Cloning and characterization of PAS5: a gene required for peroxisome biogenesis in the methylotrophic yeast Pichia pastoris

The biogenesis and maintenance of cellular organelles is of fundamental importance in all eukaryotic cells. One such organelle is the peroxisome. The establishment of a genetic system to study peroxisome biogenesis in the methylotrophic yeast Pichia pastoris has yielded many different complementation groups of peroxisomal assembly (pas) or peroxisome-deficient (per) mutants. Each appears to be deficient in functional peroxisomes. One of these mutants, pas5, has been characterized, complemented, and the gene sequenced. Ultrastructural studies show that normal peroxisomes are not present in pas5, but aberrant peroxisomal structures resembling "membranous ghosts" are frequently observed. The "peroxisome ghosts" appear to be induced and segregated to daughter cells normally. Biochemical fractionation analysis of organelles of the pas5 mutant reveals that peroxisomal matrix enzymes are induced normally but are found mostly in the cytosol. However, purification of peroxisome ghosts from the mutant shows that small amounts (< 5%) of matrix enzymes are imported. The PAS5 gene was cloned and found to encode a 127-kD protein, which contains a 200-amino acid-long region of homology with PAS1, NEM- sensitive factor (NSF), and other related ATPases. Weak homology to a yeast myosin was also observed. The gene is not essential for growth on glucose but is essential for growth on oleic acid and methanol. The role of PAS5 in peroxisome biogenesis is discussed.     

Synthesis of polyhydroxyalkanoate in the peroxisome of Pichia pastoris

Polyhydroxyalkanoates (PHAs) are polyesters naturally produced by bacteria that have properties of biodegradable plastics and elastomers. A PHA synthase from Pseudomonas aeruginosa modified at the carboxy-end for peroxisomal targeting was transformed in Pichia pastoris. The PHA synthase was expressed under the control of the promoter of the P. pastoris acyl-CoA oxidase gene. Synthesis of up to 1% medium-chain-length PHA per g dry weight was dependent on both the expression of the PHA synthase and the presence of oleic acid in the medium. PHA accumulated as inclusions within the peroxisomes. P. pastoris could be used as a model system to study how peroxisomal metabolism needs to be modified to increase PHA production in other eukaryotes, such as plants.     

PAS1, a yeast gene required for peroxisome biogenesis, encodes a member of a novel family of putative ATPases

PAS genes are required for peroxisome biogenesis in the yeast S. cerevisiae. Here we describe the cloning, sequencing, and characterization of the PAS1 gene. Its gene product, Pas1p, has been identified as a rather hydrophilic 117 kd polypeptide. The predicted Pas1p sequence contains two putative ATP-binding sites and reveals a structural relationship to three other groups of proteins associated with different biological processes such as vesicle-mediated protein transport (NSF and Sec18p), control of cell cycle (Cdc48p, VCP, and p97-ATPase), and modulation of gene expression of the human immunodeficiency virus (TBP-1). The proteins share a highly conserved domain of about 185 amino acids including a consensus sequence for ATP binding. We suggest that these proteins are members of a novel family of putative ATPases and may be descendants of one common ancestor.     

The Pichia pastoris PER6 gene product is a peroxisomal integral membrane protein essential for peroxisome biogenesis and has sequence similarity to the Zellweger syndrome protein PAF-1.

We report the cloning of PER6, a gene essential for peroxisome biogenesis in the methylotrophic yeast Pichia pastoris. The PER6 sequence predicts that its product Per6p is a 52-kDa polypeptide with the cysteine-rich C3HC4 motif. Per6p has significant overall sequence similarity with the human peroxisome assembly factor PAF-1, a protein that is defective in certain patients suffering from the peroxisomal disorder Zellweger syndrome, and with car1, a protein required for peroxisome biogenesis and caryogamy in the filamentous fungus Podospora anserina. In addition, the C3HC4 motif and two of the three membrane-spanning segments predicted for Per6p align with the C3HC4 motifs and the two membrane-spanning segments predicted for PAF-1 and car1. Like PAF-1, Per6p is a peroxisomal integral membrane protein. In methanol- or oleic acid-induced cells of per6 mutants, morphologically recognizable peroxisomes are absent. Instead, peroxisomal remnants are observed. In addition, peroxisomal matrix proteins are synthesized but located in the cytosol. The similarities between Per6p and PAF-1 in amino acid sequence and biochemical properties, and between mutants defective in their respective genes, suggest that Per6p is the putative yeast homolog of PAF-1.     

