Synthetic mutants of Clostridium pasteurianum ferredoxin: open iron sites and testing carboxylate coordination

The entire polypeptide chains for two new Clostridium pasteurianum ferredoxin (Fd) mutants were prepared with the following site-specific substitutions: Cys11Asp and Cys11 alpha-aminobutyric acid (Cys11 alpha- Aba), the latter being a non-naturally occurring amino acid. Standard t- Boc procedures were used for the synthesis and the peptides. The two apoproteins were reconstituted to the 2[4Fe-4S] holoprotein and their spectroscopic, redox and thermal properties were compared with those of native C.pasteurianum Fds. The fully reconstituted Cys11Asp and Cys11 alpha-Aba mutants were initially found to have both clusters intact, i.e. they were 2[4Fe-4S] ferredoxins. The unconventional ligands of Asp and alpha-Aba led to holo-Fds that were not very stable and easily released an iron to form the [3Fe-4S] cluster, presumably through oxidation. The Cys11 alpha-Aba mutant was somewhat more thermally stable than Cys11Asp. In contrast, while both mutants were less stable than the native protein upon exposure to oxygen, the Cys11 alpha-Aba mutant was less stable than Cys11Asp. The Cys11Gly mutant was also prepared, but all attempts, despite repeated and varied experimental conditions, at reconstitution to the Cys11Gly holo 2[4Fe-4S] Fd were unsuccessful, probably because a Gly-Gly sequence is known to break structure. This work, when compared with molecular biological site- specific mutagenesis, shows some of the advantages of chemical/in vitro reconstitution: certain mutants which cannot be detected as holoproteins by site-specific mutagenesis can be formed after all in vitro. Nonetheless, it seems apparent that altering any of the Cys coordination sites of the Fd clusters results in fundamentally more unstable ferredoxins.      

Expression of a synthetic gene coding for the amino acid sequence of Clostridium pasteurianum rubredoxin

A synthetic gene based on the published amino acid sequencefor Clostridium pasteurianum rubredoxin was constructed, clonedin Escherichia coli 71/18 and expressed using the T7 RNA polymerase/promotersystem in E.coli HMS273. UV/visible spectroseopy and metal analysesindicated that the as–isolated synthetic gene productis a mixture of holo–(i.e. iron–containing) rubredoxinand zinc–substituted rubredoxin, with the latter amountingto {small tilde} 70% of the total rubredoxin. Hie UV/visibleabsorption and resonance Raman spectra of the cloned holorubredoxinare characteristic of the native rubredoxin–type ironsite. N–terminal amino acid sequencing suggests that thegene product consists of at least three polypeptide specieswith the initial sequences (approximate relative abundances):Met–Met–Lys–... (63%), blocked (30%) and Met–Lys–...(7%). The blocked portion presumably consists of a mixture ofnMet–Met–Lys–... and nMet-Lys–..., wherenMet represents an amino–blocked methionine residue.     

重组柠檬酸杆菌合成紫色杆菌素的工艺条件优化

以L-色氨酸为前体物,对弗氏柠檬酸杆菌(Citrobacter freundii)基因工程菌株生产紫色杆菌素的工艺条件进行了优化。通过单因素实验研究了培养基种类、培养温度、碳源、溶氧、种子液的状态、接种量、诱导时机、诱导剂的浓度及初始pH对细胞生长和紫色杆菌素产量的影响,通过正交实验研究了这些因素中可能存在交互作用的4个因素(种子液OD660、接种量、诱导时机、诱导剂浓度)的影响主次,确定了这些因素、水平的最佳搭配方案。结果表明,重组柠檬酸杆菌合成紫色杆菌素的最优培养条件为:种子液培养至OD660=3.6时,以3%的接种量接种于以甘油为碳源、初始pH为6.5的磷酸盐发酵培养基E2(25μg.ml-1卡那霉素),先在37℃、200r.min-1下培养至OD660=1.4,然后加入0.5μl.ml-1的诱导剂正辛烷,同时转入20℃,在150r.min-1下诱导培养31h。在此最优条件下,紫色杆菌素粗提物(紫色杆菌素及脱氧紫色杆菌素的混合物)产量可达1.809g.L-1,比优化前(0.514g.L-1)提高了252%,是目前国际上其他研究小组报道的最高摇瓶产量(0.43g.L-1)的4.2倍。质粒稳定性实验结果表明重组柠檬酸杆菌在抗生素选择压力条件下具有良好的遗传稳定性。     

On the role of conserved proline residues in the structure and function of Clostridium pasteurianum 2[4Fe-4S] ferredoxin

