液质联用在多肽及蛋白质定性方面的研究进展

随着液质联用技术的不断发展,液相色谱—质谱联用系统广泛应用于药物分析、食品分析、环境分析等多方面,该技术将液相色谱的高分离能力与质谱强大的结构鉴定功能相结合,具备了高分离度、高灵敏度、高选择性以及提供丰富结构信息等一系列优点。这些优点决定了液相色谱—质谱联用系统将在越来越多地相关领域得到应用,尤其是近年来在生物大分子方面开展了大量研究,结合这些研究对液质联用技术在多肽及蛋白质定性方面进行了系统归纳。     

大肠杆菌BL21(DE3)膜组分相关基因的敲除对重组蛋白胞外分泌的影响

摘要:【目的】探究Escherichia coli BL21(DE3)中膜组分相关的脂多糖合成基因waaF或msbB的敲除对重组蛋白胞外分泌的影响。【方法】运用Red重组技术将E.coli BL21 (DE3)染色体上的基因waaF或msbB敲除,构建敲除菌株E.coli BL21(ΔwaaF)、E.coli BL21(ΔmsbB)。将本实验室保存的带有β-呋喃果糖苷酶(β-fructofuranosidase,β-FFase)、青霉素G 酰化酶(penicillin G acylase,PGA)基因的重组质粒pET-ffase、pET-pga分别转入敲除菌株及出发菌株中,构建工程菌株E.coli BL21(ΔmsbB)/pET-ffase、E.coli BL21(ΔwaaF)/pET-ffase、E.coli BL21(DE3)/pET-ffase、E.coli BL21(ΔmsbB)/pET-pga、E.coli BL21(ΔwaaF)/pET-pga、E.coli BL21(DE3)/pET-pga。最后通过摇瓶发酵研究敲除菌株对β-FFase、PGA胞外分泌的影响。【结果】当诱导表达4 h,以出发菌株E.coli BL21(DE3)为宿主时,β-呋喃果糖苷酶β-FFase的胞外分泌量占总表达量的2.6%,以敲除菌株ΔmsbB为宿主时,胞外分泌量达到19.7%,而以敲除菌株ΔwaaF为宿主时,胞外分泌量达到50.9%。另外,当诱导表达24 h,以敲除菌株ΔwaaF为宿主时,青霉素G酰化酶PGA的胞外酶活是出发菌株中的4.1倍,达到1708 U/L。【结论】本研究成功构建了敲除菌株ΔmsbB和ΔwaaF,ΔmsbB能明显增强β-FFase的胞外分泌,而ΔwaaF对β-FFase和PGA的胞外分泌均有显著的强化作用。     

部分革兰氏阴性菌TonB蛋白的结构特点及作用机制

摘要:在革兰氏阴性菌内,TonB系统对环境中的重要营养物质的摄取至关重要。TonB系统由锚定在内膜的ExbB-ExbD和周质蛋白TonB组成,它为TonB依赖性外膜受体(TBDTs)提供能量,使其转运营养物质。TonB系统普遍参与了铁、血红素、维生素B12、碳水化合物及多种过渡金属元素等多种重要物质的转运过程。TonB蛋白的功能与其特殊的结构密切相关,它的结构包括起固定作用的氨基端结构域、柔韧可变的脯氨酸富集的中间结构域和与TonB依赖性受体相互作用的羧基端结构域。虽然TonB蛋白结构特点较为清晰,但 其精确作用机制尚未被完全揭示。本文综述了革兰氏阴性菌TonB依赖性的营养物质摄取、TonB蛋白的结构特点、作用机制模型及表达调控,以期为进一步研究TonB蛋白功能提供理论基础和参考。     

不同营养方式对普通小球藻生长代谢及生化组分的影响

摘要:【目的】系统研究自养、混养和异养3种营养方式对真核模式微藻———普通小球藻(Chlorella vulgaris)生长特性、细胞生化组分和碳代谢途径关键酶活性的影响。【方法】以C．vulgaris为研究对象,通过设置光合自养、混养和异养3 种营养方式,采用光谱学、色谱学方法,研究不同营养方式对C．vulgaris从生长特性、细胞组分合成和碳代谢等方面的影响。【结果】C．vulgaris依次经自养至混养和异养的培养方式转变中,藻细胞的可溶性糖和油脂含量显著提高,油脂中C16、C18不饱和脂肪酸的相对含量降低,而饱和脂肪酸的含量升高;蛋白质含量、光合色素含量显著下降,18种氨基酸的相对含量也呈下降趋势;葡萄糖的添加可抑制藻细胞吸收和积累除碳元素以外的其他测试元素。在添加葡萄糖的前提下,光照可促进藻细胞的生长量、不饱和脂肪酸和氨基酸,以及除碳元素以外的其他测试参数增加。对微藻胞外碳酸酐酶和核酮糖-1,5-二磷酸 羧化酶的活性分析结果表明,异养和混养直接影响C．vulgaris的碳代谢途径。【结论】光源和葡萄糖的供给与否直接影响C．vulgaris的生长代谢和生化组分合成,葡萄糖的添加在显著促进藻细胞生物量积累的同时,刺激碳素(糖类和油脂)生化成分的合成,而抑制氮素成分(蛋白质和光合色素)的合成;在光照条件下培养基质中葡萄糖的浓度和消耗水平直接决定藻细胞主营自养或异养生长。添加有机碳源葡萄糖的混养(光照)和异养(暗处理)培养可促进藻细胞的生长,异养和自养的生物量之和接近于混养,表明混养是最佳的藻细胞营养生长方式。     

