地中海富盐菌中非编码RNA的鉴定与分析

【目的】通过转录组高通量测序技术(即RNA-seq),结合生物信息学分析和分子生物学方法,在组学水平鉴定极端嗜盐菌中可能的非编码RNA(nc RNA)。【方法】将培养至对数中期的地中海富盐菌在不同盐浓度下处理30分钟,提取RNA,进行链特异的转录组测序和5′端区分的转录组测序,通过生物信息学分析在全基因组范围内鉴定nc RNA,预测其转录边界;然后通过Northern blot和环化RNA反转录聚合酶链式反应(CR-RT-PCR)对部分预测的nc RNA进行实验验证。【结果】比较两种RNA-seq技术在不同培养条件下的RNA测序结果和对转录单元的精细分析,共鉴定到105个高可信度的nc RNA,并发现4个在不同盐度下表达差异较大的nc RNA,通过Northern blot和CR-RT-PCR验证了inc RNA1436和inc RNA1903的表达情况、转录本、转录起始位点及终止位点等。【结论】首次在组学水平鉴定了地中海富盐菌中的nc RNA,不同盐浓度刺激下部分nc RNA的转录差异暗示其有可能参与地中海富盐菌对盐胁迫的适应,高可信度nc RNA的组学发现为今后全面开展嗜盐古菌nc RNA的功能机制研究提供了基础数据及重要的切入点。     

一株聚羟基脂肪酸酯合成菌的筛选及鉴定

【背景】传统石油基塑料产品给人类和环境带来的危害日益严重,聚羟基脂肪酸酯(polyhydroxyalknoates,PHA)作为新型可降解塑料原料越来越受到青睐。但PHA生产成本过高,使其推广应用严重受限。筛选适合大规模生产PHA的高产菌株是解决这一问题的重要途径。【目的】以挖掘合成PHA的菌种资源为目标,从极端环境筛选和鉴定新的高产PHA合成菌。【方法】通过尼罗蓝平板分离法和PCR法分离纯化菌株,采用16S rRNA基因鉴定并通过MEGA 6.0软件构建系统发育树,分析菌株的进化关系,最后通过尼罗红染色定性分析和气相色谱法定量测定该菌株在不同时期的PHA积累量。【结果】从盐碱地垃圾沉积物中分离得到了一株高产PHA的菌株,PhaC的PCR扩增结果证实了该菌株是PHA合成菌,经16S rRNA基因鉴定为Pseudomonas brassicacearum,将其命名为NP-2,进一步优化了菌株NP-2的培养条件,在培养48h时PHA积累量最大,达到3.78 mg/mL。【结论】NP-2属于Pseudomonas brassicacearum,能高产PHA。本研究为生产PHA提供了极端环境的...     

产聚羟基脂肪酸酯细菌的筛选与鉴定

【目的】聚羟基脂肪酸酯(polyhydroxyalkanoates,PHAs)是一种生物可降解的天然高分子聚酯,本研究的目的是从广东省某啤酒厂废弃的活性污泥中分离筛选PHAs产生菌。【方法】首先,从活性污泥中分离PHAs产生菌。分离方法分3步:(1)富集培养PHAs产生菌;(2)通过苏丹黑B染色法进行初筛;(3)挑选PHAs产量较高的菌株,然后对细胞内提取产物进行分析,最后通过生理生化试验和16SrRNA基因序列分析法对该菌株进行鉴定。【结果】从广东省某啤酒厂的活性污泥样品中筛选获得PHAs产生菌HG-B-1,被鉴定为嗜麦芽寡养单胞菌(Stenotrophomonas maltophlia)。细胞染色分析、胞内提取物的红外光谱分析表明HG-B-1胞内贮藏物为PHAs。该菌株在以蔗糖为碳源、牛肉膏为氮源的发酵培养基中,37℃振荡培养24h,PHAs产量可达细胞干重的23.4%。【结论】本文从广东省某啤酒厂的活性污泥中筛选得到PHAs产生菌,获得了一株新型的PHAs产生菌,为进一步研究和开发新型的PHAs产生菌提供了菌源和基础资料。     

