圆红冬孢酵母基因编辑及天然产物合成的研究进展

圆红冬孢酵母(Rhodotorula toruloides)是一种能够天然合成多种类胡萝卜素和油脂的非模式酵母。该菌能够利用各种廉价原料,耐受甚至同化利用多种有毒木质纤维素水解副产物。目前,该酵母被广泛用于微生物油脂、萜烯类化合物、各种高价值酶、糖醇和聚酮化合物的生产研究。鉴于其广阔的工业应用前景,研究人员对其开展了多维度的理论和技术的探索,包括基因组、转录组、蛋白组、遗传操作平台等。本文着重阐述近年来圆红冬孢酵母的代谢工程和天然产物合成的研究进展,并展望其细胞工厂构建中面临的挑战和可能的应对决策。     

恒化培养稀释率和碳氮比对圆红冬孢酵母油脂积累的影响

采用恒化培养的方法,考察了稀释率(D)和碳氮比(mol/mol)对圆红冬孢酵母Rhodosporidiumtoruloides AS 2.138 9积累油脂的影响。结果表明:稀释率增大,油脂含量和油脂得率降低。在D=0.02 h 1时油脂得率最大,为0.18 g油/g糖;D=0.14 h 1时油脂生成速率最大,为0.09 g/(L.h)。碳氮比增大,油脂含量略有增加。在C/N=92时油脂得率最大,为0.12 g油/g糖;C/N=32时油脂生成速率最大,为0.13 g/(L.h)。碳氮比对油脂的脂肪酸组成影响不明显,油脂的棕榈酸、硬脂酸和油酸总含量超过85%。     

圆红冬孢酵母发酵菊芋块茎产油脂的研究

研究了圆红冬孢酵母Y4发酵菊芋块茎,菊芋品种及其处理方法对发酵产油的影响。结果表明,菊芋浸提汁、酸水解液或菊芋浆均可直接被圆红冬孢酵母Y4利用,发酵积累油脂,但白皮菊芋比紫皮菊芋更有利于油脂发酵。发酵菊芋浸提汁或酸水解液时,无需添加外源营养物,干菌体油脂含量可达到40%（w/w）;发酵菊芋浆时,白皮菊芋转化率达到12.1 g油/100 g去皮干菊芋。菊芋油脂发酵产品主要以16碳和18碳系脂肪酸为主,与常规植物油的脂肪酸组成相似,可作为制备生物柴油的新型替代原料。     

圆红冬孢酵母磷酸盐饥饿诱导表达载体的构建

摘要:【目的】建立一种适用于圆红冬孢酵母代谢工程的磷酸盐饥饿诱导表达系统。【方法】对圆红冬孢酵母pho89基因5'侧翼序列进行生物信息学分析,设计相应引物,PCR扩增pho89基因启动子(pPHO89)和hsp70基因终止子(tHSP),利用RF克隆方法置换出发载体上的pPGK组成型启动子和tNOS终止子,以潮霉素磷酸转移酶基因hyg为报告基因,得到响应磷酸盐饥饿诱导的单表达盒载体pZPK-pPHO89-hyg-tHSP,利用ATMT方法转化圆红冬孢酵母,通过转化子潮霉素抗性表型鉴定pPHO89和tHSP的启动子和终止子活 性。在此基础上,构建了适合外源基因表达的双表达盒诱导表达载体pZPK-HYG-pPHO89-MCS-tHSP,并利用该载体构建了苹果酸酶重组表达菌株。【结果】成功构建了响应磷酸盐饥饿的圆红冬孢酵母诱导性表达载体,该载体在圆红冬孢酵母中可表现出启动子和终止子活性。【结论】该启动子受磷酸盐浓度的严谨调节,响应度高,操作简单,无需额外诱导剂,经济便捷,为后续圆红冬孢酵母代谢工程研究提供了基本材料。     

β-1,3-葡甘露聚糖酶辅助提取圆红冬孢酵母油脂

为考察β-1,3-葡甘露聚糖酶辅助提取圆红冬孢酵母Rhodosporidium toruloides油脂工艺的应用潜力,以R. toruloides Y4发酵醪液为原料,乙酸乙酯为溶剂,在10 L规模下研究了酶解和萃取条件对油脂提取率的影响,并进行了初步物料平衡分析。结果表明：酶处理0.5 h,油脂提取率可达71.1%,酶解效率与10 mL小体系所取得的结果相当。通过多次萃取,有效缓解了乳化现象对油脂提取的影响。经过3次萃取,油脂提取率、溶剂回收率和总物料回收率分别达92.9%、87.0%和94.2%。酶辅助提取油脂工艺可直接利用油脂发酵醪液,提取率高,对设备要求低,具有很好的工业化应用潜力。     

