Enhanced 2,3-Butanediol Production by Optimizing Fermentation Conditions and Engineering Klebsiella oxytoca M1 through Overexpression of Acetoin Reductase

Microbial production of 2,3-butanediol (2,3-BDO) has been attracting increasing interest because of its high value and various industrial applications. In this study, high production of 2,3-BDO using a previously isolated bacterium Klebsiella oxytoca M1 was carried out by optimizing fermentation conditions and overexpressing acetoin reductase (AR). Supplying complex nitrogen sources and using NaOH as a neutralizing agent were found to enhance specific production and yield of 2,3-BDO. In fed-batch fermentations, 2,3-BDO production increased with the agitation speed (109.6 g/L at 300 rpm vs. 118.5 g/L at 400 rpm) along with significantly reduced formation of by-product, but the yield at 400 rpm was lower than that at 300 rpm (0.40 g/g vs. 0.34 g/g) due to acetoin accumulation at 400 rpm. Because AR catalyzing both acetoin reduction and 2,3-BDO oxidation in K. oxytoca M1 revealed more than 8-fold higher reduction activity than oxidation activity, the engineered K. oxytoca M1 overexpressing the budC encoding AR was used in fed-batch fermentation. Finally, acetoin accumulation was significantly reduced by 43% and enhancement of 2,3-BDO concentration (142.5 g/L), yield (0.42 g/g) and productivity (1.47 g/L/h) was achieved compared to performance with the parent strain. This is by far the highest titer of 2,3-BDO achieved by K. oxytoca strains. This notable result could be obtained by finding favorable fermentation conditions for 2,3-BDO production as well as by utilizing the distinct characteristic of AR in K. oxytoca M1 revealing the nature of reductase.     

Genome Sequence of the Rice Pathogen Dickeya zeae Strain ZJU1202

Dickeya zeae is a phytopathogenic bacterium causing soft rot diseases in a wide range of economically important crops. Here we present the draft genome sequence of strain ZJU1202, which is the causal agent of rice foot rot in China. The draft genome will contribute to epidemiological and comparative genomic studies and the quarantine of this devastating phytopathogen.     

海绵细菌B25W最佳产抗培养基及发酵条件的研究

从辽宁海域的繁茂膜海绵(Hymeniacidonperleve)中分离到1株解淀粉类芽孢杆菌(Paenibacillusamyloliquefaciens),定名为海绵细菌B25W。它产生的抗生素用白色念珠菌(Candidaalbicans)为指示菌,通过单因子和均匀设计实验,发现菌株最佳产抗摇瓶发酵培养基:玉米面0.34%,豆饼粉1.66%,葡萄糖0.1%,ZnSO40.04%,MgSO40.02%,KH2PO40.04%;发酵条件:种龄12h,接种量10%,发酵时间20h,初始pH6.0,250mL三角瓶内含25mL培养基,往复式摇床,116次/min,振幅11cm,培养温度28℃。应用二剂量法(以制霉菌素为标样)测定B25W抗生素的相对效价为13680u/mL,比优化前效价(8444u/mL)提高了62%。     

The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species

Background

Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known.

Results

The complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis.

Conlusion

Our findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1545-x) contains supplementary material, which is available to authorized users.     

蔗渣发酵菌剂培养基的筛选及发酵条件的优化

采用单因素和正交试验研究了蔗渣高效发酵菌剂(芽孢杆菌B-A、曲霉菌F-A、链霉菌A-B)的摇瓶发酵最佳工艺条件.结果表明:芽孢杆菌B-A的最佳培养基配方:牛肉膏0.3%、蛋白胨1%、葡萄糖1%、NaCl 0.5%、可溶性淀粉0.5%、3.08%浓度的MnSO4溶液0.1;最适发酵条件为pH7、装液量100 ml(250 ml三角瓶)、36℃培养27 h.曲霉F-A的最佳培养基配方:葡萄糖3%、豆饼粉3%、蛋白胨1.2%、酵母膏0.3%、K2HPO4 0.05%、KH2PO40.05%、CaCl20.08%、MgSO40.04%、MnSO40.04%、ZnSO40.02%;最适发酵条件为pH6、装液量50 ml、30℃培养3 d.链霉菌A-B的最佳培养基配方:可溶性淀粉4.5%、蔗糖1%、豆饼粉3%、NaNO30.2%、ZnSO40.01%、KH2PO40.001%;最适发酵条件为pH7、装液量50 ml、30℃培养3 d.     

