Komagataeibacter rhaeticus 3-15全基因组及葡萄糖脱氢酶基因缺失体的构建

细菌纤维素(BC)是一种新型的可再生、可降解的生物高分子材料。为了最大程度的发挥BC生产菌株K. rhaeticus 315的生产能力,本文首先对K. rhaeticus 315进行全基因组测序,通过功能基因的注释、分析碳源代谢流向。结果显示,该菌株碳代谢特征之一是缺乏磷酸果糖激酶的编码基因,不能通过EMP途径代谢糖类碳源,而是主要通过PPP途径和TCA途径代谢碳源,维持菌体生长和BC合成。由于葡萄糖脱氢酶的存在,该菌株在合成BC的同时生成大量副产物—葡萄糖酸。为此,本文通过敲除葡萄糖酸合成酶相关基因,即葡萄糖脱氢酶基因gcd,构建葡萄糖脱氢酶基因缺失重组株(gcd-),将葡萄糖酸的生成量降低了77%。     

构建胸膜肺炎放线杆菌apxIC基因插入突变株

目的：构建胸膜肺炎放线杆菌（APP）apxIC基因插入突变菌株,以鉴定ApxⅠ毒素的生物学特性。方法：根据apxⅠ核酸序列（U05042）设计1对引物,用于自APP血清10型参考菌株（D13039）基因组DNA中扩增apxIC基因及其上下游约2．8kb的基因片段,经克隆测序后在apxIC基因下游xbI酶切位点处插入约0．9kb的氯霉素（Chl）抗性基因表达盒,构建用于转化的转移载体pUIC-Chl^r,将转移载体DNA经电转化导入APP血清10型参考菌株中进行同源重组,以获得突变菌株。结果：在含有氯霉素的培养基中经筛选获得2株丧失溶血活性的突变菌株（D13039C-Chl^r）;利用PCR和Southern blot对突变菌株鉴定,显示氯霉素抗性基因已被插入细菌基因组中。结论：利用电转化和同源重组技术构建成功APP apxIC基因插入突变菌株,为分析ApxⅠ毒素的生物学特性,进而研制APP基因工程减毒活疫苗奠定了基础。     

白念珠菌新型耐药基因MXR1的敲除与鉴定

目的 构建用于白念珠菌MXR1基因敲除的载体质粒,并通过Ura-Blaster策略敲除MXR1两条等位基因.方法 分别扩增白念珠菌MXR1基因ORF两侧上下游的片段,通过酶切与连接反应,将上下游片段分别插入到p5921质粒的hisG-URA 3-hisG盒两端,从而形成MXR1敲除载体质粒pUC-MXR1-URA3.通过Ura-Blaster策略将载体质粒转染到白念珠菌RM 1000内,并采用PCR和Southern-blot杂交方法鉴定各步转染、复筛所得的阳性克隆.结果 成功获得MXR1基因缺失的菌株.结论 MXR1基因缺失菌株的构建,有助于深入研究白念珠菌耐药机制.     

细菌染色体第1类整合子捕获耐药性基因盒反应模型的构建

【背景】整合子在细菌耐药性的获得及传播中占据重要地位,对于整合反应检测方法的改良及反应机制的研究,可以加深我们对细菌耐药性产生和播散的理解,为遏制耐药菌株的产生和播散提供新的途径。【目的】在细菌染色体上构建第1类整合子反应模型,用于评价整合酶介导的基因盒位点特异性重组。【方法】 PCR分别扩增含氯霉素耐药基因cat的CM片段、含基因盒aadA5的LacA5片段、含整合子重组位点attI1及强可变区启动子的PcS片段和插入位点两侧的同源臂,重叠延伸聚合酶链反应连接上述5个片段制备整合子模型插入片段,通过同源重组将构建好的整合子模型片段插入大肠埃希菌JM109染色体中。转入高表达第1类整合酶的质粒pHSint,在链霉素平板上筛选发生整合的菌株,并经聚合酶链反应和测序验证。【结果】构建的整合子模型片段经测序与预期一致,整合子模型片段成功插入大肠埃希菌JM109染色体中。转入高表达整合酶的质粒pHSint后,在链霉素平板上成功筛选出基因盒aadA5发生整合的菌株,经聚合酶链反应扩增并测序与预期一致。【结论】在大肠埃希菌染色体上成功构建第1类整合酶介导基因盒位点特异性重组反应模型,为进一步揭示整合子捕获耐药性基因盒的反应机制奠定基础。     