圆红冬孢酵母新颖脂肪酸合酶的重组表达、纯化与活性检测

脂肪酸合酶(Fatty acid synthase,FAS)催化乙酰辅酶A和丙二酸单酰辅酶A反应生成脂肪酸,是油脂合成代谢途径中最重要的酶之一。在高产油脂的圆红冬孢酵母Rhodosporidium toruloides中发现了一种新颖的FAS,它含两个亚基,与其他物种的FAS相比,具有独特的结构域组成,尤其是含两个酰基载体蛋白(ACP)结构域。由于ACP在脂肪酸合成反应中起辅因子作用,推测多个ACP有利于提高FAS的催化活性,为研究该FAS的生物化学和结构特征,构建了表达FAS两个亚基的载体,并转化大肠杆菌Escherichia coli BL21(DE3),含pET22b-FAS1和pET24-FAS2质粒的重组菌株ZWE06可同时高表达两个亚基,经硫酸铵沉淀、蔗糖密度梯度离心和阴离子交换层析纯化,得到的重组FAS比活力达到548 mU/mg。纯化的FAS复合物可用于后续酶动力学和蛋白结构研究,且表达与纯化方法的建立对研究其他ACP的功能具有参考价值。     

红冬孢酵母苹果酸酶基因RKME1的克隆与表达

苹果酸酶(malic enzyme,ME)普遍存在于各种生物体中,在二价阳离子(Mg~(2+)或者Mn~(2+))的存在下,它可以催化L-苹果酸进行氧化脱羧反应,产生丙酮酸、CO_2和NADPH。前期分析结果预测红冬孢酵母YM25235菌株具有2个苹果酸酶同功酶基因RKME1和RKME2,而且RKME1基因在15℃低温条件下mRNA转录水平显著提高。为了验证RKME1的结构与功能,以红冬孢酵母YM25235 cDNA为模板,PCR扩增得到大小为1 623 bp的开放阅读框,共编码540个氨基酸。序列分析结果显示该序列含有苹果酸酶保守的4个结构域(Ⅰ~Ⅳ),同源建模结果显示该序列的三级结构和蛔虫中的苹果酸酶晶体结构有较高相似性且高度保守。进一步将RKME1插入到载体pET32a(+)中构建重组表达质粒pET32a-RKME1,然后导入大肠杆菌BL21中进行表达。经IPTG诱导,获得了相对分子质量约为70 kD的蛋白质条带。将该蛋白质进行镍柱亲和层析纯化后,酶活分析的结果表明,重组表达的RKME1蛋白可催化苹果酸脱氢生成丙酮酸,同时生成NADPH,酶活为160 U/mg以上。上述结果表明,RKME1是一个新的苹果酸酶基因,这为深入研究苹果酸酶与红冬孢酵母低温条件下生长适应性之间的关系奠定了基础。     

不同营养元素限制对圆红冬胞酵母油脂生产的影响

以产油酵母圆红冬胞酵母（Rhodosporidium toruloides）作为研究对象,系统地研究了氮、磷、硫限制对其油脂积累的影响,并在3L生物反应器上考察了R.toruloides在C/P摩尔比为1 133.3时初始葡萄糖浓度对油脂生产的影响。结果表明：氮、磷、硫中任意一种营养元素受限,均能促使R.toruloides在胞内积累高于自身干重60%的油脂;通过改变培养基的组成,可以调节油脂中脂肪酸的构成,使油脂中饱和脂肪酸比例高于70%或不饱和脂肪酸比例高于60%。就油脂生产强度及转化效率而言,磷限制优于氮限制或硫限制。当C/P摩尔比相同时,初始葡萄糖浓度越低越有利于油脂生产。对采用不同原料生产微生物油脂的技术有一定指导意义。     

