过表达carAB和pyrBI对大肠杆菌发酵胞苷的影响

为了考察氨甲酰磷酸合成酶和天冬氨酸氨甲酰转移酶对大肠杆菌发酵生产胞苷的影响,以E. coli A39 (△cdd)基因组为模板克隆carAB和pyrBI并与载体pSTV28连接构建出重组质粒pSTV28-carAB和pSTV28-pyrBI,将这两个重组质粒分别转入出发菌株A39 (△cdd)后,通过摇瓶发酵研究重组质粒对菌体的生长、胞苷和尿苷产量及副产物乙酸积累的影响。结果显示,工程菌E. coli A39-AB和A39-BI的胞苷产量分别为583.5 mg/L、408.4 mg/L,与出发菌株相比,分别提高了85.3%、29.7%。这说明过表达操纵子基因carAB和pyrBI均可促进胞苷的积累。     

嘧啶核苷的研究进展

嘧啶核苷包括尿嘧啶核苷和胞嘧啶核苷,其在食品工业和医药行业上应用广泛。介绍了嘧啶核苷的用途、测定方法、生产方法等;根据代谢控制发酵原理,以尿苷生产菌的选育为例,详细介绍了嘧啶核苷生产菌的育种策略,并对嘧啶核苷生产菌的育种实例、育种展望进行了综述。     

基于转录组学分析大肠杆菌中purR基因缺失对胞苷合成代谢的影响

胞苷可作为功能营养化学品与药物合成原料,具有重要的应用价值。大肠杆菌中由purR基因编码的DNA结合转录抑制因子对胞苷合成代谢有重要调控作用。采用CRISPR/Cas9技术敲除大肠杆菌purR基因,并通过转录组学分析突变菌株基因表达的差异。结果表明,从出发菌株E.coli NXBG-12基因组上成功敲除了purR基因,获得了突变菌株E.coli NXBG-17P。对突变菌株E.coli NXBG-17P与E.coli NXBG-12的转录组学结果进行对比分析,发现有534个差异基因,其中上调基因302个、下调基因232个;GO分析显示,差异表达基因(DEGs)主要富集于细胞膜、ATP结合、DNA结合和水解酶活性的代谢过程;KEGG分析表明,上调基因主要富集在果糖和甘露糖代谢、嘧啶代谢和磷酸转移酶系统,下调基因主要富集在氧化磷酸化、半乳糖代谢和肽聚糖的生物合成。同时,突变菌株E.coli NXBG-17P在37℃摇瓶发酵40 h,测定胞苷浓度为(3.21±0.01) g/L,是出发菌株E.coli NXBG-12的1.58倍。这表明突变菌株E.coli NXBG-17P胞苷产量升高,可能...     

胞苷生产菌的选育

目的：筛选得到胞苷发酵单位较高的菌株,并对发酵过程作初步研究。方法：以胞苷脱氨酶缺失枯草芽孢杆菌DOS7为出发菌株,对其进行紫外诱变、5-氟胞苷（5FCR＋）和2-杂氮尿嘧啶抗性（2AU＋）抗性筛选。结果：通过紫外诱变和抗性筛选得到突变株DOS7-2-1000-15,抗5-氟胞苷和2-杂氮尿嘧啶的临界浓度分别为800mg/L和1 000mg/L。同时检测了抗5-氟胞苷突变株中CTP合成酶的活性,比原始菌株提高了12.4%,突变株DOS7-2-1000-15发酵过程结果为：36℃发酵72h能积累胞苷最高为3.5g/L。结论：筛选得到的突变株DOS7-2-1000-15的遗传稳定性较好,可稳定发酵。     

大肠杆菌色氨酸转运系统多基因敲除对色氨酸生产的影响

大肠杆菌中色氨酸向胞内的转运主要是由mtr、tnaB和aroP 3个基因编码的通透酶进行调控.利用Red重组技术,在mtr单基因敲除菌的基础上,成功构建了mtr.tnaB和mtr.aroP双基因敲除菌以及mtr.tnaB.aroP三基因敲除菌,并通过发酵实验首次考察了色氨酸转运系统多基因缺失对大肠杆菌合成色氨酸的影响.发酵结果表明,mtr.tnaB和mtr.aroP双基因缺失后,色氨酸产量分别达到1.38 g/L和1.27 g/L,与出发菌株相比分别提高了17％和9％,而mtr.tnaB.aroP三基因缺失后,菌体生长受到了明显抑制,发酵后色氨酸产量仅为0.63 g/L.在补料分批发酵实验中,mtr.tnaB双基因敲除菌的色氨酸产量进一步提高至12.2 g/L,与出发菌株相比色氨酸产量提高了27％.     