The widespread occurrence of Pro residues adjacent to Cys ligandsin the sequences of [4Fe-4S] electron transfer proteins hasnot yet found a functional basis. The two such Pro of Clostridiumpasteurianum 2[4Fe-4S] ferredoxin have been probed by site-directedmutagenesis. Any one of them, but not both simultaneously, canbe substituted without impairing the proper folding of the protein.The reduction potentials of the ferredoxin variants fall ina narrow range of <20 mV above the potential of the nativeprotein. The biological activities with C.pasteurianum hydrogenaseand pyruvate-ferredoxin oxidoreductase do not change significantly,except when Lys replaces Pro. In these cases, the data suggestthat the two clusters of 2[4Fe-4S] ferredoxin may not alwaysbe equivalent in the interaction with the redox partners. Destabilizationof the structure has been observed as the consequence of theProl9 or Pro48 substitutions. Using 2-D NMR, this effect hasbeen associated with perturbations of both the hydrogen bondnetwork and one amino acid side chain around the [4Fe-4S] clusters.Thus, the conserved Pro found in the binding motif of [4Fe-4S]clusters in proteins strongly stabilizes the active site butdoes not play an essential role in the mechanism of electrontransfer.     

Adaptive evolution of Clostridium butyricum and scale-Up for high-Concentration 1,3-propanediol production

In order to obtain the excellent 1,3-propanediol (1,3-PDO) producer from wild-type Clostridium butyricum, adaptive evolution was carried out to select the strain for fast growth. The most significant change was that fermentation time decreased from 36 h to 20 h after adaptive evolution. Thus, it led to the corresponding volumetric productivity of 1,3-PDO increasing from 0.97 to 2.14 (g/L·h⁻¹) which increased by 114%. Adaptive evolution was also applied to butyric acid tolerant strain selected based on the fast-growing one through a simple equipment. 1,3-PDO concentration increased from 40.28 to 66.23 g/L through fed-batch fermentation by butyric acid tolerant strain compared with the fast-growing one. In addition, the endpoint strain was successfully and steadily used in the 50-L scale fermentation. Thus, adaptive evolution is an excellent strategy which can help us select the fast-growing strain and reduce the negative effect from substrate and metabolite inhibition. © 2018 American Institute of Chemical Engineers AIChE J, 65: 32–39, 2019     

ClostridiumsaccharobutylicumDSM13864细胞表面理化特性及固定化细胞产丁醇的性能

糖丁基梭菌Clostridium saccharobutylicum DSM 13864能利用多种糖类为底物发酵产丁醇。本文研究了该菌体细胞表面的理化特性,并以砖块作为细胞固定化材料进行丁醇发酵。采用细菌吸附有机溶剂(MATS)法证明糖丁基梭菌细胞表面有强烈的亲水性,并且等电点在pH值为3左右,这些特性有利于菌体与表面亲水多孔的砖块吸附。在60g/L葡萄糖发酵培养基中,以5～8目砖块作为固定化材料,流速为1.1L/min,发酵48h后,丁醇的浓度、得率和生产率分别达到11.02g/L、0.18g/g和0.23g/(L·h),相比悬浮细胞发酵分别提高了10.53%、5.88%和9.52%。结果表明:砖块作为一种固定化材料可有效提高糖丁基梭菌的发酵产丁醇水平。     

不同C源对丙酮丁醇梭菌产丁醇的影响

对丙酮丁醇梭菌在以葡萄糖、木糖、蔗糖、混合糖、玉米芯酸解糖液分别作C源的P2培养基中的产丁醇状况进行研究。结果表明:不同C源对丙酮丁醇梭菌发酵产丁醇有显著的影响;葡萄糖为底物时,丁醇产量最高达到13.50 g/L,总溶剂为19.66 g/L;蔗糖为底物时,丁醇所占比例都在70%以上,丁醇产量可达12 g/L;木糖、混合糖为底物时,丁醇产量在10 g/L左右;只有丙酮丁醇梭菌I4-28能利用玉米芯酸解糖液发酵产丁醇,丁醇产量为7 g/L。     

