自然环境中T4型噬菌体g23基因多样性研究进展

摘要：过去的20多年,伴随着分子生物学技术在环境微生物研究中的应用,环境中细菌和真菌群落基因多样性及与其生存环境间的关系逐渐被揭示,但对于地球上广泛存在且数量巨大的生命体-噬菌体基因多样性研究还很少。本文以编码T4型噬菌体主要壳蛋白基因g23为目标,综述了近年来T4型噬菌体在海洋、湖泊和稻田中基因多样性的研究进展。研究结果表明T4型噬菌体g23基因分布与其生存环境关系很大,许多g23基因按获取环境不同划分为几个新类群。同时文中也指出了针对环境中T4型噬菌体g23基因研究应该注意的几点问题及未来的研究发展趋势。     

纳帕海高原湿地T4类噬菌体遗传多样性分析

噬菌体在微生物中分布较广。为研究T4类噬菌体在纳帕海高原湿地的分布情况,本研究从纳帕海湿地分别采集水样和淤泥土样,采用g23基因为分子探针,利用MZIA1和MZIA6引物对其进行扩增,共获得92条基因序列,并与其他不同生境的g23基因进行比对和遗传多样性研究。结果显示,纳帕海高原湿地的T4类噬菌体与海洋基因序列相距较远,而与淡水湖泊和稻田土壤及平原基因序列相距较近。但也有部分序列独立聚簇,推测其为纳帕海地区的独有基因序列。本研究充分说明纳帕海地区拥有独特而丰富的微生物资源,为研究高原淡水湖泊中噬菌体的生态功能提供了理论依据。     

中华苜蓿根瘤菌噬菌体的分离及主要壳蛋白基因g23的系统进化分析

【目的】揭示苜蓿根瘤菌噬菌体的形态学特征及主要壳蛋白g23基因的分布地位,为根瘤菌噬菌体的生态学研究提供数据支持。【方法】以中华苜蓿根瘤菌(Sinorhizobium meliloti USDA1002T)为宿主,采用双层平板法分离土壤环境中的苜蓿根瘤菌噬菌体,利用电子显微镜观察纯化的噬菌体形态特征;提取噬菌体DNA,PCR扩增编码噬菌体壳蛋白的g23基因,构建系统进化树,以形态学鉴定和分子生物学相结合的方法,明确分离获得的苜蓿根瘤菌噬菌体g23基因的系统进化地位。【结果】分离获得了3株噬菌体,头部均呈二十面体,直径大小为81–86 nm,尾部有收缩尾鞘,长度大约为54–70 nm。克隆测序结果显示,获得的3株噬菌体g23基因株间相似度较高,但与可培养的Exo T-、Schizo T-、T-、Pseudo T-evens相似度较低。系统进化分析表明,获得的3株噬菌体不隶属于目前已划分的不同环境噬菌体g23基因的分类类群中。【结论】3株噬菌体均属于肌尾噬菌体科的裂性噬菌体,与目前获得的所有噬菌体g23基因相似性较低,属于新的侵染中华苜蓿根瘤菌的噬菌体株。     

纳帕海高原湿地噬藻体g20基因系统发育多样性分析

【背景】噬藻体是感染蓝藻的病毒,是水生系统的重要组成部分。它们对宿主种群死亡率有重要影响,是控制蓝藻水华生消的潜在因子,对蓝藻群落结构的调控具有重要意义。大量研究揭示了海洋和淡水环境中噬藻体的高度多样性,但目前对高原湿地中噬藻体的多样性知之甚少。【目的】阐明我国纳帕海高原湿地噬藻体g20基因的遗传多样性,为进一步开展高原湿地微生物资源及其生态功能研究提供理论基础。【方法】采集雨季的水体样品,以衣壳蛋白基因g20为标记基因,利用特异性引物Cps1和Cps8对其进行PCR扩增,得到26条不同的g20基因有效序列,并将其与其他生境中g20基因序列进行主坐标分析和系统发育分析。【结果】与其他海洋和淡水的噬藻体序列相比,纳帕海高原湿地中噬藻体的序列与其他稻田序列更为相近;但也存在部分序列单独聚簇,这可能为纳帕海高原湿地中独有的噬藻体类型。【结论】表明该地区的噬藻体较丰富,并具有一定的独特性。     