利用CRISPR-Cas9技术失活黑曲霉中果胶酶基因及突变株性能评价*

我国果胶酶制剂使用广泛但专一性不高,高效、专一的果胶酶制剂在市场上仍然匮乏。利用基因工程技术改造果胶酶生产菌株——黑曲霉来生产单一成分的果胶酶成为解决果胶酶应用需求的一种有效方案。构建一种高效的CRISPR-Cas9基因编辑技术,可为构建高产单一性果胶酶的黑曲霉底盘菌株提供有效的基因编辑工具。首先敲除产果胶酶黑曲霉基因组上的pyrG基因构建尿嘧啶营养缺陷型菌株AnΔpyrG,并在AnΔpyrG菌株的pyrG基因位点定点整合Cas9基因表达盒和pyrG基因表达盒,构建组成型表达Cas9基因的黑曲霉菌株AnCas9,再构建含有gpdA启动子、锤头结构核酶、HDV核酶的稳定性表达sgRNA的pLM2-sgRNA质粒,建立CRISPR-Cas9基因编辑体系。利用该技术失活AnCas9菌株中的2个聚半乳糖醛酸酶基因4978020和4983861来检测构建的CRISPR-Cas9基因编辑效率并检测4978020基因功能缺失菌株的表型变化和产酶变化,结果表明果胶酶基因编辑效率大于50%,AnΔ4978020的表型和果胶酶酶活性与出发菌株均无明显变化。在黑曲霉中成功构建了高效的Cas9基因编辑技术,4978020基因功能缺失也不影响菌株表型,为构建高产单一性果胶酶黑曲霉底盘菌株奠定基础。     

大肠杆菌hfq和rne-710基因的双质粒无痕敲除技术

基因敲除技术是了解基因功能的重要技术手段。以大肠杆菌K-12 MG1655基因组hfq(309 bp)和rne-710(1056 bp)基因为模型,首先构建Δhfq∷Spe和Δrne-710∷Spe菌株,通过融合PCR方法分别构建缺失hfq(309 bp)和rne-710(1056 bp)的融合片段并连接至辅助质粒,缺失hfq和rne-710的片段经重组分别替换壮观霉素抗性盒,得到无痕敲除株Δhfq和Δrne-710。双质粒无痕敲除和融合PCR方法相结合为大片段基因缺失开辟了新的途径。     

北京棒杆菌芳香族氨基酸转运蛋白基因敲除对L-色氨酸积累的影响

[目的]为了减少北京棒杆菌PD-67(Corynebacterium pekinense PD-67)从细胞外吸收色氨酸,降低细胞内色氨酸库的浓度,从而使色氨酸的反馈控制作用减弱,增加胞外L-色氨酸的积累量,构建北京棒杆菌PD-67的芳香族氨基酸转运蛋白基因aroP敲除的菌株,研究aroP基因敲除对菌株L-色氨酸积累的影响.并进一步研究在aroP敲除菌株中表达邻氨基苯甲酸合成酶(AS)基因对L-色氨酸积累的影响.[方法]运用PCR技术扩增aroP基因,与整合质粒连接后,用限制性内切酶法构建带有内部片段缺失的aroP基因的敲除载体.利用同源重组技术,敲除北京棒杆菌PD-67的aroP基因,构建菌株PD-67 ΔaroP,并用带有aroP基因的表达载体对PD-67ΔaroP进行互补验证.采用PCR技术扩增AS基因,与表达载体连接构建重组质粒.将重组质粒转入菌株PD-67ΔaroP,构建工程菌株PD-67 ΔaroP/pXAS.通过摇瓶发酵研究PD-67 AaroP和PD-67 ΔaroP/pXAS的发酵特性.[结果]经PCR验证获得了aroP基因缺陷的菌株.摇瓶发酵结果表明,与出发菌株相比,PD-67ΔaroP的L-色氨酸的积累量提高了65％.酶活分析结果表明,AS基因在菌株PD-67 △aroP中得到表达.AS基因表达使工程菌单位菌体产酸率提高了25.6％.[结论]北京棒杆菌PD-67中芳香族氨基酸转运蛋白基因arop的敲除能够提高胞外L-色氨酸的积累量.在arop基因敲除菌中表达AS基因,可以进一步提高工程菌的产酸率.     