产L—肉碱的菌种筛选及发酵条件优化

将D,L-肉碱(carnitine,β-羟基-γ-三甲胺丁酸)用浓硫酸脱水获得反-巴豆甜菜碱(trans-crotonobetaine),从本室保藏的菌株中筛选出1株能将反-巴豆甜菜碱非对称合成L-肉碱的菌株E.coliK74.利用它的休止细胞立体选择性地水合反-巴豆甜菜碱产生L-肉碱,起催化作用的酶是L-肉碱脱水酶,是一种可诱导的胞内酶,当培养基中加入反-巴豆甜菜碱并在部分厌氧条件下可诱导产生.如培养基中含有葡萄糖、硝酸盐或氧时,酶的合成受到抑制,在磷酸缓冲液中,E.coliK74休止细胞的最适反应条件是pH为7.8,温度为37～42℃.     

Production of the Monamycins, Novel Depsipeptide Antibiotics

Methods are described for the production of the monamycins by Streptomyces jamaicensis in shake flasks and jar fermentors. The effects on the fermentation of variations in pH, temperature, medium composition, volume of inoculum, and strain of the organism are discussed. The methods employed for the extraction and for the microbiological assay of the antibiotics are outlined.     

Potential of bulb-associated bacteria for biocontrol of hyacinth soft rot caused by Dickeya zeae

Aims:  Dickeya zeae is a pectinolytic bacterium responsible for soft rot disease in flower bulb crops. In this study, the possibility of controlling soft rot disease in hyacinth by using antagonistic bacteria isolated from hyacinth bulbs was explored.
Methods and Results:  Bacterial isolates with potential for biocontrol were selected on the basis of antibiosis against D. zeae , siderophore production, and the N -acyl homoserine lactones (AHLs)-inactivation. In in vitro assays, 35 out of 565 hyacinth-associated bacterial isolates produced antimicrobial substances against D. zeae, whereas 20 degraded AHLs, and 35 produced siderophores. Isolates of interest were identified by 16S rDNA sequence analysis and reaction in BIOLOG™ tests. Twenty-six isolates that differed in characteristics were selected for pathogenicity testing on hyacinth cultivars, Pink Pearl and Carnegie. Two strains identified as Rahnella aquatilis and one as Erwinia persicinus significantly reduced tissue maceration caused by D. zeae 2019 on hyacinth bulbs, but not on leaves.
Conclusions:  Hyacinth bulbs harbour bacteria belonging to different taxonomic groups that are antagonistic to D. zeae , and some can attenuate decay of bulb tissue.
Significance and Impact of the Study:  Selected hyacinth-associated bacterial isolates have potential for control of soft rot disease caused by D. zeae in hyacinth bulb production.     

菜籽粕制备复合氨基酸螯合铜的工艺优化

发酵工艺已成功开发并用于生产大部分必需氨基酸,但蛋氨酸却是例外.尽管已经尝试利用微生物法生产蛋氨酸,但至今未能实现商业化生产.本文详细讨论了大肠杆菌、棒状杆菌和短杆菌等有潜在产蛋氨酸能力的菌株体内的蛋氨酸生物合成调节机制,阐述了微生物发酵法产蛋氨酸的研究进展,对蛋氨酸发酵生产的发展前景进行了展望.     