极端嗜盐古菌中CRISPR结构的生物信息学分析

摘要：【目的】利用生物信息学方法了解目前拥有全基因组序列的极端嗜盐古菌中CRISPR结构的特征。【方法】通过比对,保守性分析,GC含量分析,RNA结构预测等方法对已有全基因组序列的嗜盐古菌基因组进行研究。【结果】在5株嗜盐古菌基因组中发现CRISPR结构,在leader序列内得到具有回文性质的保守motif。发现在大CRISPR结构内repeat序列具有很强的保守性。同时根据第四位碱基的不同,repeat序列可形成两类不同的RNA二级结构。【结论】leader序列中回文结构的发现对其可能为蛋白结合位点的假     

盐芥miR396的表达分析、前体克隆及靶基因预测

利用实时定量PCR的方法分析了tsa-mi R396在盐芥不同组织的表达情况及盐、冷胁迫下的表达量变化,结果显示tsami R396在盐芥的不同组织均有表达,且在盐芥幼苗受盐、冷胁迫处理2 h后其表达量明显上升,随后呈波动性变化。利用在线软件ps RNATarget预测到25个tsa-mi R396的靶基因并进行功能分类。成功克隆tsa-mi R396前体,并利用Mfold在线软件分析该前体能够折叠形成茎环结构。     

基于PHA颗粒-PhaP标签和内含肽元件的极端嗜盐古菌蛋白的表达纯化系统

【目的】建立一个基于PHA颗粒-PhaP标签的简便实用的极端嗜盐古菌蛋白表达纯化系统,并探讨嗜盐古菌内含肽在该系统优化中的应用。【方法】以嗜盐古菌-大肠杆菌穿梭载体pWL502为基本骨架,构建带有嗜盐古菌强启动子和PhaP融合标签的表达载体;在地中海富盐菌phaP缺陷株(ΔphaP)中融合表达目的基因,通过蔗糖密度梯度离心分离纯化结合于PHA颗粒上的PhaP融合蛋白;在phaP基因与多克隆位点之间引入特定的嗜盐古菌内含肽元件,尝试通过定点突变改变该内含肽的剪切活性。【结果】成功构建了以PhaP作为N端融合标签的表达载体pPM以及作为C端融合标签的载体pIP;在phaP基因簇强启动子控制下,二者均实现了目标蛋白的高效表达;通过PHA颗粒介导的蛋白分离纯化策略,实现了以PhaP为融合标签的目标蛋白的分离纯化;发现内含肽序列Hbt21在地中海富盐菌中保持了高效的剪接活性,通过定点突变其C端末位氨基酸天冬酰胺(N182)及邻位的丝氨酸(S183)失活了该内含肽的C端剪接活性。【结论】首次建立了一个基于PHA颗粒-PhaP标签的简便节约的极端嗜盐古菌蛋白表达纯化系统,并确定了嗜盐古菌型内含肽C端剪接的活性位点,为该内含肽将来应用于PhaP融合蛋白的标签去除奠定了基础。     

嗜盐菌中甘氨酸甜菜碱的合成途径及其生物学功能

在嗜盐菌长期的盐适应或短期的盐胁迫过程中,甘氨酸甜菜碱(又名三甲基甘氨酸,N,N,N-trimethylglycine)发挥着极为重要的作用。甘氨酸甜菜碱在嗜盐菌中的生物合成有2种途径:胆碱氧化途径和甘氨酸甲基化途径。前者以胆碱为底物,由胆碱脱氢酶(cholinedehydrogenase,BetA)和甜菜碱乙醛脱氢酶(betaine aldehyde dehydrogenase,BetB)经2次氧化生成甜菜碱;后者以甘氨酸作为底物,由甘氨酸肌醇甲基转移酶(glycine sarcosine N-methyltransferase,GSMT)和肌氨酸二甲基甘氨酸甲基转移酶(sarcosine dimethylglycine N-methyltransferase,SDMT)经3次N-甲基化生成甜菜碱。目前在JGI-IMG和EZBioCloud数据库中公布了134株嗜盐菌标准菌株的全基因组序列。其中,约56.0%的嗜盐细菌和约39.6%的嗜盐古菌拥有胆碱氧化途径所需的2个基因;约9.7%的嗜盐细菌和约0.7%的嗜盐古菌携带甲基化途径所需的2个基因。其中,8株嗜盐细菌同时拥有胆碱氧化途径和甘氨酸甲基化途径所需的全部基因。甘氨酸甜菜碱生物合成基因在典型微生物菌株或经济作物中的表达可以提高其耐盐抗逆能力,这种独特的优势已经引起科学家们强烈的兴趣,相信未来,嗜盐菌中甘氨酸甜菜碱生物合成领域内的科学理论和技术应用会有重大的突破。     