毕赤酵母基因编辑技术研究进展

巴斯德毕赤酵母是一种重要的蛋白表达系统,基因编辑技术作为代谢工程的基本工具,对于毕赤酵母的代谢改造十分重要。近十年基因编辑技术发展迅速,除传统的同源重组和Cre/loxP重组外,相继出现了许多新的基因编辑技术,例如ZFN、TALEN和CRISPR/Cas9等,这些技术的出现使基因编辑更加简便高效。本文对毕赤酵母中传统和新型基因编辑技术的原理应用和研究进展进行了简要综述,并结合相关领域的发展对毕赤酵母基因编辑技术的发展进行了展望。     

PAS3, a Saccharomyces cerevisiae gene encoding a peroxisomal integral membrane protein essential for peroxisome biogenesis

Saccharomyces cerevisiae pas3-mutants are described which conform the pas-phenotype recently reported for the peroxisomal assembly mutants pas1-1 and pas2 (Erdmann, R., M. Veenhuis, D. Mertens, and W.-H Kunau, 1989, Proc. Natl. Acad. Sci. USA. 86:5419-5423). The isolation of pas3-mutants enabled us to clone the PAS3 gene by functional complementation. DNA sequence analysis revealed a 50.6-kD protein with at least one domain of sufficient length and hydrophobicity to span a lipid bilayer. To verify these predictions antibodies were raised against a truncated portion of the PAS3 coding region overexpressed in E. coli. Pas3p was identified as a 48 kD peroxisomal integral membrane protein. It is shown that a lack of this protein causes the peroxisome-deficient phenotype and the cytosolic mislocalization of peroxisomal matrix enzymes. Based on protease digestion experiments Pas3p is discussed to be anchored in the peroxisomal membrane by its amino-terminus while the bulk of the molecule is exposed to the cytosol. These findings are consistent with the possibility that Pas3p is one component of the peroxisomal import machinery.     

Positive selection of novel peroxisome biogenesis-defective mutants of the yeast Pichia pastoris

We have developed two novel schemes for the direct selection of peroxisome-biogenesis-defective (pex) mutants of the methylotrophic yeast Pichia pastoris. Both schemes take advantage of our observation that methanol-induced pex mutants contain little or no alcohol oxidase (AOX) activity. AOX is a peroxisomal matrix enzyme that catalyzes the first step in the methanol-utilization pathway. One scheme utilizes allyl alcohol, a compound that is not toxic to cells but is oxidized by AOX to acrolein, a compound that is toxic. Exposure of mutagenized populations of AOX-induced cells to allyl alcohol selectively kills AOX-containing cells. However, pex mutants without AOX are able to grow. The second scheme utilizes a P. pastoris strain that is defective in formaldehyde dehydrogenase (FLD), a methanol pathway enzyme required to metabolize formaldehyde, the product of AOX. AOX-induced cells of fld1 strains are sensitive to methanol because of the accumulation of formaldehyde. However, fld1 pex mutants, with little active AOX, do not efficiently oxidize methanol to formaldehyde and therefore are not sensitive to methanol. Using these selections, new pex mutant alleles in previously identified PEX genes have been isolated along with mutants in three previously unidentified PEX groups.     