引起芭蕉芋细菌性软腐病的玉米迪基氏菌(Dickeya zeae)CE1的全基因组序列及比较基因组学分析

【背景】玉米迪基氏菌(Dickeya zeae)可引起香蕉、水稻等重要作物的细菌性软腐病,并造成巨大的损失。芭蕉芋抗性较好且与病虫害相关的报道很少,本研究团队首次报道了由D.zeae CE1引起的芭蕉芋细菌性软腐病。【目的】揭示CE1菌株的全基因组序列,并与同样来源于广东香蕉和水稻的D. zeae菌株作比较基因组学分析,初步探讨D. zeae种内不同病原细菌在与寄主互作过程中可能存在的遗传分化机制。【方法】采用三代测序结合二代测序对CE1菌株进行完整基因组测序,利用比较基因组学方法分析该菌株与香蕉和水稻菌株的进化关系和基因组特征差异。【结果】细菌基因组测序表明,CE1菌株的完整基因组大小为4 714 731 bp,注释预测到4 052个编码基因。与芭蕉芋和香蕉两个寄主亲缘关系类似,基因组比较分析发现来自芭蕉芋和香蕉的病菌菌株亲缘关系较近,它们在遗传进化上明显不同于水稻菌株。基因家族分析表明,编码重要致病因子如细菌分泌系统、鞭毛蛋白、胞外多糖、规律间隔成簇短回文重复序列(clustered regularly interspaced short palindromic repeats,C...     

Comparative analysis of two members of the metal ion-containing group III-alcohol dehydrogenases from Dickeya zeae

Purpose of work

A pair of NAD⁺- and NADP⁺-dependent group III-alcohol dehydrogenases was characterized from the enterobacterium, Dickeya zeae, to expand our understanding of the distribution and biochemical properties of this interesting group of enzymes. Two putative group III-alcohol dehydrogenases (ADHs) were identified in the genome of Dickeya zeae. Amino acid alignments and phylogenetic analysis revealed that Adh3.1 and Adh3.2 are only distantly related (~25 % identity at the protein level). Both proteins were purified to homogeneity after heterologous expression in E. coli. A specific activity of 1.8 U/mg was measured for the NAD⁺-dependent enzyme Adh3.1 with ethanol used as substrate, while NADPH-dependent Adh3.2 preferred butanal (29.1 U/mg) as substrate. Maximum activity for Adh3.1 was at 50 °C and pH 10 and for Adh3.2 at 70 °C and pH 6. Cell viability assays were used to confirm activity towards butanal and glyoxals. Biochemical characterization and phylogenetic analyses led to the hypothesis that Adh3.1 and Adh3.2 are probably the result of an ancient gene duplication event followed by functional diversification.     

短小芽胞杆菌产碱性木聚糖酶发酵条件的研究

碱性木聚糖酶在碱性条件下催化水解木聚糖,广泛应用于造纸、纺织等领域.着重对短小芽胞杆菌M-11产碱性木聚糖酶的发酵条件进行初步的探索.研究了菌株的生长曲线、确定最佳接种龄为16 h、最佳接种量为1％;确定最适碳源浓度为7％、最适单一氮源为氯化铵、其浓度为1.0％、最适无机盐为氯化铁、其浓度为3 mmol/L;在此基础之上进行6因素3水平的正交试验,确定最适产酶培养基组成:麸皮5％,接种量3％,氯化铵1.2％,氯化铁3.5 mmol/L,硫酸镁0.03％,氯化钠5 mmol/L,磷酸氢二钾0.4％;最适培养条件:接种龄16 h,初始pH 8.0,温度37℃,300 mL摇瓶装液量50 mL,摇床转速220 r/min,发酵周期48 h.通过对发酵条件的优化使发酵液酶活达613 IU/mL.无机氮源为其最适氮源,因此短小芽胞杆菌M-11在碱性木聚糖酶的产品开发上优于短小芽胞杆菌M -26.     

一株根霉产脂肪酶发酵条件的研究

通过对筛选出的一株根梅ＲｈｉｚｏｐｕｓＹ－９２产旨肪肪酶发酵２基组成（Ｃ,Ｎ,无机盐）及工艺条件的探索,并经正交实验,得到较优培养基配方为：蛋白胨６％,豆饼粉４％,葡萄糖１％,ＭｇＳＯ４·７Ｈ２Ｏ０．１％,ＫＨ２ＰＯ４０．３％,起始ＰＨ８．０,在此条件下,发酵液酶活可达９９．１５ｕ／ｍｌ,是初始酶活的１７８％。     

A novel multidomain polyketide synthase is essential for zeamine production and the virulence of Dickeya zeae