地中海拟无枝菌酸菌U32中生物素羧基载体蛋白结构基因的克隆、表达及转录

乙酰辅酶A羧化酶(Acetyl CoA Carboxylase EC 6.4.1.2, ACC)催化依赖于ATP的乙酰辅酶A羧化形成丙二酸单酰辅酶A,该反应是脂肪酸生物合成途径中的第一步,也是受到调控的关键一步。根据结核分枝杆菌(M. tuberculosis)和天蓝色链霉菌(S. coelicolor)中ACC-α亚基的氨基酸保守序列和地中海拟无枝菌酸菌U32对氨基酸密码子的使用偏好,设计简并引物以U32基因组DNA为模板扩增出一条约250bp的片段,并以此片段作探针成功地从U32基因组cosmid文库中克隆到相应的ACC-α亚基的编码基因accA。该基因对应的ORF长1797bp,编码一个598个氨基酸的蛋白,推算出的分子量是63,714Da;基因G+C mol%含量为70.1%,符合U32基因结构特征,距起始密码子GTG上游6个碱基处有链霉菌典型的RBS序列AGGAGG,并有生物素羧化酶特征的ATP结合区。利用pET28(b)系统构建表达载体,在E. coli BL21(DE3)中实现了accA的诱导表达,产物大部分以可溶形式存在,并通过Western Blot证明该蛋白上确有共价结合的生物素。Northern Blot分析了各种氮源对accA基因转录水平的不同影响。     

地中海拟无枝菌酸菌U32中amrC／amkC基因的序列分析及在大肠杆 …

从力复霉素ＳＶ产生菌－－地中海拟无枝菌酸菌（Ａｍｙｃｏｌａｔｏｐｓｉｓ ｍｅｄｉｔｅｒｒａｎｅｉ）Ｕ３２的硝酸盐同化基因簇的上游克隆了一个２．６ｋｂ的ＥｃｏＲＩ－ＸｈｏＩ ＤＮＡ片段并测定其序列。序列分析表明,该ＤＮＡ片段编码两个完整的开放阅读框架（ＯＲＦ）,ＯＲＦ２的起始密码子ＧＴＧ与ＯＲＦ１的终止密码子ＴＧＡ在ＴＧ处重叠。ＯＲＦ１编码一个含２２４个氨基酸的多肽,它同放线菌中典型的应答调节蛋白包     

来源于马赛菌(Massilia sp.) UMI-21的ACSMU和PhaCMU体外表达及功能研究

【目的】构建马赛菌(Massilia sp.) UMI-21来源乙酰辅酶A合成酶ACS_MU和聚羟基脂肪酸酯(polyhydroxyalkanoate, PHA)合酶PhaC_MU的体外重组表达体系并过表达2种酶,利用体外合成体系确定2种酶在Massilia sp. UMI21聚3-羟基丁酸(polyhydroxybutyrate, PHB)合成途径中的主要功能。【方法】利用无缝克隆技术将来源于Massilia sp. UMI-21的乙酰辅酶A合成酶基因acs_MU和PHA合酶基因phaC_MU扩增后与pQE-80L质粒连接,转导大肠杆菌(Escherichia coli) BL21(DE3)构建2个基因的重组表达体系;利用6×His标签纯化蛋白ACS_MU和PhaC_MU,并采用5,5′-二硫双(2-硝基苯甲酸) [5,5′-dithiobis-(2-nitrobenzoic acid), DTNB]法测定其活性;使用体外单相合成系统(one-phase reaction system, OPRS),以(R)-3HB为底物,验证ACS_MU和PhaC_MU这2种酶在合成PHB途径中的功能。【结果】成功构建了ACS_MU和PhaC_MU蛋白重组表达菌株BL21-pQE-80L-acs_MU和BL21-pQE-80L-phaC_MU,提纯得到过表达蛋白ACS_MU和PhaC_MU产率分别为24.8 mg/L和25.6 mg/L;ACS_MU酶比活力为(0.148±0.011) U/mg。PhaC_MU酶对(R)-3HBCoA的比活力为(0.102±0.011) U/mg;核磁共振氢谱(nuclear magnetic resonance hydrogen spectroscopy, ¹H-NMR)分析结果表明,使用ACS_Pt-PCT_CP-PhaC_Re、ACS_MU-PCT_CP-PhaC_Re和ACS_MU-PCT_CP-PhaC_MU这3条OPRS途径均能合成PHB,产量分别为0.62、0.76和0.64 g/L。【结论】acs_MU和phaC_MU基因可利用大肠杆菌表达体系过表达并可获得具有活性的可溶性蛋白;对比ACS_Pt-PCT_CP-PhaC_Re合成体系,ACS_MU替代ACS_Pt合成PHB产量增加22.58%,在聚合酶相同的情况下,PHB的合成产量依赖乙酰辅酶A合成酶(acetyl-CoA synthase, ACS)合成乙酰辅酶A的稳定性。使用PhaC_MU代替PhaC_Re,对比ACS_MU-PCT_CP-PhaC_Re组合,合成PHB产量减少了15.79%。在聚合前体浓度相同的情况下,PHB合成量依赖聚合酶的活性。     

