Engineering of enzymes using non-natural amino acids

In enzyme engineering, the main targets for enhancing properties are enzyme activity, stereoselective specificity, stability, substrate range, and the development of unique functions. With the advent of genetic code extension technology, non-natural amino acids (nnAAs) are able to be incorporated into proteins in a site-specific or residue-specific manner, which breaks the limit of 20 natural amino acids for protein engineering. Benefitting from this approach, numerous enzymes have been engineered with nnAAs for improved properties or extended functionality. In the present review, we focus on applications and strategies for using nnAAs in enzyme engineering. Notably, approaches to computational modelling of enzymes with nnAAs are also addressed. Finally, we discuss the bottlenecks that currently need to be addressed in order to realise the broader prospects of this genetic code extension technique.     

Relationships between biological soil crusts,bacterial diversity and abundance,and ecosystem functioning: Insights from a semi‐arid Mediterranean environment

Questions: To what degree do biological soil crusts (BSCs), which are regulators of the soil surface boundary, influence associated microbial communities? Are these associations important to ecosystem functioning in a Mediterranean semi‐arid environment? Location: Gypsum outcrops near Belmonte del Tajo, Central Spain. Methods: We sampled a total of 45 (50 cm × 50 cm) plots, where we estimated the cover of every lichen and BSC‐forming lichen species. We also collected soil samples to estimate bacterial species richness and abundance, and to assess different surrogates of ecosystem functioning. We used path analysis to evaluate the relationships between the richness/abundance of above‐ and below‐ground species and ecosystem functioning. Results: We found that the greatest direct effect upon the ecosystem function matrix was that of the biological soil crust (BSC) richness matrix. A few bacterial species were sensitive to the lichen community, with a disproportionate effect of Collema crispum and Toninia sedifolia compared to their low abundance and frequency. The lichens Fulgensia subbracteata and Toninia spp. also had negative effects on bacteria, while Diploschistes diacapsis consistently affected sensitive bacteria, sometimes positively. Despite these results, very few of the BSC effects on ecosystem function could be ascribed to changes within the bacterial community. Conclusion: Our results suggest the primary importance of the richness of BSC‐forming lichens as drivers of small‐scale changes in ecosystem functioning. This study provides valuable insights on semi‐arid ecosystems where plant cover is spatially discontinuous and ecosystem function in plant interspaces is regulated largely by BSCs.     

保护性耕作对紫色水稻土团聚体组成和有机碳储量的影响

通过长期定位试验,研究了保护性耕作对四川盆地紫色水稻土耕层团聚体组成和有机碳储量的影响.结果表明,保护性耕作显著影响耕层团聚体组成及其有机碳含量.油菜免耕、厢作免耕、绿肥免耕、垄作翻耕和厢作翻耕0～10 cm土壤大团聚体分别比对照(12%)增加23%、69%、9%、36%和28%,而10～20 cm土壤大团聚体比对照低9%～38%.冬水免耕、油菜免耕和绿肥免耕0～10 cm土壤大团聚体中有机碳含量分别比对照增加13%、31%和32%,而10～20 cm土壤各处理有机碳含量低于对照28%～54%,其土壤大团聚体和微团聚体中碳浓度差异低于0～10cm土壤.各处理0～10 cm土壤总有机碳储量比对照增加8%～28%,而10～20 cm土壤总有机碳储量低于对照4%～22%.传统耕作转变为保护性耕作13年后0～10和10～20 cm土壤有机碳固定率分别为53和25 g·m^-2·a^-1,传统耕作有机碳固定率分别为26和33 g·m^-2·a^-1.保护性耕作有利于紫色水稻土表层大团聚体的形成和土壤总有机碳储量的提高.     

Immobilized Enzyme Three-Phase Reactors for Oxidation of Cephalosporin C

The enzymatic oxidation of Cephalosporin C (CEPHC) was catalyzed by D-aminoacid oxidase, from the red yeast Trigonopsis variabilis, immobilized on Duolite A365. The study was performed in two different three phase bioreactors, gas-liquid-solid (immobilized enzyme): the fluidized-bed batch reactor, fed continuously with oxygen and discontinuously with CEPHC, and the UF-membrane reactor continuously fed with both substrates. Only the first reactor allowed significant product yield (>70%) while the second was a very useful tool for laboratory investigation of both bioconversion kinetics and enzyme stability.

Optimum reaction temperature was 15d`C for the control of CEPHC spontaneous degradation (roughly 15% in 30 h), and enzyme deactivation (half-life greater than 30 h). Immobilization improved (one order of magnitude longer half-life) enzyme resistance to mechanical stresses induced by liquid stirring and gas bubbling. Roughly 0.04g of CEPHC was adsorbed per gram of enzyme carrier. The limiting step in oxygen transfer was the gas to liquid transport. In order to attain kinetic control of the bioconversion the mildest conditions were atmospheric gas pressure and oxygen flow rate equal to 2 × 10 ²NmL/s per mL of liquid phase.     

