Directed Evolution of Enzymes for Biocatalytic Applications

Directed molecular evolution is a rapidly growing field revolutionizing the development of biocatalysts with improved properties. This review describes methods to create mutant libraries and assays for rapid screening or selection of desired variants. Selected examples emphasizing the evolution of enzymes for applications in biocatalysis show that it is possible to alter substrate specificity, modulate enantioselectivity and increase enzyme performance under process conditions.     

Directed enzyme evolution

Laboratory evolutionists continue to generate better enzymes for industrial and research applications. Exciting developments include new biocatalysts for enantioselective carbon-carbon bond formation and fatty acid production in plants. Creative contributions to the repertoire of evolutionary methods will ensure further growth in applications and expand the scope and complexity of biological design problems that can be addressed. Researchers are also starting to elucidate mechanisms of enzyme adaptation and natural evolution by testing evolutionary scenarios in the laboratory.     

Directed Evolution of the Epoxide Hydrolase from Aspergillus niger

An efficient and genetically stable expression system for the directed evolution of epoxide hydrolase from Aspergillus niger (ANEH) has been constructed. Error prone polymerase chain reaction (PCR) with defined mutation rates was used to create biodiversity in two libraries of mutants. Screening for activity allowed the isolation of clones with improved properties. One of these clones shows an expression level 3.4 higher than the original wild type clone in E. coli SG13009 and a 3.3 fold increased catalytic efficiency on 4-(p-nitrophenoxy)-1,2-epoxybutane. In addition, a screening assay for determining the enantioselectivity in the kinetic resolution of styrene oxide has been established using mass spectrometry.     

Directed Evolution of the Epoxide Hydrolase from Aspergillus niger

An efficient and genetically stable expression system for the directed evolution of epoxide hydrolase from Aspergillus niger (ANEH) has been constructed. Error prone polymerase chain reaction (PCR) with defined mutation rates was used to create biodiversity in two libraries of mutants. Screening for activity allowed the isolation of clones with improved properties. One of these clones shows an expression level 3.4 higher than the original wild type clone in E.?coli SG13009 and a 3.3 fold increased catalytic efficiency on 4-(p-nitrophenoxy)-1,2-epoxybutane. In addition, a screening assay for determining the enantioselectivity in the kinetic resolution of styrene oxide has been established using mass spectrometry.     

Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily

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蛋白质定向进化的研究技术及应用

蛋白质定向进化是在人类改造蛋白质的过程中产生的。蛋白质定向进化通常分三步进行,即随机诱变、体外重组和筛选。每一步都有多种研究技术。蛋白质定向进化大大加速了人类改造蛋白质的步伐,在实际应用研究和基础理论研究中都具有重要意义。     

甲壳素酶Chisb的定向进化及生物转化合成几丁寡糖

甲壳素酶具有广泛的工业应用前景,如可将虾壳、蟹壳和其他甲壳废物降解成以几丁寡糖为主的高附加值产品,但野生型甲壳素酶催化效率低,大大限制了几丁寡糖的生产。笔者在前期研究中表达了一个具有较高效催化效率的甲壳素酶Chisb,并对其酶学性质进行了初步研究。为进一步提高甲壳素酶Chisb的催化效率,以R13NprB-C-SP-H为亲本,采用易错PCR(Error-pronePCR)技术构建随机突变体文库,对甲壳素酶Chisb进行定向进化。经过96孔板初筛和摇瓶复筛,获得了两个催化效率进一步提高的突变体C43D和E336R。对突变体的酶学性质进行分析, C43D和E336R的最适催化温度为55℃, C43D的最适pH为5.0,E336R的最适pH为9.0;其催化效率相比对照分别提高了1.35倍和1.57倍;而E336R和C43D催化产几丁寡糖的含量分别为2.53 g/L和2.06 g/L,相比对照(0.89 g/L)分别提高了2.84倍和2.31倍;底物转化率分别为84.3%和68.7%,相比对照(29.7%)分别提高了54.6%和39%。研究表明,通过易错PCR引入随机突变的方法能够有效提高甲壳素酶Chisb的催化效率。上述研究获得的催化效率提高的正向突变体及其酶学性质分析对生物转化合成几丁寡糖具有重要研究意义和应用价值。     

蛋白质定向进化的研究进展

在工业生物催化过程和生物细胞工厂构建方面,蛋白质定向进化被广泛地应用于酶的分子改造.蛋白质定向进化不仅可以针对某一目的蛋白进行改造,还可以改善代谢途径、优化代谢网络、获得期望表型细胞.为了获得更高效的突变效率,快捷、高通量的筛选方法,提高蛋白质定向进化的效果,研究者不断开发蛋白质体内、体外进化方法,取得了新的进展和应用.本文介绍了最近发展的蛋白质定向进化技术的原理、方法及特点,总结了突变文库的筛选方法和蛋白质定向进化的最新应用,最后讨论了蛋白质定向进化存在的挑战和未来发展方向.     