Accumulation of zirconium and nickel by Citrobacter sp

Zirconium in aqueous flows was moderately biomineralized by immobilized Citrobacter N14 cells, in the form of gel‐like deposits, probably comprising a mixture of zirconium hydrogen phosphate (Zr(HPO₄)₂) and hydrated zirconia (ZrO₂). The simultaneous presence of uranyl ion (UO) did not facilitate zirconium deposition and the biomineralization of uranium itself as HUO₂PO₄ was repressed by zirconium in the presence of excess inorganic phosphate, liberated enzymatically. Nickel (Ni²⁺) was not significantly removed from aqueous flows by sorption into cell‐bound zirconium deposits, although cell‐bound hydrogen uranyl phosphate (HUP) facilitated nickel removal via intercalative ion exchange into its polycrystalline lattice. A preformed layer of HUP also promoted zirconium removal, at 100% efficiency at pH 2.6, maintained over 38 column fluid‐volumes before saturation. © 1999 Society of Chemical Industry     

Lipidomic Analysis of Clostridium cadaveris and Clostridium fallax

The lipidomes of Clostridium fallax and Clostridium cadaveris were studied using thin-layer chromatography (TLC) and normal phase liquid chromatography/mass spectrometry (NPLC/MS). Both species contain diradylglycerol (DRG), monohexosyldiradylglycerol (MHDRG), monohexosyl monoacylglycerol (MHMAG), phosphatidylglycerol (PtdGro), and phosphatidylethanolamine (PtdEtn). DRG, MHDRG, PtdEtn, and PtdGro are present in both diacyl and alk-1-enyl acyl (plasmalogen) forms. Both species contain cardiolipin (Ptd₂Gro), which is present in tetraacyl, monoalkenyl-triacyl, and dialkenyl-diacyl forms. Both species contain small amounts of phosphatidylcholine (PtdCho). The presence of octadecadienoic (18:2) acyl chains in some PtdCho species indicates that they arise from the medium because no 18:2 is seen in the other lipids and clostridia generally lack the capacity to synthesize polyunsaturated fatty acids. The major lipidomic differences between these two species are that C. fallax contains a glycerolacetal of plasmenylethanolamine while C. cadaveris contains an ethanolamine-phosphate-modified diacylglycerol. The significance of these lipid compositions is discussed.     

A novel kinetic model to describe 1,3-propanediol production fermentation by Clostridium butyricum

Clostridium butyricum is one of the best 1,3-propanediol producers due to the nonpathogenic, less byproducts, and energy-efficient fermentation process. In fermentation process, the relationship among substrate, product, and byproducts is intricate and hard to be analyzed. The present study is aimed at establishing a novel kinetic model not only based on biomass, substrate, and 1,3-propanediol, but also considering the byproduct concentration to describe 1,3-propanediol fermentation process by C. butyricum. The simulative result of the model fit well with that in the batch fermentation process. Furthermore, the model was also used to predict the result of fed-batch fermentation process after some modifications. The predicted result of model fit well with the data in experiment when glycerol was controlled at around 10 g/L. Thus, this novel kinetic model could serve as a tool for further optimization of the fermentation process, and could be improved for some other similar processes.     

Citrobacter farmeri降解间甲酚的特性分析

从某焦化厂废水好氧生物处理的污泥中分离出一株能以间甲酚为唯一碳源、能源生长代谢的菌株Citrobacter farmeri.考察了间甲酚在不同初始浓度下Citrobacter farmeri细菌生长动力学,4种等浓度酚类物质的降解先后顺序,分别添加共基质葡萄糖和蛋白胨对低浓度和高浓度间甲酚降解的影响,以及在添加共基质葡...     

响应面法优化甘露醇产丁醇的发酵条件

以褐藻的主要成分甘露醇为底物,利用丙酮丁醇梭菌ATCC824发酵生产丁醇。采用Plackett-Burman（P-B）和Box-Behnken优化发酵条件。在Plackett-Burman实验设计时,考察牛肉膏、酵母浸粉、胰蛋白胨、乙酸铵、 KH2PO4、MgSO4?7H2O、FeSO4?7H2O、接种量、发酵温度、初始pH值这10个因素对丁醇产量影响,筛选出影响丁醇发酵的重要参数是发酵温度、初始pH值、乙酸铵浓度,利用Box-Behnken设计确定最优发酵条件为发酵温度37.3 ℃、初始pH值6.38、乙酸铵浓度2.82 g/L。数学模型分析预测最大丁醇产量为8.47 g/L。经实验验证表明,在优化条件下的丁醇产量平均值达到8.52±0.55 g/L。这说明利用统计学方法优化甘露醇的丁醇发酵条件是有效的。     