金黄色葡萄球菌中PVL基因与噬菌体DNA的同源性*

为了探讨金黄色葡萄球菌PVL基因与噬菌体的相关性 ,从 4株含有PVL基因的菌株中分离出DNA ,用HindⅢ或EcoRⅠ酶切后 ,分别与PVL和LukM-lukF-PV探针进行Southern印迹杂交 ,以及对含有PVL基因及其下游区域的片段克隆、测序和同源性分析。结果表明3株菌的PVL基因及其下游区域的序列与V8菌株噬菌体∮PVL的PVL基因及其下游噬菌体attsite的序列     

利用T4噬菌体展示猪瘟病毒E2抗原

利用重组PCR技术将猪瘟病毒 (CSFV )E2蛋白主要抗原编码区基因 (mE2 )与T4噬菌体SOC基因融合 ,构建了大小为 643bp的SOC/mE2融合基因 ,再将其插入携带T4溶菌酶基因 (e)和(denV)基因的T4重组载体 (PRH) ,构建了重组载体pRsmE2。通过重组载体与缺失突变型T4发生同源重组 ,可将SOC/mE2融合基因整合入T4的基因组中 ,并成功地将大小约 2 1 5aaSOC/mE2融合蛋白展示于T4噬菌体衣壳表面。经Westernblot、胶体金免疫电镜等免疫学检测证实 ,展示于T4表面的mE2融合蛋白具有CSFV免疫学活性。     

人工湿地植物种类及多样性对甲烷释放及功能基因丰度的影响

为了研究人工湿地处理中碳/氮水平的废水时植物种类及多样性对系统甲烷释放及功能基因丰度的影响,我们构建了实验尺度的人工湿地微宇宙实验系统。选取千屈菜(Lythrum salicaria L.)和海寿花(Pontederia cordata L.)2种人工湿地常用、景观效果好的植物,在系统中配置了单种处理和两物种混种处理。结果表明:千屈菜与海寿花混种系统的甲烷释放强度(8.78 mg CH_4 m~(-2) d~(-1))高于两物种单种系统的平均值(6.97 mg CH_4 m~(-2) d~(-1))(P0.001),同甲烷释放一样,混种系统的mcrA基因绝对丰度(977541.6 copies/g dw soil)也高于两物种单种系统的平均值(585146.8 copies/g dw soil),但混种系统的pmoA基因绝对丰度(326956.6 copies/g dw soil)低于两物种单种系统的平均值(1043616.0 copies/g dw soil)(P0.001)。此外,混种系统的微生物量、植物生物量高于两物种单种系统的平均值(P0.01),但出水铵态氮浓度低于两物种单种系统的平均值(P0.05),出水总有机碳浓度和硝态氮浓度在单混种系统间无显著差异(P0.05)。千屈菜单种系统和海寿花单种系统间的甲烷释放强度、pmoA基因绝对丰度、微生物量、植物生物量和出水铵态氮浓度存在显著差异(P0.05),但mcrA基因绝对丰度、出水总有机碳和硝态氮浓度无显著差异(P0.05)。为了达到人工湿地的高净化效率,需要将千屈菜与海寿花混合种植,但混合种植强化甲烷释放。通过植物种类和丰富度对各指标变异的解释度(ω~2)分析发现,植物种类对甲烷释放、pmoA基因绝对丰度、出水铵态氮的影响大于植物丰富度,但对mcrA基因绝对丰度的影响小于植物丰富度。     

