Restriction enzyme-mediated DNA family shuffling

Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy

Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues affecting the optimum pH of Staphylococcal lipases, chimeric lipases from homologous lipases were generated via a DNA shuffling strategy. Chimeric 1 included mutations of G166S, K212E, T243A, H271Y. Chimeric 2 consisted of substitutions of K212E, T243A, H271Y. Chimeric 3 contained substitutions of K212E, R359L. From the screening results, the pH profiles for chimeric 1 and 2 lipases were shifted from pH 7 to 6. While the pH of chimeric 3 was shifted to 8. It seems the mutation of K212E in chimeric 1 and 2 decreased the pH to 6 by changing the electrostatic potential surface. Furthermore, chimeric 3 showed 10 ˚C improvement in the optimum temperature due to the rigidification of the catalytic loop through the hydrophobic interaction network. Moreover, the substrate specificity of chimeric 1 and 2 was increased towards the longer carbon length chains due to the mutation of T243A adjacent to the lid region through increasing the flexibility of the lid. Current study illustrated that directed evolution successfully modified lipase properties including optimum pH, temperature and substrate specificity through mutations, especially near catalytic and lid regions.

GH2 family β-galactosidases evolution using degenerate oligonucleotide gene shuffling

OBJECTIVES

To improve the biochemical characteristics of the GH2 family β-galactosidases using a family shuffling method based on degenerate oligonucleotide gene shuffling.

RESULTS

Four β-galactosidase genes from the genus Alteromonas were divided into 14 gene segments, and each included the homologous sequence in the adjacent segments. The gene segments were regenerated into complete β-galactosidase genes and amplified by PCR. The obtained chimeric genes were cloned into a plasmid and screened for β-galactosidase activity. Approximately 320 positive clones were observed on the screening plate, of which nine sequenced genes were chimera. Additionally, the M22 and M250 mutants were expressed, purified, and characterized. The optimal temperature and substrate specificity of the recombinant M22 and M250 were consistent with those of the wild-type enzymes. The catalytic efficiency of recombinant M22 enzyme was higher than that of the wild-type enzymes, and the recombinant M250 displayed weak transglycosylation activity.

CONCLUSIONS

The chimeric genes of GH2 β-galactosidase were obtained using a controlled family shuffling that will provide an enzyme evolutionary method to obtain the β-galactosidases with excellent characteristics for laboratory and industrial purposes.

Problem of Domain/Building Block Preservation in the Evolution of Biological Macromolecules and Evolutionary Computation

Structurally and functionally isolated domains in biological macromolecular evolution, both natural and artificial, are largely similar to "schemata", building blocks (BBs), in evolutionary computation (EC). The problem of preserving in subsequent evolutionary searches the already found domains / BBs is well known and quite relevant in biology as well as in EC. Both biology and EC are seeing parallel and independent development of several approaches to identifying and preserving previously identified domains / BBs. First, we notice the similarity of DNA shuffling methods in synthetic biology and multi-parent recombination algorithms in EC. Furthermore, approaches to computer identification of domains in proteins that are being developed in biology can be aligned with BB identification methods in EC. Finally, approaches to chimeric protein libraries optimization in biology can be compared to evolutionary search methods based on probabilistic models in EC. We propose to validate the prospects of mutual exchange of ideas and transfer of algorithms and approaches between evolutionary systems biology and EC in these three principal directions. A crucial aim of this transfer is the design of new advanced experimental techniques capable of solving more complex problems of in vitro evolution.

Voltammetric determination of human papillomavirus 16 DNA by using interdigitated electrodes modified with titanium dioxide nanoparticles

A gene sensor for rapid detection of the Human Papillomavirus 16 (HPV 16) which is associated with the appearance of cervical cancer was developed. The assay is based on voltammetric determination of HPV 16 DNA by using interdigitated electrodes modified with titanium dioxide nanoparticles. Titanium dioxide nanoparticles (NPs) were used to modify a semiconductor-based interdigitated electrode (IDE). The surface of the NPs was then functionalized with a commercial 24-mer oligomer DNA probe for HPV 16 that was modified at the 5' end with a carboxyl group. If the probe interacts with the HPV 16 ssDNA, the current, best measured at a working voltage of 1.0 V, increases. The gene sensor has has a ∼ 0.1 fM limit of detection which is comparable to other sensors. The dielectric voltammetry analysis was carried out from 0 V to 1 V. The electrochemical sensitivity of the IDE is 2.5 × 10^-5 μA·μM^-1·cm^-2. Graphical abstract Schematic of an interdigitated electrode (IDE) modified with titanium dioxide nanoparticles for voltammetric determination of HPV 16 DNA by using an appropriate DNA probe.

Directed Evolution of Proteins Based on Mutational Scanning

Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.

DNA shuffling of uricase gene leads to a more "human like" chimeric uricase with increased uricolytic activity

Urate oxidase (Uox) is the enzyme involved in purine metabolism. Pseudogenization of Uox gene is the underlying mechanism of hyperuricemia and gout in human. Although Uox from various microorganisms has been used in clinical practice for many years, its application is limited by potential immunogenicity. In order to develop a more "human like" uricase, DNA shuffling was used to create chimeric uricase with both improved enzymatic activity and increased homology with deduced human uricase (dHU) gene. By using wild porcine uricase (wPU) gene and dhu as parental genes, a diverse chimeric library was generated. After preliminary screening by a "homebrew" high throughput protocol, approximately 100 chimeras with relatively high enzymatic activity were obtained. By further activity comparison of the purified enzymes, chimera-62 with increase in both activity and homology with dHU compared with wPU was selected. Its Km and catalytic efficiency were determined as 9.43±0.04μM and 2.67s(-1)μM(-1) respectively. There were 33 amino acid substitutions in chimera-62 when compared with dHU and 5 substitutions when compared with wPU. By homology modeling and 3-D structure analysis, it was speculated that mutations G248S and L266F contributed to the increased activity of chimera-62 by increasing the stability of α-helix and surface polarity respectively.

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.