拟南芥硫酯酶基因在毕赤酵母中的表达

硫酯酶在生物体内能催化水解脂酰酰基载体蛋白和饱和脂肪脂酰链,对中链脂肪酸(Medium chain fatty acids,MCFAs)的积累起着关键作用。为获得具有生产中链脂肪酸能力的工程菌,以拟南芥c DNA为模板,PCR扩增得到其脂酰-ACP硫酯酶基因At Fat A,经Eco RⅠ/XbaⅠ双酶切后连接至同样双酶切的质粒中,获得重组质粒p PICZαA-At Fat。将重组质粒电击转入毕赤酵母GS115中,通过Zeocin抗性筛选,挑选出阳性克隆子并摇瓶发酵诱导,SDS-聚丙烯酰胺凝胶电泳分析获得明显目的蛋白条带,首次成功构建At Fat A的真菌表达系统。气质联用法检测发酵产物胞外游离脂肪酸,发现毕赤酵母At Fat A重组菌株比起始GS115菌株胞外游离MCFAs(主要是辛酸)产量增加51%,MCFAs产量占胞外总脂肪酸产量的28.7%,而野生菌中这一比例仅有18.1%,这为日后生产安全无毒害的MCFAs探索了一条新的途径。     

蚓激酶基因的克隆及在毕赤酵母中的表达

以赤子爱胜蚓(Eisenia fetida)体内的总RNA为模板,通过RT-PCR方法扩增含自身信号肽的蚓激酶基因F238,将其克隆到pUCm-T载体上,并进行测序。GenBank登录号为:DQ202401。测序结果表明基因全长为738bp,共编码245个氨基酸,包括7个氨基酸的信号肽序列和238个氨基酸的成熟肽序列。与粉正蚓(Lumbricus rubellus)F-III-2相比,核苷酸与氨基酸序列的同源性均为99%,仅存在2个碱基的差异,导致2个氨基酸的突变。通过生物信息学方法对蛋白质的理化及结构特性进行分析预测,F238的等电点为4.61,含有11个半胱氨酸,形成3个二硫键。蛋白质分子主要由β折叠组成,具有丝氨酸活性中心,属丝氨酸蛋白酶超家族胰蛋白酶类。以重组质粒pUCm-T-F238为模板,通过PCR方法扩增去信号肽的蚓激酶基因F238-m,构建毕赤酵母(Pichia pastoris)表达载体pPIC9-F238-m,将其线性化后用电穿孔法导入酵母宿主菌GS115中。在MM和MD平板上筛选表型,经甲醇诱导后,SDS-PAGE分析显示表达产物的分子量为28kDa左右,纤维平板法测定活力最高可达100U/mL。     

纳豆激酶基因的克隆及其在毕赤酵母中的表达

纳豆激酶纳是从日本传统食品纳豆中发现的一类具有溶栓效果的蛋白酶,由于其具有安全,高效,作用时间长,易吸收,廉价等优点,现在正成为一个开发治疗血栓类疾病药物的研究热点。从本实验室保存的一株高溶栓的纳豆杆菌N07出发,提取总基因组DNA,利用PCR手段扩增获得了纳豆激酶长为825bp的成熟肽基因片段。构建重组表达质粒pPICZaA-NK,经EcoR I、Xba I双酶切、PCR、测序验证得出重组表达质粒上的外源基因即为825bp的目的片段;将重组质粒pPICZaA-NK用内切酶Sac I线性化后电击导入毕赤酵母X33,通过含Zeocin的YPDS平板筛选获得重组酵母。重组酵母在BMMY培养基中发酵培养,用1%甲醇诱导目的蛋白表达。用纤维蛋白平板法检测发现发酵上清具有纤溶活性,经硫酸铵盐析、透析、Sephadex-G50过柱等步骤分离得到纳豆激酶蛋白,进行SDS-PAGE鉴定表明,表达的纳豆激酶蛋白分子量为27KD。以尿激酶为标准,实验所得纳豆激酶发酵上清液溶栓活性约为195U/mL。成功的将纳豆激酶成熟肽基因在毕赤酵母X33中表达,为纳豆激酶基因工程进一步研究奠定基础。     