ccpA基因对蜡样芽胞杆菌氨肽酶生产的影响

【目的】构建蜡样芽胞杆菌(Bacillus cereus)ccp A缺失菌株,并初步探索ccp A基因对其碳代谢及氨肽酶生产的影响。【方法】利用温敏型质粒p KSV7构建蜡样芽胞杆菌CZ ccp A基因缺失突变株CZΔccp A,通过回补菌株对敲除株表型进行验证;不同碳源发酵对比菌株碳代谢的变化,进行氨肽酶发酵优化。【结果】成功构建ccp A缺失菌株CZΔccp A与回补菌株CZ1,三株菌在LB培养基中生长无差异;在柠檬酸钠以及甘露低聚糖为碳源时,菌株的代谢产生明显变化;以D-木糖为单一碳源时,氨肽酶的产量提高48.25%。【结论】CZ ccp A基因对柠檬酸钠、甘露低聚糖、D-木糖为单一碳源时的代谢可能具有调控作用,ccp A基因缺失可以提高蜡样芽胞杆菌CZ的氨肽酶产量。     

解淀粉芽孢杆菌高效合成胞苷的代谢调控机制及育种策略

胞苷是合成抗病毒、抗肿瘤药物的良好中间体,也是核苷酸类保健食品和功能性食品的重要原料。主要论述了解淀粉芽孢杆菌高效合成胞苷的代谢调控机制和构建胞苷高产菌株的育种策略。重点阐述了通过提高解淀粉芽孢杆菌嘧啶操纵子转录水平,增强胞苷合成代谢途径、阻断胞苷降解途径、增大磷酸戊糖途径向胞苷合成途径的分流量、提高胞苷合成前端代谢物PRPP的合成量、增强中心碳代谢流向胞苷合成途径、减少旁路代谢途径及促进胞苷的分泌等方法,选育出胞苷高产菌株,不仅为胞苷高产菌株的选育提供参考,也为解决目前胞苷工业化生产中存在的问题提供思路。     

比较pta及ack敲除对钝齿棒杆菌产L-精氨酸生理代谢的影响

旁支代谢途径的截断有利于目的氨基酸合成途径的集流。基于基因组尺度代谢网络模型的预测,以钝齿棒杆菌(Corynebacterium crenatum)MT-M4为出发菌株,通过无痕敲除技术分别敲除了编码磷酸乙酰基转移酶的pta基因及编码乙酸激酶的ack基因,阻断了乙酸的合成。摇瓶发酵结果表明,pta缺失菌株精氨酸产量较出发菌株提高了25.60%,达15.46g/L。葡萄糖转化率提高了29.41%;ack缺失菌株精氨酸产量达13.82g/L,较出发菌株提高了12.81%,葡萄糖转化率提高了26.02%。同时,pta及ack敲除菌株的细胞生长较出发菌株均分别提高了9.19%及7.71%。因此,pta、ack的敲除不仅有利于精氨酸的合成,而且对菌体生长具有促进作用;但pta的敲除更有利于精氨酸的积累。     

代谢工程方法改造大肠杆菌生产胸苷

胸苷是抗艾滋病药物司他夫定(3′-脱氧-2′,3′-双脱氢胸苷)和叠氮胸苷的重要前体物质。应用代谢工程方法对大肠杆菌Escherichia coli BL21(DE3)生物合成胸苷进行了研究。通过敲除E.coli BL21嘧啶回补途径的deo A、tdk和udp三个基因,BS03工程菌株能够积累21.6 mg/L胸苷。为了增加合成胸苷前体物核糖-5-磷酸和NADPH的供给,进一步敲除pgi和pyr L使工程菌BS05胸苷的产量提高到90.5 mg/L。而通过过表达胸苷合成途径的ush A、thy A、dut、ndk、nrd A和nrd B六个基因,菌株BS08胸苷的产量能达到272 mg/L。通过分批补料发酵,BS08最终可以积累1 248.8 mg/L的胸苷。本研究结果表明经过代谢工程改造的E.coli BL21具有良好的胸苷合成能力和应用潜力。     