Alignment of genes and SwaI restriction sites to the BamHI genomic map of Haloferax mediterranei

Abstract Eleven Swa I restriction sites and ten genes have been aligned to the Bam HI physical map of the main chromosome of the halobacterium Haloferax mediterranei ATCC33500, using two-dimensional pulsed field gel electrophoresis and hybridization experiments.     

Adaptive response of Haloferax mediterranei to low concentrations of NaCl (< 20%) in the growth medium

Halobacteria require 20–25% NaCl for optimal growth and lyse when the salt concentration falls below 10%. The response of Haloferax mediterranei cells to low concentrations of NaCl (< 20%) in the medium was studied. The cells adapted to and grew in concentrations of NaCl as low as 10% and survived in concentrations lower than 5%. The cells synthesised a red pigment, bacterioruberin, in response to stress caused by a low concentration of NaCl (< 20%). Received: 3 January 1997 / Accepted: 18 April 1997     

Immobilization of Haloferax mediterranei aldolase by cross-linking in a proteinic matrix: stability and halophilic characteristics

Fructose-1,6-bisphosphate (FBP) aldolase (EC 4.1.2.13) of Haloferax mediterranei was immobilized by treating the cell extract in the presence of 10% BSA, with the cross-linking reagent, 0.5% glutaraldehyde for 15min, with the retention of 60% of its original activity. The immobilized preparation exhibited a shift in the temperature optimum from 55°C to 65°C. The enzyme showed enhanced stability towards inactivation by radiation and storage (0–5°C) on immobilization. Immobilization also made the enzyme less halophilic, reducing its denaturation on prolonged storage in a non-salt medium, as well as exhibiting optimal activity at a lower KCl concentration (0.5m) as compared to the soluble enzyme (1–2m).     

Identification of several intracellular carbohydrate-degrading activities from the halophilic archaeon Haloferax mediterranei

Three different amylolytic activities, designated AMY1, AMY2, and AMY3 were detected in the cytoplasm of the extreme halophilic archaeon Haloferax mediterranei grown in a starch containing medium. This organism had also been reported to excrete an α-amylase into the external medium in such conditions. The presence of these different enzymes which are also able to degrade starch may be related to the use of the available carbohydrates and maltodextrins, including the products obtained by the action of the extracellular amylase on starch that may be transported to the cytoplasm of the organism. The behavior of these intracellular hydrolytic enzymes on starch is reported here and compared with their extracellular counterpart. Two of these glycosidic activities (AMY1, AMY3) have also been purified and further characterized. As with other halophilic enzymes, they were salt dependent and displayed maximal activity at 3 M NaCl, and 50°C. The purification steps and molecular masses have also been reported. The other activity (AMY2) was also detected in extracts from cells grown in media with glycerol instead of starch and in a yeast extract medium. This enzyme was able to degrade starch yielding small oligosaccharides and displayed similar halophilic behavior with salt requirement in the range 1.5–3 M NaCl. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparison of four phaC genes from Haloferax mediterranei and their function in different PHBV copolymer biosyntheses in Haloarcula hispanica

Background

Cyanobacteria are recognized as the primordial organisms to grace the earth with molecular oxygen ~3.5 billion years ago as a result of their oxygenic photosynthesis. This laid a selection pressure for the evolution of antioxidative defense mechanisms to alleviate the toxic effect of active oxygen species (AOS) in cyanobacteria. Superoxide dismutases (SODs) are metalloenzymes that are the first arsenal in defense mechanism against oxidative stress followed by an array of antioxidative system. Unlike other living organisms, cyanobacteria possess multiple isoforms of SOD. Hence, an attempt was made to demonstrate the oxidative stress tolerance ability of marine cyanobacterium, Leptolyngbya valderiana BDU 20041 and to PCR amplify and sequence the SOD gene, the central enzyme for alleviating stress.