构建可合成非天然辅酶的圆红冬孢酵母工程菌*

烟酰胺腺嘌呤二核苷酸(nicotinamide adenine dinucleotide,NAD)及其还原态是生物体通用的氧化还原辅酶和重要小分子,参与胞内众多代谢反应,因此调控NAD水平不仅难以选择性作用于代谢途径,还常常产生意外的生物学效应。最近研究发现利用非天然辅酶烟酰胺胞嘧啶二核苷酸(nicotinamide cytosine dinucleotide,NCD),可构建正交的氧化还原催化体系,为调控胞内代谢提供了新机遇。为实现在产油酵母圆红冬孢酵母中建立NCD介导的氧化还原代谢,采用农杆菌介导转化方法,在基因组整合表达密码子优化的NCD合酶(NcdS)编码基因NCDS,获得系列有效表达NcdS的工程菌株。酶偶联法分析发现,工程菌细胞裂解液NcdS酶活达8.1×10^-3 U/OD_{600 nm}。通过高效液相色谱法(HPLC)和超高分辨率质谱检测,确定细胞裂解液可催化合成NCD。在培养基内补加5.0 mmol/L烟酰胺核糖后,工程菌胞内合成NCD达41.6 μmol/L。对工程菌进行发酵和油脂提取,发现胞内表达NCD合酶未导致细胞产油性能降低,后续可通过表达其他NCD偏好性酶,有望在圆红冬孢酵母中建立受NCD调控的油脂合成代谢体系。     

高山被孢霉Δ~6-脂肪酸脱氢酶基因在红冬孢酵母中的表达

以绿色荧光蛋白(green fluorescent protein,GFP)作为报告基因,将质粒pRH2304转化红冬孢酵母YM25235进行表达分析,荧光显微观察结果表明GFP在YM25235获得表达,建立了红冬孢酵母YM25235遗传转化方法。在此基础上,以高山被孢霉Δ6-脂肪酸脱氢酶基因取代pRH2304中的GFP基因,构建重组质粒pRH2304MAD6,将其转化红冬孢酵母YM25235进行表达分析。PCR结果表明,高山被孢霉Δ6-脂肪酸脱氢酶基因已经整合到YM25235基因组中,进一步的脂肪酸气相色谱分析结果表明,该基因编码产物催化n-6途径中的亚油酸转化成γ-亚麻酸,占细胞总脂肪酸的4.35%,但没有检测到催化n-3途径中的α-亚麻酸转化成十八碳四烯酸。     

在无天然游离质粒产甘油假丝酵母中非整合表达合成咖啡酸

【背景】咖啡酸（3,4-二羟基肉桂酸）是一种有多种生物活性和药用价值的天然酚类化合物,产甘油假丝酵母（Candida glycerinogenes）具有咖啡酸前体代谢途径,高耐酸且生长与发酵速率快,是潜在高产咖啡酸的底盘细胞,但无游离载体将影响咖啡酸合成的深入研究。【目的】探索在无天然游离质粒的C. glycerinogenes中构建操作更简便、表达能力更强的游离载体合成咖啡酸的可行性。【方法】筛选自主复制序列（autonomously replicating sequence,ARS）,构建适用于C. glycerinogenes合成咖啡酸的游离载体,并通过改造其ARS位置、标记基因URA5启动子长度、基因表达元件和利用Kozak序列优化表达并合成咖啡酸。【结果】构建的5个分别含不同ARS的载体中,pTGAPU-CA-AOX1t-KLARS在C. glycerinogenes中能自我复制并表达合成咖啡酸的基因,而且当ARS位于目的基因表达元件上游、URA5启动子截短250 bp,或分别采用Kozak序列与终止子URA5t后,咖啡酸产量较改造前均有明显提升,最高产量为初始产量的3.73倍,达29.1 mg/L,高于前期整合表达产量。【结论】在C. glycerinogenes中非整合表达合成咖啡酸且优于整合表达,为今后利用游离载体改造咖啡酸合成代谢途径提供了新工具,同时为其他无游离质粒菌株构建非整合表达体系提供参考。     

Isolation and nucleotide sequence of an autonomously replicating sequence (ARS) element functional in Candida albicans and Saccharomyces cerevisiae