乙醛脱氢酶2基因在毕赤酵母中的表达和分离纯化

将乙醛脱氢酶2（ALDH2）基因整合到质粒pPIC9K上,构建重组表达载体pPIC9K-coALDH2,用电转导将表达质粒pPIC9K-coALDH2转化至毕赤酵母GS115中,在毕赤酵母中表达经密码子改造的ALDH2。结果表明：重组基因工程菌GS115（pPIC9K-coALDH2）发酵液中蛋白质量浓度为8.40 mg/L,1 mL发酵液中酶活为11.35 mU。     

脂肪酶1在毕赤酵母中的高效表达

根据褶皱假丝酵母脂肪酶CRL中LIP1的成熟多肽序列 ,人工合成了由毕赤酵母 (Pichiapastoris)中偏爱密码子组成的lip1基因序列。该基因以N端融合的方式分别正确插入毕赤酵母诱导型表达载体pPICZαA与组成型表达载体pGAPZαA中。通过电激将线性化的上述两种重组质粒分别转化毕赤酵母SMD116 8H细胞 ,筛选获得两株分别具有诱导型表达和组成型表达生物活性LIP1能力的高产菌株。其中 ,组成型表达菌株CHT II换液后 4 8h上清液中含脂肪酶活力为 2 .0 0× 10 5u/L ,表达产物在pH 4～ 8与温度 30～ 5 0℃范围内具有较高的脂肪酶活性 ;高密度发酵条件下 ,发酵 72h ,上清液中含脂肪酶活力可达 1.395× 10 6u/L ,表明构建的重组菌株具有更大的工业化生产优势。     

影响外源基因在巴氏毕赤酵母中表达的因素

要在一种宿主表达系统中成功表达外源蛋白并获得较高产量,必须要较为全面地了解影响其表达的许多因素。影响外源基因在巴氏毕赤酵母中表达的因素主要包括：外源基因的特性、表达框的染色体整合位点和方式、宿主菌的甲醇利用表型、基因剂量、分泌信号、产物稳定性和翻译后修饰等。本文就这些因素进行分析,并提出一定的对策和建议。     

Role of Vac8 in Cellular Degradation Pathways in Pichia pastoris

We have identified the Pichia pastoris Vac8 homolog, a 60-64 kDa armadillo repeat protein, and have examined the role of PpVac8 in the degradative pathways involving the yeast vacuole. We report here that PpVac8 is required for glucose-induced pexophagy and mitophagy, but not ethanol-induced pexophagy or starvation-induced autophagy. This has been demonstrated by the persistence of peroxisomal alcohol oxidase activity and GFP-labeled mitochondria in mutants lacking PpVac8 during glucose adaptation. During glucose-induced micropexophagy, in the absence of PpVac8, the vacuole was invaginated with arm-like “segmented” extensions that almost completely surrounded the adjacent peroxisomes. PpVac8-GFP was found at the vacuolar membrane and concentrated at the base of the sequestering membranes that extend from the vacuole to engulf the peroxisomes. The localization of PpVac8-GFP to the vacuolar membrane occurred independent of PpAtg1, PpAtg9 or PpAtg11. Mutagenesis of the palmitoylated cysteines to alanines or deletion of the myristoylation and palmitoylation sites of PpVac8, resulted in an impaired vacuolar association and decreased degradation of alcohol oxidase. Deletion of the central armadillo repeat domains of the PpVac8 did not alter its association with the vacuolar membrane, but resulted in a nonfunctional protein that suppressed the formation of the arm-like extensions from the vacuole to engulf the peroxisomes. PpVac8 is essential for the trafficking of PpAtg11, but not PpAtg1 or PpAtg18, to the vacuole membrane. Together, our results support a role for PpVac8 in early (formation of sequestering membranes) and late (post-MIPA membrane fusion) molecular events of glucose-induced pexophagy.     