基于MS2噬菌体lys基因的质粒型条件自溶菌的构建与应用

【背景】传统外源蛋白的原核表达通常需要以超声破碎或者酶解的方式破碎菌体,过程比较烦琐。【目的】构建基于MS2噬菌体lys基因的质粒型条件自溶菌,以简化外源蛋白的获取流程。【方法】从MS2噬菌体中克隆lys基因,构建重组表达质粒,并在大肠杆菌BL21(DE3)中异源表达,以此构建质粒型条件自溶菌,通过生长曲线和菌落形成单位反映自溶菌裂解效率,利用SDS-PAGE检测外源蛋白释放情况。【结果】构建了pBAD-lys BL21(DE3)、pBAD-Opti-lys BL21(DE3)及pCDF-BAD-Opti-lys BL21(DE3)这3种质粒型条件自溶菌。以上自溶菌在阿拉伯糖诱导后其宿主裂解效率均为99.99%以上,CFU结果显示含pCDF-BAD-Opti-lys质粒的宿主裂解效果更优,在此自溶菌BL21(DE3)中表达含His标签的重组绿色荧光蛋白(enhanced green fluorescent protein,eGFP),经阿拉伯糖诱导后菌体中约63.00%以上的eGFP释放至胞外,利用Ni-NTA可以直接从培养基中纯化得到约30 kDa的单一目的蛋白。【结论】基于MS2噬菌体lys基因成功构建了阿拉伯糖诱导的质粒型条件自溶菌,此自溶菌能够以自我裂解的方式释放大部分胞内外源蛋白,简化传统外源蛋白获取流程。     

向日葵MADS-Box基因HAM23-like克隆和表达分析

为了解MADS-box基因在向日葵(Helianthus annuus)花发育过程中的作用,采用RT-PCR技术克隆了1个MADS-box基因新成员HAM23-like,开放阅读框为831bp,编码276个氨基酸,相对分子量为30.52k D,理论等电点为9.42。系统发育分析表明,HAM23-like与拟南芥的AGL18聚于同一分支,具有较近的亲缘关系。qRT-PCR分析表明,HAM23-like基因在花和成熟果实(籽粒饱满期)中的表达量较高;HAM23-like在开花当天的雄蕊中的表达量最高;随着花的发育,HAM 23-like表达量逐渐升高,在开花后5 d (果实形成早期)达到最高表达水平。因此,推断HAM23-like基因可能与向日葵花器官后期发育和瘦果早期发育相关。     

拟南芥AtCIPK23基因对烟草抗旱能力的影响

为了探索拟南芥AtCIPK23基因对烟草耐旱能力的影响,对3个转AtCIPK23基因阳性纯合株系KA13、KA14和KA44与野生型烟草K326（对照）进行了自然干旱处理,测定离体叶片的失水速率、叶绿素含量、相对电导率、脯氨酸和可溶性糖含量,并分析了转基因及野生型材料对活性氧的清除能力,对活性氧清除基因NtSOD、NtCAT和NtAPX及干旱胁迫相关基因NtDREB、NtLEA5和NtCDPK2的表达量进行检测。结果表明：（1）转基因烟草离体叶片的失水速率明显低于K326;自然干旱7 d后,野生型K326出现了明显的干旱胁迫症状;干旱7 d进行复水后,转基因株系的复水存活率明显高于K326。（2）转基因株系中的叶绿素、脯氨酸及可溶性糖含量比K326显著提高,电导率则明显降低。（3）野生型烟草K326中H₂O₂的积累量明显高于3个转基因株系,转基因株系中ROS清除机制的3个关键基因NtSOD、NtCAT和NtAPX被诱导上调表达。（4）抗旱相关基因NtDREB、NtLEA5和NtCDPK2仅在转基因烟草中受干旱诱导。研究认为,AtCIPK23基因可能具有提高植物抗旱能力的功能。     