酿酒酵母adh2和ald6双基因缺失突变株的构建

酿酒酵母乙醇合成代谢过程中, 阻断或削弱乙醛至乙酸代谢流不但能增强乙醇合成流, 同时还能降低发酵乙酸含量。本研究以乙醇脱氢酶Ⅱ(adh2)基因缺陷型酿酒酵母YS2-Dadh2为出发菌株, 应用长侧翼同源两步PCR(LFH-PCR)策略构建乙醛脱氢酶Ⅵ(ald6)基因敲除组件, 转化酿酒酵母YS2-Dadh2敲除ald6基因, 之后转入表达质粒pSH65到阳性克隆中, 半乳糖诱导表达Cre重组酶切除Kanr基因筛选标记, 最后, 传代丢失质粒pSH65获得单倍体ald6基因缺失突变株。利用同样的敲除组件和技术再次敲除其等位基因, 最终获得双基因缺失突变株YS2-△adh2-Dald6。发酵实验表明与出发菌株YS2相比, 突变株乙酸合成量降低18%, 乙醇最高产量提高12.5%。     

枯草芽孢杆菌产胞苷的初步研究

目的:通过对野生型枯草芽孢杆菌NO122的诱变筛选,选育出胞苷产生菌株。方法:以野生型枯草芽孢杆菌为出发菌株进行紫外线、硫酸二乙酯诱变,经3-脱杂氮尿嘧啶、5-氟胞苷结构类似物平板定向筛选产胞苷突变株;研究碳源、氮源、温度、初始pH值等发酵条件对该突变菌株产胞苷的影响。结果:经诱变传代后得到突变株TZM1012,该突变株在发酵温度37℃、初始pH7.2、摇床转速220r/min的条件下,摇瓶发酵72h,发酵液中的胞苷可达1.873g/L,并具有较好的遗传稳定性。结论:获得产胞苷生产菌株,并具有较好的遗传稳定性。     

Arabidopsis thaliana cytidine deaminase 1 shows more similarity to prokaryotic enzymes than to eukaryotic enzymes

Two Expressed Sequence Tagged (EST) clones were identified from the Arabidopsis database as encoding putative cytidine deaminases. Sequence analysis determined that the two clones overlapped and encoded a single cDNA. This cytidine deaminase corresponds to theArabidopsis thaliana gene,cda1. The deduced amino acid sequence was more closely related to prokaryotic cytidine deaminases than to eukaryotic enzymes. The cDNA shares 44% amino acid identity with theEscherichia coli cytidine deaminase but only 26 and 27% identity with human and yeast enzymes. A unique zinc-binding domain of the Ecoli enzyme forms the active site. A similar putative zinc-binding domain was identified in the Arabidopsis enzyme based upon primary sequence similarities. These similarities permitted us to model the active site of the Arabidopsis enzyme upon that of the Ecoli enzyme. In this model, the active site zinc is coordinated by His⁷³, Cys¹⁰³, Cys¹⁰⁷, and an active site hydroxyl. Additional residues that participate in catalysis, Asn⁶⁴, Glu⁶⁶, Ala⁷⁸, Glu⁷⁹, and Pro¹⁰², are conserved between the Arabidopsis and Ecoli enzymes suggesting that the Arabidopsis enzyme has a catalytic mechanism similar to the Ecoli enzyme. The two overlapping ESTs were used to prepare a single, full-length clone corresponding to theA thaliana cda1 cDNA. This cDNA was subcloned into pProExHtb and expressed as a fusion protein with an N-terminal His₆ tag. Following purification on a Ni-NTA-Agarose column, the protein was analyzed for its kinetic properties. The enzyme utilizes both cytidine (K_m = 226 μand 2’-deoxycytidine (K_m= 49 μM) as substrates. The enzyme was unable to deaminate cytosine, CMP or dCMP. journal Paper Number J-18324 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa Project No. 3340.     

Screening the Fusarium graminearum inhibitory mutant strain from Bacillus subtilis by atmospheric-pressure plasma jet

Aims:  The aim of this study was to improve the antagonistic activity of Bacillus subtilis JA towards Fusarium graminearum by screening high-yielding mutant using the atmospheric-pressure plasma jet (APPJ).
Methods and Results:  Atmospheric-pressure plasma jet was applied as mutagenic source for breeding high-yielding mutant strain. Helium was used as APPJ operating gas. The mutation effects of different treatment times of APPJ were studied. The mutant strain designated as B. subtilis B06 was successfully screened out, which showed higher antagonistic activity against F. graminearum in vitro . Its inhibition zone against the indicator fungus increased by 23% compared to the original one. HPLC and ESI (electrospray ionization) mass spectrometry analysis indicated that antifungal compounds produced by the mutant and original strain belonged to the lipopeptide, surfactin and iturin families. The mutant strain showed favourable properties of faster growth in the fermentation process and higher production of antibiotics. The lipopeptide production of the mutant was 2·3-fold as that of the original strain.
Conclusions:  A mutant strain with strong antagonistic activity and high yielding of antibiotics was obtained by APPJ in this study. The mutant could be used as a promising biocontrol agent in agriculture.
Significance and Impact of Study:  This study provides a novel mutagenic source for breeding high-yielding microbial mutant, which would be very useful in the application of some valuable metabolites from micro-organism.     