OSF1在毕赤酵母菌中的分泌表达及其生物活性

为了研究人成骨细胞刺激因子(Human osteoblast-stimulating factor,OSF-1)的生物学活性,构建OSF-1高效毕赤酵母表达菌株并表达纯化具有生物活性的OSF-1。首先通过全基因人工合成的方法合成人osf-1基因,并克隆至毕赤酵母分泌表达载体pPIC9K,构建重组表达质粒pPIC9K/osf-1,线性化后电转化酵母宿主菌GS115,构建P.pastoris GS115/pPIC9K/osf-1,经MD、G418-YPD平板和PCR法筛选,获得多拷贝转化子。阳性表达菌株在25℃,经1%的甲醇诱导表达96 h,重组蛋白的表达量达到最大。经SDS-PAGE电泳分析所表达的重组蛋白约为18 kDa,与人成骨细胞刺激因子相符。表达上清经SP-Sephadex C-50离子交换层析进行纯化,得到纯度达98%以上的OSF-1。Western blotting鉴定该蛋白对人成骨细胞刺激因子抗体具有良好的抗原性。生物活性测定表明提纯的OSF-1能促进鼠成骨细胞MC3T3-E1的增殖和分化。利用重组毕赤酵母高效分泌表达了有生物活性的OSF-1,为进一步开展其抗骨质疏松活性研究及产业化开发奠定了基础。     

耐热羧肽酶Taq基因在毕赤酵母中的表达

为了获取表达羧肽酶Taq毕赤酵母工程菌,通过密码子优化,依据毕赤酵母密码子偏爱性,在体外合成了栖热水生菌的耐热羧肽酶Taq基因。将该基因克隆到毕赤酵母表达载体p HBM905A上并引入6×His标签,构建了重组质粒p HBM905A-Cpase Taq。将该重组质粒转化毕赤酵母GS115,经1%甲醇诱导表达72 h,酶产量达0.1 mg/m L。对纯化的重组酶进行酶活性分析表明在75℃,p H为7.5时,该酶比酶活性为80 U/mg。本研究首次证明了羧肽酶Taq能在毕赤酵母中有效分泌表达,可以被大量制备,进而为多肽水解为氨基酸奠定工业基础。     

中性内切型纤维素酶在毕赤酵母中高水平表达的研究

中性内切型纤维素酶在纺织及造纸工业具有重要的应用,为了进一步提高从我国草菇中克隆的一种新的中性内切型纤维素酶(EG1)在Pichiapastoris中的表达水平,我们进行了提高基因拷贝数及高密度发酵等多种手段实现其高水平表达的研究。在前期研究的基础上,利用对已整合eg1的重组子再转化的方法,从含有2000μgLZeocin的YPDSZ平板上筛选到高抗Zeocin转化子,在摇瓶培养条件下,该转化子表达量比原来提高了3.8倍,在pH4～8条件下均有稳定表达,接种量(OD600=5.0)表达水平最好,提高甲醇的诱导浓度对表达有显著的促进作用。用3.2L发酵罐进行了高密度发酵,甲醇诱导95.5h后达到最高值,比摇瓶培养再提高了6.4倍,因此利用高抗Zeocin转化子及高密度发酵的手段,使EG1的表达水平提高了34倍,蛋白表达量达8.80mgmL,EG1酶活达到543.36IUmL,实现了中性内切纤维素酶的高水平表达,本研究将大大促进建立我国纺织用纤维素酶大规模高效生产技术。     

过氧化物酶体生物发生研究进展

过氧化物酶体是存在于真核细胞中的一种亚细胞器,主要功能是参与脂肪酸等脂质的代谢过程和氧化应激的调节。近年来研究发现,多种疾病都与过氧化物酶体的生物发生异常有关。过氧化物酶体的生物发生指过氧化物酶体的形成过程,包括从头合成和分裂增殖两条途径。两条途径中,参与过氧化物酶体生物发生的蛋白质,即peroxin(PEX)的基因发生突变,会导致过氧化物酶体生成障碍,引起疾病的发生。因此,就过氧化物酶体生物发生的研究进展进行综述,有助于为相关疾病的诊断和治疗提供参考和依据。