Dickeya zeae is the causal agent of the rice foot rot disease, but its mechanism of infection remains largely unknown. In this study, we identified and characterized a novel gene designated as zmsA. The gene encodes a large protein of 2,346 amino acids in length, which consists of multidomains arranged in the order of N-terminus, β-ketoacyl synthase, acyl transferase, acyl carrier protein, β-ketoacyl reductase, dehydratase. This multidomain structure and sequence alignment analysis suggest that ZmsA is a member of the polyketide synthase family. Mutation of zmsA abolished antimicrobial activity and attenuated the virulence of D. zeae. To determine the relationship between antimicrobial activity and virulence, active compounds were purified from D. zeae EC1 and were structurally characterized. This led to identification of two polyamino compounds, i.e., zeamine and zeamine II, that were phytotoxins and potent antibiotics. These results have established the essential role of ZmsA in zeamine biosynthesis and presented a new insight on the molecular mechanisms of D. zeae pathogenicity.     

酵母菌产麦角固醇发酵条件的研究

为了提高酵母菌麦角固醇的产量,采用摇瓶培养法,对筛选出的一株酵母菌YN2产麦角固醇发酵条件进行了研究。结果表明,酵母菌YN2产麦角固醇适宜的培养基配方为：酵母粉1％,牛肉膏2．5％,葡萄糖8％,K2HPO4 0．3％,MgSO4 0．15％,该菌株产麦角固醇最适培养条件为：培养温度28℃,起始pH6．5,发酵时间72h。在优化的实验条件下,麦角固醇含量可达2．2％,100ml发酵液中麦角固醇产量达25．30mg。     

L-缬氨酸发酵生产的育种思路及发酵条件优化策略

L-缬氨酸在医药及饲料领域中有着广泛的用途,根据L缬氨酸的生物合成途径及其代谢调节机制,利用代谢调控理论,重点阐述了L缬氨酸生产菌的育种思路及培养条件的优化,为缬氨酸发酵生产提供理论指导。     

Novel Method of Lactic Acid Production by Electrodialysis Fermentation

In lactic acid fermentation by Lactobacillus delbrueckii, the produced lactic acid affected the lactic acid productivity. Therefore, for the purpose of alleviating this inhibitory effect, an electrodialysis fermentation method which can continuously remove produced lactic acid from the fermentation broth was applied to this fermentation process. As a result, the continuation of fermentation activity was obtained, and the productivity was three times higher than in non-pH-controlled fermentation. In electrodialysis fermentation, the amount of produced lactic acid was 82.2 g/liter, which was about 5.5 times greater than that produced in non-pH-controlled fermentation. It was concluded that these good results were obtained on account of alleviating the lactic acid inhibitory effect by electrodialysis fermentation. However, the fouling of anion-exchange membranes by cells was observed in electrodialysis fermentation.     

腺苷蛋氨酸发酵条件及发酵培养基的优化

腺苷蛋氨酸具有转甲基、转硫和转氨丙基等重要生理作用 ,已成为治疗疾病的重要药物。研究了腺苷蛋氨酸发酵条件及发酵培养基的优化。结果表明 :发酵培养基的最适初始pH值为5.0 ;最佳发酵温度为 30℃ ;最适底物浓度为 1 % ;8%蔗糖为最佳碳源 ;0.5 %的NH4NO3 为最佳氮源 ;无机离子的最佳组合为 0.01 %MgSO4·7H2 O、0.03%CaCl2 、0.04%FeSO4·7H2 O和 0.01%LiCl。     

粘质沙雷氏菌产几丁质酶发酵条件的研究

目的：通过对粘质沙雷氏菌发酵条件的优化,提高其产几丁质酶的能力。方法：以实验室保存菌种粘质沙雷氏菌S418为对象,通过单因素试验和三因素三水平正交试验筛选出了菌株S418产几丁质酶的最佳培养基配方及培养条件。结果：该菌种产酶的最佳发酵条件：0.2%（w/v）胶体几丁质,1%蛋白胨,0.05%KH2PO4,在28℃、pH7.0、接种量6%,培养72h,酶活达到5.49U/mL。结论：优化后菌株S418产几丁质酶的条件。