Genetic mapping in Bacillus subtilis 168 of the aadK gene which encodes aminoglycoside 6-adenylyltransferase

Abstract Bacillus subtilis 168 has an aadK gene, which encodes aminoglycoside 6-adenylyltransferase, a streptomycin-modifying enzyme, on its chromosome. To characterize the aadK gene, we con tructed a B. subtilis 168 strain that carried the chloramphenicol resistance gene near the aadK on the chromosome and an aadK deletion mutant using an integration technique. The aadK gene was mapped between azlB and pheA on the chromosome of B. subtilis 168. The aadK deletion mutant was slightly more susceptible to streptomycin than the original strain. The result indicates that the aadK gene contributes low-level resistance to streptomycin in B. subtilis 168.     

Cytidine deamination assay to differentiate Staphylococcus aureus from other staphylococci

AIMS: Adoption of the property of cytidine (cytosine-beta-d-riboside) deamination in staphylococci to distinguish Staphylococcus aureus from other staphylococci. METHODS AND RESULTS: A total of 560 staphylococcal strains were examined. The test demonstrated a sensitivity of 97.1% and a specificity of 98.8%. Of the 249 S. aureus strains (115 oxacillin-resistant) 58 strains were coagulase-negative S. aureus and another 16 strains were clumping factor-negative S. aureus. The 74 deficient S. aureus strains were identified by 16S rRNA gene sequencing and further investigated by spa typing and 13 spa types were found. CONCLUSIONS: The cytidine deaminase test (CDT) is useful especially for distinguishing coagulase- and clumping factor-negative S. aureus from other staphylococci and the results correlated well with 16S rRNA sequencing and the polymerase chain reaction (PCR) amplification of the nuc gene. SIGNIFICANCE AND IMPACT OF THE STUDY: Cytidine deamination assay differentiates S. aureus from other staphylococci. This method is fast (6 h) and reliable in distinguishing between non-S. aureus and the defective (coagulase-negative, clumping factor-negative) S. aureus isolates which could have major consequences for therapy.     

Modulation of human cytidine deaminase by specific aminoacids involved in the intersubunit interactions

An investigation was made of the role exerted by some residues supposed to be involved in the intersubunit interaction and also in the catalytic site of homotetrameric human cytidine deaminase (T-CDA). Attention was focused on Y33, Y60, R68, and F137 residues that are a part of a conserved region in most T-CDAs. Hence, a series of site-directed mutagenesis experiments was set up obtaining seven mutants: Y60G, Y33G, Y33F Y33S, F137A, R68G, and R68Q. Each active purified mutant protein was characterized kinetically, with a series of substrates and inhibitors, and the effect of temperature on enzyme activity and stability was also investigated. Circular dichroism (CD) experiments at different temperatures and in presence of small amounts of sodium dodecyl sulphate (SDS) were performed in all the soluble mutant CDAs. The results obtained by site-directed mutagenesis studies were compared to the crystallographic data of B. subtilis CDA and E. coli CDA and to molecular modeling studies previously performed on human CDA. The mutation of Y60 to glycine produced an enzyme with a more compact quaternary structure with respect to the wild-type; this mutation did not have a dramatic effect on cytidine deamination, but it slightly affected the binding with the substrate. None of the mutant CDAs in Y33 showed enzymatic activity; they existed only as monomers, indicating that this residue, located at the intersubunit interface, may be responsible for the correct folding of human CDA. The insertion of an alanine instead of phenylalanine at position 137 led to a soluble but completely inactive enzyme unable to form a tetramer, suggesting that F137 residue may be important for the assembling of the tetramer and also for the arrangement of the CDA active site. Finally, R68G and R68Q mutations revealed that the presence of the amino group seems to be important for the catalytic process but not for substrate binding, as already shown in B. subtilis CDA. The quaternary structure of R68Q was not affected by the mutation, as shown by the SDS-induced dissociation experiments and CD studies, whereas R68G dissociated very easily in presence of small amounts of SDS. These experiments indicated that in the human CDA, the side chain of arginine 68 involved in the catalytic process in one subunit active site might come from another subunit. The data obtained from these studies confirmed the presence of a complicated set of intersubunit interactions in the active site of human CDA, as shown in other T-CDAs.     