A New Screening Method for the Directed Evolution of Thermostable Bacteriolytic Enzymes

Directed evolution is defined as a method to harness natural selection in order to engineer proteins to acquire particular properties that are not associated with the protein in nature. Literature has provided numerous examples regarding the implementation of directed evolution to successfully alter molecular specificity and catalysis¹. The primary advantage of utilizing directed evolution instead of more rational-based approaches for molecular engineering relates to the volume and diversity of variants that can be screened². One possible application of directed evolution involves improving structural stability of bacteriolytic enzymes, such as endolysins. Bacteriophage encode and express endolysins to hydrolyze a critical covalent bond in the peptidoglycan (i.e. cell wall) of bacteria, resulting in host cell lysis and liberation of progeny virions. Notably, these enzymes possess the ability to extrinsically induce lysis to susceptible bacteria in the absence of phage and furthermore have been validated both in vitro and in vivo for their therapeutic potential^3-5. The subject of our directed evolution study involves the PlyC endolysin, which is composed of PlyCA and PlyCB subunits⁶. When purified and added extrinsically, the PlyC holoenzyme lyses group A streptococci (GAS) as well as other streptococcal groups in a matter of seconds and furthermore has been validated in vivo against GAS⁷. Significantly, monitoring residual enzyme kinetics after elevated temperature incubation provides distinct evidence that PlyC loses lytic activity abruptly at 45 °C, suggesting a short therapeutic shelf life, which may limit additional development of this enzyme. Further studies reveal the lack of thermal stability is only observed for the PlyCA subunit, whereas the PlyCB subunit is stable up to ~90 °C (unpublished observation). In addition to PlyC, there are several examples in literature that describe the thermolabile nature of endolysins. For example, the Staphylococcus aureus endolysin LysK and Streptococcus pneumoniae endolysins Cpl-1 and Pal lose activity spontaneously at 42 °C, 43.5 °C and 50.2 °C, respectively^8-10. According to the Arrhenius equation, which relates the rate of a chemical reaction to the temperature present in the particular system, an increase in thermostability will correlate with an increase in shelf life expectancy¹¹. Toward this end, directed evolution has been shown to be a useful tool for altering the thermal activity of various molecules in nature, but never has this particular technology been exploited successfully for the study of bacteriolytic enzymes. Likewise, successful accounts of progressing the structural stability of this particular class of antimicrobials altogether are nonexistent. In this video, we employ a novel methodology that uses an error-prone DNA polymerase followed by an optimized screening process using a 96 well microtiter plate format to identify mutations to the PlyCA subunit of the PlyC streptococcal endolysin that correlate to an increase in enzyme kinetic stability (Figure 1). Results after just one round of random mutagenesis suggest the methodology is generating PlyC variants that retain more than twice the residual activity when compared to wild-type (WT) PlyC after elevated temperature treatment.     

改进酶稳定性的定向进化技术

酶作为一种生物催化剂,以其独特的优良特性,在绿色化学和清洁生产中得到了广泛的应用。随着酶定向进化技术的建立和发展,通过定向进化改进酶稳定性的研究越来越多。详细综述了各种定向进化方法的特点及在提高酶稳定性方面的应用,并从结构和功能的角度进一步解释了相关机理。     

蛋白质定向进化技术的研究进展

蛋白质定向进化技术是蛋白质分子改造的一个重要策略.重点介绍了易错PCR、DNA改组等对编码蛋白质的基因进行随机突变和重组的技术,以及构建突变体库和高通量筛选的方法,并探讨了定向进化技术在蛋白质工程中的应用及前景.     

蛋白质定向进化及其在微生物代谢调控中的应用

蛋白质定向进化是非理性改造蛋白质的一种有效方法。利用蛋白质定向进化技术可以改变代谢流,扩展或构建新的代谢途径,弱化或消除不必要或有害的代谢途径,从而达到提高某种代谢产物产率或降解有害物质的目的。蛋白质定向进化技术在代谢调控中的应用有效拓宽了代谢工程的应用范围。本文介绍了主要的蛋白质定向进化技术如易错PCR技术、DNA改组技术、交错延伸技术和临时模板随机嵌合技术等,评述了蛋白质定向进化技术对微生物细胞代谢中的关键蛋白进行定向改造,从而改善其代谢能力,调控微生物代谢等的应用。     

Directed polymerase evolution

Polymerases evolved in nature to synthesize DNA and RNA, and they underlie the storage and flow of genetic information in all cells. The availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. To circumvent these limitations, researchers have turned to directed evolution to tailor the properties and/or substrate repertoire of polymerases for different applications, and several systems have been developed for this purpose. These systems draw on different methods of creating a pool of randomly mutated polymerases and are differentiated by the process used to isolate the most fit members. A variety of polymerases have been evolved, providing new or improved functionality, as well as interesting new insight into the factors governing activity.     