油菜叶绿体基因组同源重组片段的克隆及phb基因定点整合载体的构建

利用叶绿体基因组在进化过程中高度保守的特点,根据烟草、水稻和玉米叶绿体基因组全序列资料,设计合成引物,PCR扩增并克隆了油菜叶绿体两个重要的功能基因rbcL和atpB(GenBank登录号分别为AF267640和AF267641）,并以此作为定点整合源基因的同源重组片段。以来自叶绿体的强启动子PpsbA和Prrn等驱动PHB合成途径中3个关键酶基因phbA、phbB和phbC,分别构建表达盒,并将它们按照其在原始菌株中的自然转录顺序phbC-phbA-phbB相串联,最后连同选择标记基因aadA表达盒一起,克隆到油菜叶绿体同源片段中,构建成pgb基因定点整合载体pRCABZ和pRCABF.酶切及Southem杂交结果证明所构建的转化载体符合预期设计。叶绿体转化及后续工作目前正在进行之中。     

利用可重复使用的URA3标记基因建立热带假丝酵母基因敲除系统

热带假丝酵母(Candida tropicalis)在发酵工业中具有重要的应用潜力,但二倍体遗传结构和较低的遗传转化效率限制了其代谢工程育种技术的应用。建立可靠的遗传转化技术并高效的删除目的基因是代谢工程改造热带假丝酵母的重要前提。文章以C. tropicalis ATCC 20336为出发菌株,通过化学诱变筛选获得了尿嘧啶缺陷型突变株C. tropicalis XZX(ura3/ura3)。以丙酮酸脱羧酶(Pyruvate decarboxylase,PDC)基因作为靶基因构建了两端包含同源臂并在选择性标记C. tropicalis URA3(Orotidine-5′-phosphate decarboxylase,乳清酸核苷-5-磷酸脱羧酶)基因两侧同向插入源于沙门氏菌(Salmonella typhimurium)的hisG序列的基因敲除盒PDC1-hisG-URA3-hisG- PDC1(PHUHP),并转化宿主菌株C. tropicalis XZX,筛选获得PHUHP片段正确整合到染色体的PDC基因位点的转化子XZX02。在此基础上,将转化子XZX02涂布于5-FOA(5-氟乳清酸)选择培养基上,筛选得到URA3基因从PHUHP片段中丢失的营养缺陷型菌株XZX03。进一步构建了第2个PDC等位基因的删除表达盒PDCm- URA3-PDCm,并转化C. tropicalis XZX03菌株,获得转化子C. tropicalis XZX04。经PCR和DNA测序确认转化子C. tropicalis XZX04细胞染色体上的两个PDC等位基因被成功敲除。文章建立了一种营养缺陷型标记可重复使用的热带假丝酵母遗传转化技术,利用该技术成功敲除了细胞的PDC基因,为进一步利用代谢工程改造热带假丝酵母奠定了基础。     