Multiplex Gene Disruption by Targeted Base Editing of Yarrowia lipolytica Genome Using Cytidine Deaminase Combined with the CRISPR/Cas9 System

The oleaginous yeast Yarrowia lipolytica has a tendency to use the non‐homologous end joining repair (NHEJ) over the homology directed recombination as double‐strand breaks (DSB) repair system, making it difficult to edit the genome using homologous recombination. A recently developed Target‐AID (activation‐induced cytidine deaminase) base editor, designed to recruit cytidine deaminase (CDA) to the target DNA locus via the CRISPR/Cas9 system, can directly induce C to T mutation without DSB and donor DNA. In this study, this system is adopted in Y. lipolytica for multiplex gene disruption. Target‐specific gRNA(s) and a fusion protein consisting of a nickase Cas9, pmCDA1, and uracil DNA glycosylase inhibitor are expressed from a single plasmid to disrupt target genes by introducing a stop codon via C to T mutation within the mutational window. Deletion of the KU70 gene involved in the NHEJ prevents the generation of indels by base excision repair following cytidine deamination, increasing the accuracy of genome editing. Using this Target‐AID system with optimized expression levels of the base editor, single gene disruption and simultaneous double gene disruption are achieved with the efficiencies up to 94% and 31%, respectively, demonstrating this base editing system as a convenient genome editing tool in Y. lipolytica.     

Affinity maturation of anti-TNF-alpha scFv with somatic hypermutation in non-B cells

Activation-induced cytidine deaminase (AID) is required for the generation of antibody diversity through initiating both somatic hypermutation (SHM) and class switch recombination. A few research groups have successfully used the feature of AID for generating mutant libraries in directed evolution of target proteins in B cells in vitro. B cells, cultured in suspension, are not convenient for transfection and cloning. In this study, we established an AID-based mutant accumulation and sorting system in adherent human cells. Mouse AID gene was first transfected into the human non-small cell lung carcinoma H1299 cells, and a stable cell clone (H1299-AID) was selected. Afterwards, anti-hTNF-αscFv (ATscFv) was transfected into H1299-AID cells and ATscFv was displayed on the surface of H1299-AID cells. By 4-round amplification/flow cytometric sorting for cells with the highest affinities to hTNF-alpha, two ATscFv mutant gene clones were isolated. Compared with the wild type ATscFv, the two mutants were much more efficient in neutralizing cytotoxicity of hTNF-alpha. The results indicate that directed evolution by somatic hypermutation can be carried out in adherent non-B cells, which makes directed evolution in mammalian cells easier and more efficient.     

Intersubunit interactions in human cytidine deaminase

In order to design new efficient cytidine based drugs, an intersubunit interactions study related to the active site has been performed on the wild-type cytidine deaminase (CDA) and on the mutant enzyme F137W/W113F. F137 is the homologous to the Bacillus subtilis CDA F125 involved in the subunit interactions. In presence of the dissociating agent SDS, wild-type human CDA dissociate into enzymatically inactive monomers without intermediate forms via a non-cooperative transition. Extensive dialysis or dilution of the inactivated monomers restores completely the activity. The presence of the strong human CDA competitive inhibitor 5-fluorozebularine disfavour dissociation of the tetramer into subunits in the wild-type CDA but not in mutant enzyme F137W/W113F.     

C-terminal deletion of AID uncouples class switch recombination from somatic hypermutation and gene conversion

Class-switch recombination (CSR), somatic hypermutation (SHM), and antibody gene conversion are distinct DNA modification reactions, but all are initiated by activation-induced cytidine deaminase (AID), an enzyme that deaminates cytidine residues in single-stranded DNA. Here we describe a mutant form of AID that catalyzes SHM and gene conversion but not CSR. When expressed in E. coli, AID(delta189-198) is more active in catalyzing cytidine deamination than wild-type AID. AID(delta189-198) also promotes high levels of gene conversion and SHM when expressed in eukaryotic cells, but fails to induce CSR. These results underscore an essential role for the C-terminal domain of AID in CSR that is independent of its cytidine deaminase activity and that is not required for either gene conversion or SHM.