Summary An 8.6-kb fragment was isolated from an EcoRI digest of Candida albicans ATCC 10261 genomic DNA which conferred the property of autonomous replication in Saccharomyces cervisiae on the otherwise non-replicative plasmid pMK155 (5.6 kb). The DNA responsible for the replicative function was subcloned as a 1.2-kb fragment onto a non-replicative plasmid (pRC3915) containing the C. albicans URA3 and LEU2 genes to form plasmid pRC3920. This plasmid was capable of autonomous replication in both S. cerevisiae and C. albicans and transformed S. cerevisiae AH22 (leu2 ^–) to Leu⁺ at a frequency of 2.15 × 10³ transformants per pg DNA, and transformed C. albicans SGY-243 (ura3) to Ura⁺ at a frequency of 1.91 × 10³ transformants per g DNA. Sequence analysis of the cloned DNA revealed the presence of two identical regions of eleven base pairs (5TTTTATGTTTT3) which agreed with the consensus of autonomously replicating sequence (ARS) cores functional in S. cerevisiae. In addition there were two 10/11 and numerous 9/11 matches to the core consensus. The two 11/11 matches to the consensus, CaARS1 and CaARS2, were located on opposite strands in a non-coding AT-rich region and were separated by 107 bp. Also present on the C. albicans DNA, 538 by from the ARS cores, was a gene for 5S rRNA which showed sequence homology with several other yeast 5S rRNA genes. A sub-fragment (494 bp) containing the 5S rRNA gene (but not the region containing the ARS cores) hybridized to genomic DNAs from a number of yeast species, including S. cerevisiae, C. tropicalis, C. pseudotropicalis, C. parapsilosis, C. kruseii, C. (Torulopsis) glabrata and Neurospora crassa. The 709-bp ARS element (but not the 5S rRNA gene) was necessary for high-frequency transformation and autonomous plasmid replication in both S. cerevisiae and C. albicans.EMBL/GenBank database accession number: X16634 (5S rRNA)     

Bending of DNA segments with Saccharomyces cerevisiae autonomously replicating sequence activity, isolated from basidiomycete mitochondrial linear plasmids

Summary Previous studies have indicated that DNA bending is a general structural feature of sequences (ARSs) from cellular DNAs of yeasts and nuclear and mitochondrial genomic DNAs of other eukaryotes that are capable of autonomous replication in Saccharomyces cerevisiae. Here we showed that bending activity is also tightly associated with S. cerevisiae ARS function of segments cloned from mitochondrial linear DNA plasmids of the basidiomycetes Pleurotus ostreatus and Lentinus edodes. Two plasmids, designated pLPO2-like (9.4 kb), and pLPO3 (6.6 kb) were isolated from a strain of P. ostreatus. A 1029 by fragment with high-level ARS activity was cloned from pLPO3 and it contained one ARS consensus sequence (A/T)TTTAT(A/G)TTT(A/T) indispensable for activity and seven dispersed ARS consensus-like (10/11 match) sequences. A discrete bent DNA region was found to lie around 500 by upstream from the ARS consensus sequence (T-rich strand). Removal of the bent DNA region impaired ARS function. DNA bending was also implicated in the ARS function associated with a 1430 by fragment containing three consecutive ARS consensus sequences which had been cloned from the L. edodes plasmid pLLE1 (11.0 kb): the three consecutive ARSs responsible for high-level ARS function occurred in, and immediately adjacent to, a bent DNA region. A clear difference exists between the two plasmid-derived ARS fragments with respect to the distance between the bent DNA region and the ARS consensus sequence(s).     

Characterization of an autonomously replicating sequence in Candida guilliermondii

Candida guilliermondii is an ascomycetous yeast widely studied due to its clinical importance, biotechnological interest, and biological control potential. During a series of preliminary experiments aiming at optimizing the electroporation procedure of C. guilliermondii cells, we observed that the efficiency of transformation of an ura5 recipient strain with the corresponding dominant marker URA5 was more than a thousand fold higher as compared with the transformation of an ura3 strain with the URA3 wild type allele. This result allowed the identification of an autonomously replicating sequence (ARS) within an A/T rich region located upstream of the URA5 open reading frame (ORF). Interestingly, linear double strand DNAs (dsDNAs) containing this putative ARS are circularized and then autonomously replicated in C. guilliermondii transformed cells. We demonstrated that the C. guilliermondii Lig4p ligase, involved in the canonical non-homologous end-joining (NHEJ) pathway, was responsible for this phenomenon since a lig4 mutant was unable to circularize and to autonomously maintain transforming dsDNAs containing the putative ARS. Finally, a functional dissection of the C. guilliermondii A/T rich region located upstream of the URA5 ORF revealed the presence of a 60 bp-length sequence essential and sufficient to confer ARS properties to shuttle plasmid and linear dsDNAs.     