黑曲霉菌株柠檬酸合成酶基因的敲除及功能分析

【背景】柠檬酸合成酶是碳代谢途径的中心酶,其在三羧酸循环(tricarboxylic acid cycle,TCA)、氨基酸合成和乙醛酸循环中发挥着重要作用,是柠檬酸合成的关键酶。本论文所选用的是一株高产柠檬酸的黑曲霉菌株CGMCC10142。【目的】克隆柠檬酸合成酶关键基因,构建柠檬酸合成酶的敲除菌株并鉴定其在黑曲霉菌株高产柠檬酸过程中的功能及影响。【方法】采用根癌农杆菌转化方法并利用同源重组原理,采用抗性筛选和致死型反向筛选的双重筛选方法获得正确敲除株。对转化子在不同碳源下的生长情况进行观察并对柠檬酸发酵过程中菌丝球变化和产酸量进行分析,最后通过荧光定量PCR分析柠檬酸合成酶基因对黑曲霉积累柠檬酸的影响,及其对主要代谢途径中重要酶相关基因和其他的表达量的影响。【结果】以柠檬酸高产菌株黑曲霉CGMCC10142为出发菌,构建一株遗传稳定的柠檬酸合成酶敲除的菌株T1-2。结果发现该菌株在以葡萄糖为碳源的培养基上生长缓慢并且产生孢子量减少。通过摇瓶发酵产酸实验,结果表明敲除菌在84 h产酸量为64.3 g/L,相对于出发菌的98.7g/L降低了34.85%。通过荧光定量PCR发现柠檬酸合成酶的表达量是下降的,同时重要酶的表达量都下降。【结论】该菌株的柠檬酸合成酶基因对柠檬酸积累具有重要作用,但存在其他同工酶基因,该基因敲除仅使产酸合成降低34.85%,同时发现该柠檬酸合成酶的顺畅表达有助于主代谢途径中各关键酶的高效表达,本研究可为研究黑曲霉高产柠檬酸机理奠定基础。     

High-throughput PCR screening of genes for three-component regulatory system putatively involved in quorum sensing from low-G + C gram-positive bacteria

Quorum sensing of gram-positive bacteria is often regulated by three-component regulatory system composed of autoinducing peptide, sensor kinase and response regulator. We used PCR to study a gene cassette encoding this three-component regulatory system. Degenerate primers were designed from consensus amino acid sequences in the HPK10 subfamily, mostly involved in quorum sensing. Products amplified from genomic DNA of Lactobacillus, Enterococcus, and Clostridium species were cloned and sequenced; their deduced amino acid sequences were similar to those of members of the HPK10 subfamily. Complete genes for the putative gene cassette were cloned by inverse PCR from L. paracasei E93490 and L. plantarum WCFS6. Phylogenetic analysis grouped the cloned putative HPKs into the HPK10 subfamily. These results indicated the usefulness of this high-throughput gene screening and suggested that the three-component regulatory gene cassette are widely present.     

Characterization of the gene for fructose-1,6-bisphosphatase from Saccharomyces cerevisiae and Schizosaccharomyces pombe. Sequence, protein homology, and expression during growth on glucose

We have determined the nucleotide sequence of the gene for fructose-1,6-bisphosphatase from both Saccharomyces cerevisiae and Schizosaccharomyces pombe. The predicted protein sequence for fructose-1,6-bisphosphatase from S. cerevisiae contains 347 amino acids and has a molecular weight of 38,100; that from S. pombe, contains 346 amino acids and has a molecular weight of 38,380. Comparison of these amino acid sequences with each other and that of pig kidney fructose-1,6-bisphosphatase shows several regions of strong homology separated by regions of divergence. These homologous regions are likely candidates for functional domains. A gene cassette was constructed for fructose-1,6-bisphosphatase from S. cerevisiae and the gene cassette expressed from the regulated PHO5 and GAL1 promoters of yeast. Yeast cells expressing fructose-1,6-bisphosphatase, while growing on glucose, accumulated large amounts of enzyme intracellularly, suggesting that glucose-regulated proteolytic inactivation does not operate efficiently under these conditions. Growth on glucose was not inhibited by the expression of fructose 1,6-bisphosphatase.     