严格厌氧发酵体系在线尾气监测系统的设计及在梭菌生产生物能源丁醇的应用

目前关于有氧或微氧的乙醇发酵的尾气检测系统已经建立,但是对于丙酮丁醇梭菌等严格厌氧菌发酵尾气的在线监测鲜见文献报道。因此,本研究以丙酮丁醇梭菌生产丁醇的严格厌氧发酵体系为研究对象,研究了传统有氧或微氧尾气检测方法在丙酮丁醇梭菌厌氧发酵体系中的检测结果,设计并建立了适合厌氧菌发酵的尾气在线监测系统,对丙酮丁醇梭菌的发酵过程实时监测。在建立有效的厌氧发酵尾气分析系统的条件下,比较了丙酮丁醇梭菌在游离细胞条件下和高细胞密度条件下的发酵性能。相比较于游离发酵,高细胞密度发酵的发酵周期明显缩短,丁醇生产强度显著提高。丁醇最高产量为15.4g/L,生产强度0.64g/（L·h）,分别比对照组提高了12.4%和106%,CO₂和H₂最高产气速率分别提高60%和9%,产气量分别提高了20.7%和41.3%。尾气分析系统采集的气体数据为丙酮丁醇梭菌的代谢分析提供了重要依据。     

A mathematical model of a fluidized bed reactor for the continuous production of solvents by immobilized Clostridium acetobutylicum

A fluidized bed reactor has been employed for the continuous production of solvents from whey permeate using cells of Clostridium acetobutylicum immobilized by adsorption onto bonechar. Substrate diffusion equations have been developed for the bioparticles, and a mathematical model has been advanced to describe the operation of the reactor. The model was fitted to the experimental data using the concept that not all of the biomass within the reactor was active in solvent production. On this basis, less than 5% was ‘active’ biomass.     

The effect of raw glycerol concentration on the production of 1,3‐propanediol by Clostridium butyricum

Raw glycerol, the main by‐product of the bio‐diesel production process, was converted to 1,3‐propanediol by Clostridium butyricum F2b. In batch cultures, 47.1 g dm^?3 of 1,3‐propanediol were produced. Continuous cultures were conducted at a constant dilution rate (= 0.04 h^?1) and various inlet glycerol concentrations with 1,3‐propanediol produced at levels up to 44.0 g dm^?3. At increasing glycerol concentrations in the inlet medium, biomass yield decreased. This decrease was attributed to the microbial metabolism being directed towards the biosynthesis of organic acids (and hence carbon losses as CO₂) instead of biochemical anabolic reactions. An autonomous analytical model was developed, and quantified the effect of inlet glycerol concentration on the production of biomass and metabolites. Indeed, high inlet substrate concentrations positively affected the biosynthesis, principally of butyric acid and to a lesser extent that of acetic acid. In contrast, at increased glycerol concentrations, the relative increase of 1,3‐propanediol production per unit of substrate consumed was lower as compared with that of acetic and, mainly, butyric acid. This could be explained by the fact that the butyric acid pathway represents an alternative and competitive one to that of 1,3‐propanediol for re‐generation of NADH₂ equivalents in the microbial cell. Copyright © 2004 Society of Chemical Industry     

Protective and Anti-Inflammatory Effects of Protegrin-1 on Citrobacter rodentium Intestinal Infection in Mice

Infectious intestinal colitis, manifesting as intestinal inflammation, diarrhea, and epithelial barrier disruption, affects millions of humans worldwide and, without effective treatment, can result in death. In addition to this, the significant rise in antibiotic-resistant bacteria poses an urgent need for alternative anti-infection therapies for the treatment of intestinal disorders. Antimicrobial peptides (AMPs) are potential therapies that have broad-spectrum antimicrobial activity due to their (1) unique mode of action, (2) broad-spectrum antimicrobial activity, and (3) protective role in GI tract maintenance. Protegrin-1 (PG-1) is an AMP of pig origin that was previously shown to reduce the pathological effects of chemically induced digestive tract inflammation (colitis) and to modulate immune responses and tissue repair. This study aimed to extend these findings by investigating the protective effects of PG-1 on pathogen-induced colitis in an infection study over a 10-day experimental period. The oral administration of PG-1 reduced Citrobacter rodentium intestinal infection in mice as evidenced by reduced histopathologic change in the colon, prevention of body weight loss, milder clinical signs of disease, and more effective clearance of bacterial infection relative to challenged phosphate-buffered saline (PBS)-treated mice. Additionally, PG-1 treatment altered the expression of various inflammatory mediators during infection, which may act to resolve inflammation and re-establish intestinal homeostasis. PG-1 administered in its mature form was more effective relative to the pro-form (ProPG-1). To our knowledge, this is the first study demonstrating the protective effects of PG-1 on infectious colitis.