DNA改组技术在水蛭素实验进化中的应用

蛋白质的改造是生物工程的重大研究课题.由于结构和功能预测的不精确性,而使按照三维结构信息进行定位诱变往往达不到预期的目的.近年来,另一条改造蛋白质的途径有较大的发展,即在实验室条件下模拟生物分子的自然进化,通过变异和靶功能的选择来获得改进性能的蛋白质[1],此过程称为生物分子实验定向进化.DNA改组(DNAshuffling)是一种改造基因和蛋白质的有效实验进化技术[2].它是在体外进行基因随机片段的重组,从而增加基因的多样性,促使有利变异与不利变异分离,通过选择使有利变异得到优化组合[3].DNA改组包含3个步骤:基因的随机片段化,自身引发PCR和重组合PCR.经过DNA改组的突变体库有可能选择到性能更优的突变体.为进行亲和淘选,需将突变体展示在噬菌体的表面[4].     

大肠杆菌碱性磷酸酶的体外定向进化研究

大肠杆菌碱性磷酸酶（E.coli alkaline phosphatase, EAP, EC 3.1.3.1）是一个非特异性二聚体磷酸单酯酶. 采用易错聚合酶链反应(error prone PCR)的方法,在原有高活力突变株的基础上,对EAP远离活性中心催化三联体的区域进行定向进化,经两轮error prone PCR,获得催化活力较亲本D101S突变株提高3倍、较野生型酶提高35倍的进化酶4-186,并对该酶的催化动力学特征进行了分析. 进化酶基因的DNA测序表明4-186含两个有义氨基酸置换：K167R和S374C,二者既不位于底物结合位点,也不位于酶的金属离子结合位点.     

酶的分子定向进化及其应用

酶的分子定向进化是20世纪90年代初兴起的一种蛋白质工程的新策略,是一种在生物体外模拟自然进化过程的、具有一定目的性的快速改造蛋A质的方法.该方法引起了生物催化技术领域的又一次革命.目前分子定向进化技术已被广泛应用于工业、农业及制药业等的相关领域.本文详细综述了酶的分子定向进化的概念、过程、基本策略及其核心技术,并着重介绍了酶的分子定向进化技术在提高酶的活力、稳定性、底物特异性和对映体选择性等几方面的应用及取得的相关成果.     

微生物酶的分子改性和人工进化的研究进展

运用分子生物学技术对微生物来源的酶进行分子改性和人工进化在过去几年中取得了令人瞩目的进展。本文综述了用于酶分子改性和人工进化的主要分子生物学方法,如易错PCR技术、DNA体外随机拼接技术等及其在酶的分子进化和改性中应用成就。     

Directed Evolution of an Enantioselective Bacillus subtilis Lipase

Chiral compounds are of steadily increasing importance to the chemical industry, in particular for the production of pharmaceuticals. Where do these compounds come from? Apart from natural resources, two synthetic strategies are available: asymmetric chemical catalysis using transition metal catalysts and biocatalysis using enzymes. In the latter case, screening programs have identified a number of enzymes. However, their enantioselectivity is often not high enough for a desired reaction. This problem can be solved by applying directed evolution to create enantioselective enzymes as shown here for a lipase from Bacillus subtilis. The reaction studied was the asymmetric hydrolysis of meso-1,4-diacetoxy-Zcyclopentene with the formation of chiral alcohols which were detected by electrospray ionization mass spectrometry. Iterative cycles of random mutagenesis and screening allowed the identification of several variants with improved enantioselectivities. In parallel, we have started to use X-ray structural data to simulate the Bacillus subtilis lipase A-catalyzed substrate hydrolysis by using quantum mechanical and molecular mechanical calculations. This combined approach should finally enable us to devise more efficient strategies for the directed evolution of enantioselective enzymes.     

基于易错PCR技术的黏质沙雷氏菌脂肪酶基因LipA的定向进化

利用易错PCR技术对黏质沙雷氏菌脂肪酶基因LipA进行定向进化,经过筛选最终获得一个比活力比野生酶提高了425 U/mg的突变体ep1,测序分析ep1有5个氨基酸发生了突变,与野生酶相比ep1的最适pH值由原来的8.5降低为7.5,Tm值提高3℃,Km值由原来的40 mg/mL降低为12.5 mg/mL.对其三维结构进行分析,推测酶学性质的改变可能与处在活性中心右前方双螺旋发卡结构上的158A、和处在下部β卷曲折叠拐角处的S375G的突变有关.