High-level secretion of biologically active aprotinin from the yeastPichia pastoris

Summary A synthetic gene encoding aprotinin (bovine pancreatic trypsin, inhibitor) was fused to theSaccharomyces cerevisiae prepro alpha mating factor leader sequence at the dibasic amino acid processing site.Pichia pastoris strains were developed to'express one or multiple copies of a methanol-inducible expression cassette containing the gene fusion.P. pastoris containing a single copy of the vector secreed approximately 150 mg/l of immunoreactive protein. A construct bearing five copies of the expression cassette secreted 930 mg/l of aprotinin. The purified aprotinin molecule was equipoten with the native molecule in a trypsin inhibition assay. Protein sequence analysis showed that the alpha factor-aprotinin fusion was not processed at the basic amino acid residues Lys-Arg. Instead, recombinant aprotinin had additional N-terminal amino acids derived from prepro alpha factor. The N-terminal extension was variably 11 or 4 amino acids. Inclusion of the spacer DNA sequence encoding Glu and Ala between aprotinin and the Lys-Arg processing site led to the secretion of a biologically active aprotinin containing only a Glu-Ala N-terminal extension.     

IntI2 integron integrase in Tn7

Integrons can insert and excise antibiotic resistance genes on plasmids in bacteria by site-specific recombination. Class 1 integrons code for an integrase, IntI1 (337 amino acids in length), and are generally borne on elements derived from Tn5090, such as that found in the central part of Tn21. A second class of integron is found on transposon Tn7 and its relatives. We have completed the sequence of the Tn7 integrase gene, intI2, which contains an internal stop codon. This codon was found to be conserved among intI2 genes on three other Tn7-like transposons harboring different cassettes. The predicted peptide sequence (IntI2*) is 325 amino acids long and is 46% identical to IntI1. In order to detect recombination activity, the internal stop codon at position 179 in the parental allele was changed to a triplet coding for glutamic acid. The sequences flanking the cassette arrays in the class 1 and 2 integrons are not closely related, but a common pool of mobile cassettes is used by the different integron classes; two of the three antibiotic resistance cassettes on Tn7 and its close relatives are also found in various class 1 integrons. We also observed a fourth excisable cassette downstream of those described previously in Tn7. The fourth cassette encodes a 165-amino-acid protein of unknown function with 6.5 contiguous repeats of a sequence coding for 7 amino acids. IntI2*179E promoted site-specific excision of each of the cassettes in Tn7 at different frequencies. The integrases from Tn21 and Tn7 showed limited cross-specificity in that IntI1 could excise all cassettes from both Tn21 and Tn7. However, we did not observe a corresponding excision of the aadA1 cassette from Tn21 by IntI2*179E.     

15种氨基酸随机肽库的小盒式DNA编码文库的构建

采用小盒式DNA编码文库的构建策略,选取在进化上可能起源较早的15种氨基酸,按照其简并密码子合成了一个为10个随机氨基酸编码的小盒式DNA模板,经过连续3轮的PCR扩增、酶切及连接的小盒式文库组装过程,成功构建了一个文库容量达1.31×10¹²/ml,随机编码区长达97个氨基酸的小盒式DNA编码文库。     

Characterization of transposon Tn5086, carrying the site-specifically inserted gene dhfrVII mediating trimethoprim resistance.

Two different enteric plasmids of widely separate origins were observed to carry a new 15.3-kb trimethoprim resistance transposon, Tn5086, also mediating resistance to mercuric ions and to a low level of sulfonamide. The trimethoprim resistance gene characterized from Tn5086 was found to be distinct from those found earlier and was designated type VII. Molecular analysis demonstrated that Tn5086 is closely related to Tn21. The internal part of Tn21 and Tn5086, the element referred to as the integron, was found to be different. First, the integron of Tn5086 contains a 0.62-kb cassette formed by the trimethoprim resistance gene dhfrVII and its immediate surroundings instead of the 0.86-kb aadA1 cassette of Tn21. Second, the integron of Tn5086 lacks a 4.2-kb segment 3' of sulI in Tn21. The dhfrVII gene commences with a UUG codon but was otherwise seen to be markedly related to the cassette genes dhfrI, dhfrV, and dhfrVI. The four related dihydrofolate reductases of 157 amino acids encoded by these genes contain a glutamate instead of the aspartic acid residue found at position 27 of the active center of the chromosomal enzyme from Escherichia coli.     