Result

L. valderiana BDU 20041, a filamentous, non-heterocystous marine cyanobacterium showed tolerance to the tested dye (C.I. Acid Black 1) which is evident by increased in biomass (i.e.) chlorophyll a. The other noticeable change was the total ROS production by culture dosed with dye compared to the control cultures. This prolonged incubation showed sustenance, implying that cyanobacteria maintain their antioxidant levels. The third significant feature was a two-fold increase in SOD activity of dye treated L. valderiana BDU20041 suggesting the role of SOD in alleviating oxidative stress via Asada-Halliwell pathway. Hence, the organism was PCR amplified for SOD gene resulting in an amplicon of 550 bp. The sequence analysis illustrated the presence of first three residues involved in motif; active site residues at H4, 58 and D141 along with highly conserved Mn specific residues. The isolated gene shared 63.8% homology with MnSOD of bacteria confirmed it as Mn isoform. This is the hitherto report on SOD gene from marine cyanobacterium, L. valderiana BDU20041 of Indian subcontinent.

Conclusion

Generation of Reactive Oxygen Species (ROS) coupled with induction of SOD by marine cyanobacterium, L. valderiana BDU20041 was responsible for alleviating stress caused by an azo dye, C. I. Acid Black 1. The partial SOD gene has been sequenced and based on the active site, motif and metal specific residues; it has been identified as Mn metalloform.     

The effect of ammonium on assimilatory nitrate reduction in the haloarchaeon Haloferax mediterranei

Physiology, regulation and biochemical aspects of the nitrogen assimilation are well known in Prokarya or Eukarya but they are poorly described in Archaea domain. The haloarchaeon Haloferax mediterranei can use different nitrogen inorganic sources (NO₃⁻, NO₂⁻ or NH₄⁺) for growth. Different approaches were considered to study the effect of NH₄⁺ on nitrogen assimilation in Hfx. mediterranei cells grown in KNO₃ medium. The NH₄⁺ addition to KNO₃ medium caused a decrease of assimilatory nitrate (Nas) and nitrite reductases (NiR) activities. Similar effects were observed when nitrate-growing cells were transferred to NH₄⁺ media. Both activities increased when NH₄⁺ was removed from culture, showing that the negative effect of NH₄⁺ on this pathway is reversible. These results suggest that ammonium causes the inhibition of the assimilatory nitrate pathway, while nitrate exerts a positive effect. This pattern has been confirmed by RT-PCR. In the presence of both NO₃⁻ and NH₄⁺, NH₄⁺ was preferentially consumed, but NO₃⁻ uptake was not completely inhibited by NH₄⁺ at prolonged time scale. The addition of MSX to NH₄⁺ or NO₃⁻ cultures results in an increase of Nas and NiR activities, suggesting that NH₄⁺ assimilation, rather than NH₄⁺ per se, has a negative effect on assimilatory nitrate reduction in Hfx. mediterranei. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Purification and characterisation of a possible assimilatory nitrite reductase from the halophile archaeon Haloferax mediterranei

The nitrite reductase from the extreme halophilic archaeon, Haloferax mediterranei, has been purified and characterised. H. mediterranei is capable of growing in a minimal medium (inorganic salts and glucose as a carbon source) with nitrate as the only nitrogen source. The overall purification was 46-fold with about 4% recovery of activity. The enzyme is a monomeric protein of approximately 66 kDa. A pH of 7.5 and high temperatures up to 60 degrees C are necessary for optimum activity. Reduced methyl viologen has been found to be an electron donor as effective as ferredoxin. NADPH and NADH, which are electron donors in nitrite reductases from different non-photosynthetic bacteria, were not effective with nitrite reductase from H. mediterranei.