一新中温碱性蛋白酶基因的克隆及原核表达

摘要:【目的】从环境中分离筛选产蛋白酶、降解蛋白质的菌株,寻找使用价值较高的碱性蛋白酶。【方法】通过酪蛋白平板法分离筛选产蛋白酶菌株,经生理生化方法及16S rDNA 基因序列鉴定菌株;利用简并引物及基因组步移克隆蛋白酶完整开放阅读框;蛋白酶前体蛋白及成熟肽序列在大肠杆菌(Escherichia coli) BL21(DE3)中进行重组表达;纯化活性蛋白酶后,利用化学合成多肽底物(succinyl-Ala-Ala-Pro-Phe-p-nitroanilide)检测酶活性质及其催化活力。【结果】分离到的菌株L010被鉴定命名为芽胞杆菌( Bacillus sp.)L010;蛋白酶开放阅读框包含了1149个碱基,编码382个氨基酸,氨基酸序列按其功能分为N端的30个氨基酸残基组成的信号肽,77个氨基酸残基构成的前导肽,C端275个氨基酸残基组成的成熟肽;此蛋白属于丝氨酸蛋白酶家族中枯草杆菌蛋白酶类(Subtilisins)成员,并命名为SprD;SprD的前体蛋白在大肠杆菌(Escherichia coli)BL21(DE3)中重组表达时,在前导肽辅助下自加工为活性蛋白酶;SprD呈现出较高的催化活力,其反应最适条件为温度70℃,pH9－10。【结论】SprD在碱性(pH 7.0－ 10.0)、中高温(25℃－60℃)条件下的稳定性及较高的催化能力使其具有一定的研究和潜在利用价值。     

Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli

The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.     

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli

The 106 small molecule metabolic (SMM) pathways in Escherichia coli are formed by the protein products of 581 genes. We can define 722 domains, nearly all of which are homologous to proteins of known structure, that form all or part of 510 of these proteins. This information allows us to answer general questions on the structural anatomy of the SMM pathway proteins and to trace family relationships and recruitment events within and across pathways. Half the gene products contain a single domain and half are formed by combinations of between two and six domains. The 722 domains belong to one of 213 families that have between one and 51 members. Family members usually conserve their catalytic or cofactor binding properties; substrate recognition is rarely conserved. Of the 213 families, members of only a quarter occur in isolation, i.e. they form single-domain proteins. Most members of the other families combine with domains from just one or two other families and a few more versatile families can combine with several different partners.Excluding isoenzymes, more than twice as many homologues are distributed across pathways as within pathways. However, serial recruitment, with two consecutive enzymes both being recruited to another pathway, is rare and recruitment of three consecutive enzymes is not observed. Only eight of the 106 pathways have a high number of homologues. Homology between consecutive pairs of enzymes with conservation of the main substrate-binding site but change in catalytic mechanism (which would support a simple model of retrograde pathway evolution) occurs only six times in the whole set of enzymes. Most of the domains that form SMM pathways have homologues in non-SMM pathways. Taken together, these results imply a pervasive "mosaic" model for the formation of protein repertoires and pathways.     

Involvement of lactaldehyde dehydrogenase in several metabolic pathways of Escherichia coli K12

Lactaldehyde dehydrogenase (E.C. 1.2.1.22) of Escherichia coli has been purified to homogeneity. It has four apparently equal subunits (molecular weight 55,000 each) and four NAD binding sites per molecule of native enzyme. The enzyme is inducible, only under aerobic conditions, by at least three different types of molecules, the sugars fucose and rhamnose, the diol ethylene glycol and the amino acid glutamate. The enzyme catalyzes the irreversible oxidation of several aldehydes with a Km in the micromolar range for alpha-hydroxyaldehydes (lactaldehyde, glyceraldehyde, or glycolaldehyde) and a higher Km, in the millimolar range, for the alpha-ketoaldehyde methylglyoxal. It displays substrate inhibition with all these substrates. NAD is the preferential cofactor. The functional and structural features of the enzyme indicate that it is not an isozyme of other E. coli aldehyde dehydrogenases such as glyceraldehyde phosphate dehydrogenase, glycolaldehyde dehydrogenase, or acetaldehyde dehydrogenase. The enzyme, previously described as specific for lactaldehyde, is thus identified as a dehydrogenase with a fairly general role in aldehyde oxidation, and it is probably involved in several metabolic pathways.     

A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

Transformation of engineered Escherichia coli into a robust microbial factory is contingent on precise control of metabolism. Yet, the throughput of omics technologies used to characterize cell components has lagged far behind our ability to engineer novel strains. To expand the utility of quantitative proteomics for metabolic engineering, we validated and optimized targeted proteomics methods for over 400 proteins from more than 20 major pathways in E. coli metabolism. Complementing these methods, we constructed a series of synthetic genes to produce concatenated peptides (QconCAT) for absolute quantification of the proteins and made them available through the Addgene plasmid repository (www.addgene.org). To facilitate high sample throughput, we developed a fast, analytical-flow chromatography method using a 5.5-min gradient (10 min total run time). Overall this toolkit provides an invaluable resource for metabolic engineering by increasing sample throughput, minimizing development time and providing peptide standards for absolute quantification of E. coli proteins.