过表达乙酰辅酶A乙酰基转移酶2基因(RKAcat2)对红冬孢酵母产类胡萝卜素的影响

[背景] 乙酰辅酶A乙酰基转移酶（Acetyl Coenzyme A Acyltransferase,Acat）是硫解酶家族的一员,分为I型和II型,而II型作为甲羟戊酸（Mevalonate,MVA）途径的第一个限速酶,其表达水平和催化活性会影响萜类及其衍生物的合成量。[目的] 分析Acat II型基因的过表达对红冬孢酵母产类胡萝卜素的影响。[方法] 从红冬孢酵母YM25235菌株中克隆编码Acat II型的基因RKAcat2,将其回转到红冬孢酵母YM25235菌株中,构建一株RKAcat2基因过表达菌株进行分析。[结果] 与对照菌株相比,RKAcat2基因过表达使YM25235菌株中类胡萝卜素含量提高了50.53%,而菌株中油脂含量降低了22.80%,脂肪酸组成中油酸含量显著下降了17.78%,而且菌株中乙酰辅酶A （Coenzyme A,CoA）的含量也下降了13.64%。[结论] 过表达RKAcat2基因促进更多乙酰CoA进入MVA途径中,从而提高了类胡萝卜素的合成水平,这与部分MVA途径和类胡萝卜素合成途径中基因的转录分析结果一致。研究结果可为进一步通过代谢工程手段提高产油红酵母中类胡萝卜素及其特定组分含量的研究提供参考。     

Isolation and sequence analysis of a small cryptic plasmid pRK10 from a corrosion inhibitor degrading strain Serratia marcescens ACE2

The nucleotide sequence of a smallest cryptic plasmid pRK10 of Serratia marcescens ACE2 was determined. When compared to the all other plasmids reported so far from S. marcescens in sizes of over 70 kb, pRK10 is only 4241 bp long with 53% G + C content and has five coding sequences representing a coding percentage of 65.41. This small plasmid consists of one Tdh gene, four mobilization genes, mobCABD, and an origin of replication homologous to those of ColE1-type plasmids. Analysis of the five open reading frames identified on the plasmid suggests the presence of genes involved in replication and mobilization containing sequences homologous to the bom region and mobCABD genes of ColE1 and Tdh from Acinetobacter baumannii str. AYE. Results also indicate that pRK10 does not encode any gene for antibiotic/heavy metal resistance. Copy number and incompatibility of the plasmid with plasmids of ColE1 origin of replication was determined and it is quite stable in its natural host as well as in Escherichia coli DH5α. This relatively small plasmid will be useful for construction of shuttle vectors to facilitate the genetic analysis.     

The function of the nuclear matrix attachment region of silkworm rDNA as an autonomously replicating sequence in plasmid and chromosomal replication origin in yeast

Nuclear matrix attachment regions (MARs) play a crucial role in chromatin architecture, gene expression, and DNA replication. Although it is well known that yeast autonomously replicating sequences (ARSs) bind nuclear matrix and MARs also function as ARS elements in yeast, whether a heterologous MAR or ARS element acts as a replication origin in the chromosome has not been elucidated. We previously identified a MAR (rMAR) located in the nontranscribed spacer (NTS) of silkworm Attacus ricini rDNA. We report here that this rMAR contains 10 copies of ARS consensus sequence (ACS) and several DNA unwinding regions. The rMAR employs ARS activity in yeast and a rARS element locates in the 3(') region of the rMAR. Furthermore, we have also revealed that either the rMAR or the rARS element functions as a replication origin in the chromosome. Our results provide the first direct evidence to demonstrate that heterologous rMAR and rARS display chromosomal origin activity, suggesting that the chromosome structure and replication origin of rDNA reserve some common features during evolution.     

In addition to the ARS core, the ARS box is necessary for autonomously replicating sequences

Summary Autonomously replicating sequences (ARSs) were cloned from nuclear and mitochondrial DNA of D. melanogaster using YIp5, which is composed of pBR322 and the yeast ura3 gene, as the cloning vector and YNN27, a Ura^- yeast strain as the recipient. The nucleotide sequences of six ARSs, two from nuclear bulk, two from the nuclear 1.688 satellite, and two from mitochondorial DNA, were determined. The relationship between the transformation frequency and the inclusion of the ARS core, 5 _T ^A TT-TAT _A ^G TTT _T ^A 3, of these fragments was analysed. All the ARSs contained an ARS core or a single base change of it. However, not all the fragments that contained a single base change of the ARS core were able to transform the recipient cells, suggesting that certain bases in the ARS core were not exchangeable. It is suggested by transformation experiments with subfragments that in addition to an ARS core, an ARS box which is located within 25 bp upstream of the ARS core and whose sequence is composed of 5TNT _G ^A AA 3, is necessary for autonomous replication.