Construction and characterization of ack knock-out mutants of Propionibacterium acidipropionici for enhanced propionic acid fermentation

Propionibacterium acidipropionici produces propionic acid from glucose with acetic acid, succinic acid, and CO2 as byproducts. In this work, inactivation of ack gene, encoding acetate kinase (AK), by gene disruption and integrational mutagenesis was studied as a method to reduce acetate formation in propionic acid fermentation. The partial ack gene of approximately 750 bp in P. acidipropionici was cloned using a PCR-based method with degenerate primers and sequenced. The deduced amino acid sequence had 88% similarity and 76% identity with the amino acid sequence of AK from Bacillus subtilis. The partial ack gene was used to construct a linear DNA fragment with an inserted tetracycline resistance cassette and a nonreplicative integrational plasmid containing a tetracycline resistance gene cassette. These DNA constructs were then introduced into P. acidipropionici by electroporation, resulting in two mutants, ACK-Tet and TAT-ACK-Tet, respectively. Southern hybridization confirmed that the ack gene in the mutant ACK-Tet was disrupted by the inserted tetracycline resistance gene. As compared to the wild-type, the activities of AK were reduced by 26% and 43% in ACK-Tet and TAT-ACK-Tet mutants, respectively. The specific growth rate of these mutants was reduced by approximately 25% to 0.10/h (0.13/h for the wild-type), probably because of reduced acetate and ATP production. Both mutants produced approximately 14% less acetate from glucose. Although ack disruption alone did not completely eliminate acetate production, the propionate yield was increased by approximately 13%.     

Information content of amino acid residues in putative helix VIII of the lac permease from Escherichia coli

Mutants in putative helix VIII of lactose permease that retain the ability to accumulate lactose were created by cassette mutagenesis. A mutagenic insert encoding amino acid residues 259-278 was synthesized chemically by using reagents contaminated with 1% each of the other three bases and ligated into a KpnI/BclI site in the lacY gene in plasmid pGEM-4. Mutants that retain transport activity were selected by transforming a strain of Escherichia coli containing a wild-type lacZ gene, but deleted in lacY, with the mutant library and identifying colonies that transport lactose on indicator plates. Sequencing of the mutated region in lacY in 129 positive colonies reveals 43 single amino acid mutations at 26 sites and 26 multiple mutations. The variable amino acid positions are largely on one side of the putative alpha-helix, a stripe opposite Glu269. This mutable stripe of low information content is probably in contact with the membrane phospholipids.     

Control of gene expression in plant cells using a 434:VP16 chimeric protein

The herpes simplex virus type 1 VP16 polypeptide is a potent trans-activator of viral gene expression. We have tested the ability of the VP16 activation domain to activate gene expression in plant cells. A plasmid encoding a translational fusion between the full-length 434 repressor and the C-terminal 80 amino acids of VP16, was constructed. When expressed in Escherichia coli, the chimeric protein binds efficiently to 434-binding motifs (operators). For expression in plant cells, the chimeric activator gene was placed between the cauliflower mosaic virus (CaMV) 35S promoter and nos terminator sequences in a pUC-based plasmid. The 434 operators were placed upstream of a minimal CaMV 35S promoter linked to the E. coli gus reporter gene. This reporter-expression cassette was then incorporated into the same plasmid as the 434 cI/VP16 activator-expression cassette. Two control plasmids were also constructed, one encoding the 434 protein with no activator domain and the second a chimeric activator with no DNA-binding domain. The chimeric activator was tested for its ability to activate gene expression in a tobacco protoplast transient assay system. Results are presented to show that we can obtain in plant cells significant activation of gene expression that is dependent on both DNA-binding and the presence of the activator domain.