) trinucleotide repeats located in coding sequences, which are sufficient for binding to both Gis2p and ZNF9, thus implying strong structural conservation. Predicted ZNF9 targets belong to the same functional categories as seen in yeast, indicating functional conservation, which is further supported by complementation of the large cell-size phenotype of gis2 mutants with ZNF9. We further applied a matched-sample proteome-transcriptome analysis suggesting that Gis2p differentially coordinates expression of RNA regulons, primarily by reducing mRNA and protein levels of genes required for ribosome assembly and by selectively up-regulating protein levels of myosins. CONCLUSIONS: This integrated systematic exploration of RNA targets for homologous RNA-binding proteins indicates an unexpectedly high conservation of the RNA-binding properties and of potential targets, thus predicting conserved RNA regulons. We also predict regulation of muscle-specific genes by ZNF9, adding a potential link to the myotonic dystrophy related phenotypes seen in ZNF9 mouse models.