Properties of L-arabinose isomerase from Escherichia coli as biocatalyst for tagatose production

L-arabinose isomerase (EC 5.3.1.4) mediates the isomerization of D-galactose into D-tagatose as well as the conversion of L-arabinose into L-ribulose. To investigate the properties of L-arabinose isomerase as a biocatalyst for the conversion of galactose to tagatose, the L-arabinose isomerase of Escherichia coli was characterized. The substrate specificity for L-arabinose was 166-fold higher than that for D-galactose. The optimal pH and temperature for the galactose isomerization reaction were 8.0 and 30 °C, respectively. The enzyme activity was stable for 1 h at temperatures below 35 °C and within a pH range of 8–10. The Michaelis constant, K _m, for galactose was 1480 mM, which is 25-fold higher than that for arabinose. The addition of Fe²⁺ and Mn²⁺ ions enhanced the conversion of galactose to tagatose, whereas the addition of Cu²⁺, Zn²⁺, Hg²⁺, and Fe³⁺ ions inhibited the reaction completely. In the presence of 1 mM Fe²⁺ ions, the K _m for galactose was found to be 300 mM.     

微生物来源的尿酸氧化酶的研究进展及应用前景

尿酸氧化酶是一种重要的医药用酶,它催化嘌呤代谢途径中的尿酸氧化生成尿囊素和过氧化氢,因而被广泛用于治疗痛风,检测血液尿酸浓度,预防和治疗由于肿瘤化学治疗引起的高尿酸血症。综述了尿酸氧化酶的来源、酶学性质、基因克隆与表达及其用途,并对其在应用中存在的问题和前景作了展望。     

Multi-point enzyme immobilization,surface chemistry,and novel platforms: a paradigm shift in biocatalyst design

Engineering enzymes with improved catalytic properties in non-natural environments have been concerned with their diverse industrial and biotechnological applications. Immobilization represents a promising but straightforward route, and immobilized biocatalysts often display higher activities and stabilities compared to free enzymes. Owing to their unique physicochemical characteristics, including the high-specific surface area, exceptional chemical, electrical, and mechanical properties, efficient enzyme loading, and multivalent functionalization, nano-based materials are postulated as suitable carriers for biomolecules or enzyme immobilization. Enzymes immobilized on nanomaterial-based supports are more robust, stable, and recoverable than their pristine counterparts, and are even used for continuous catalytic processes. Furthermore, the unique intrinsic properties of nanomaterials, particularly nanoparticles, also confer the immobilized enzymes to be used for their broader applications. Herein, an effort has been made to present novel potentialities of multi-point enzyme immobilization in the current biotechnological sector. Various nano-based platforms for enzyme/biomolecule immobilization are discussed in the second part of the review. In summary, recent developments in the use of nanomaterials as new carriers to construct robust nano-biocatalytic systems are reviewed, and future trends are pointed out in this article.     

Inactivation of de novo DNA methyltransferase activity by high concentrations of double-stranded DNA

The activity of eukaryotic DNA methyltransferase diminishes with time when the enzyme is incubated with high concentrations (200–300 μg/ml) of unmethylated double-stranded Micrococcus luteus DNA. Under similar conditions, single-stranded DNA induces only a limited decrease of enzyme activity. The inactivation process is apparently due to a slowly progressive interaction of the enzyme with double-stranded DNA that is independent of the presence of S-adenosyl-l-methionine. The inhibited enzyme cannot be reactivated either by high salt dissociation of the DNA-enzyme complex or by extensive digestion of the DNA. Among synthetic polydeoxyribonucleotides both poly(dG-dC) · poly(dG-dC) and poly(dA-dT) · poly(dA-dT), but not poly(dI-dC) · poly(dI-dC), cause inactivation of DNA methyltransferase. This inactivation process may be of interest in regulating the ‘de novo’ activity of the enzyme.     

Desert soil fungi isolated from Saudi Arabia: cultivable fungal community and biochemical production

Desert soils harbor fungi that have survived under highly stressed conditions of high temperature and little available moisture. This study was designed to survey the communities of cultivable fungi in the desert soils of the Arabian Peninsula and to screen the fungi for the potentially valuable antioxidants (flavonoids, phenols, saponins, steroids, tannins, terpenoids, and alkaloids) and enzymes (cellulase, laccase, lipase, protease, amylase, and chitinase). Desert soil was sampled at 30 localities representing different areas of Saudi Arabia and studied for physico-chemical soil properties. Five types of soil texture (sand, loamy sand, sandy loam, silty loam, and sandy clay loam) were observed. A total of 25 saprotrophic species was identified molecularly from 68 isolates. Our survey revealed 13 culturable fungal species that have not been reported previously from Arabian desert soils and six more species not reported from Saudi Arabian desert soils. The most commonly recorded genera were Aspergillus (isolated from 20 localities) and Penicillium (6 localities). The measurements of biochemicals revealed that antioxidants were produced by 49 and enzymes by 52 isolates; only six isolates did not produce any biochemicals. The highest biochemical activity was observed for the isolates Fusarium brachygibbosum and A. phoenicis. Other active isolates were A. proliferans and P. chrysogenum. The same species, for instance, A. niger had isolates of both high and low biochemical activities. Principal component analysis gave a tentative indication of a relationship between the biochemical activity of fungi isolated from soil and soil texture variables namely the content of silt, clay and sand. However, any generalizable relation between soil properties and fungal biochemical activities cannot be suggested. Each fungal isolate is probable to produce several antioxidants and enzymes, as shown by the correlation within the compound groups. Desert soil warrants further research as a promising source of biochemicals.