Lysis protein T of bacteriophage T4

Summary Lysis protein T of phage T4 is required to allow the phage's lysozyme to reach the murein layer of the cell envelope and cause lysis. Using fusions of the cloned gene t with that of the Escherichia coli alkaline phosphatase or a fragment of the gene for the outer membrane protein OmpA, it was possible to identify T as an integral protein of the plasma membrane. The protein was present in the membrane as a homooligomer and was active at very low cellular concentrations. Expression of the cloned gene t was lethal without causing gross leakiness of the membrane. The functional equivalent of T in phage is protein S. An amber mutant of gene S can be complemented by gene t, although neither protein R of (the functional equivalent of T4 lysozyme) nor S possess any sequence similarity with their T4 counterparts. The murein-degrading enzymes (including that of phage P22) have in common a relatively small size (molecular masses of ca. 18 000) and a rather basic nature not exhibited by other E. coli cystosolic proteins. The results suggest that T acts as a pore that is specific for this type of enzyme.     

Isolation and genetic characterization of new uvsW alleles of bacteriophage T4

Summary TheuvsW gene of bacteriophage T4 is required for wild-type levels of recombination, for normal survival and mutagenesis after UV irradiation, and for wild-type resistance to hydroxyurea. Additionally,uvsW mutations restore the arrested DNA synthesis caused by mutations in any of several genes that block secondary initiation (recombination-primed replication, the major mode of initiation at late times), but only partially restore the reduced burst size. AuvsW deletion mutation was constructed to establish the null-allele phenotype, which is similar but not identical to the phenotype of the canonicaluvsW mutation, and to demonstrate convincingly that theuvsW gene is non-essential (althoughuvsW mutations severely compromise phage production). In an attempt to uncouple the diverse effects ofuvsW mutations, temperature-sensitiveuvsWts mutants were isolated. Recombination and replication effects were partially uncoupled in these mutants, suggesting distinct and separable roles foruvsW in the two processes. Furthermore, the restoration of DNA synthesis but not recombination in the double mutantsuvsW uvsX anduvsW uvsY prompts the hypothesis that the restored DNA synthesis is not recombinationally initiated.     

Characterization of a novel T4-type Stenotrophomonas maltophilia virulent phage Smp14

Stenotrophomonas maltophilia (Sm), with most of the isolates being resistant to multidrugs, is an opportunistic bacterium causing nosocomial infections. In this study, a novel virulent Sm phage, Smp14, was characterized. Electron microscopy showed that Smp14 resembled members of Myoviridae and adsorbed to poles of the host cells during infection. It lysed 37 of 87 clinical Sm isolates in spot test, displayed a latent period of ca. 20 min, and had a burst size of ca. 150. Its genome (estimated to be 160 kb by PFGE), containing m4C and two unknown modified bases other than m5C and m6A as identified by HPLC, resisted to digestion with many restriction endonucleases except MseI. These properties indicate that it is a novel Sm phage distinct from the previously reported phiSMA5 which has a genome of 250 kb digestible with various restriction enzymes. Sequencing of a 16 kb region revealed 12 ORFs encoding structural proteins sharing 15-45% identities with the homologues from T4-type phages. SDS-PAGE displayed 20 virion proteins, with the most abundant one being the 39 kDa major capsid protein (gp23), which had the N-terminal 52 amino acids removed. Phylogenetic analysis based on gp23 classified Smp14 into a novel single-membered T4-type subgroup.     

Structure and location of gene product 8 in the bacteriophage T4 baseplate

Many bacteriophages, such as T4, T7, RB49, and phi29, have complex, sometimes multilayered, tails that facilitate an almost 100% success rate for the viral particles to infect host cells. In bacteriophage T4, there is a baseplate, which is a multiprotein assembly, at the distal end of the contractile tail. The baseplate communicates to the tail that the phage fibers have attached to the host cell, thereby initiating the infection process. Gene product 8 (gp8), whose amino acid sequence consists of 334 residues, is one of at least 16 different structural proteins that constitute the T4 baseplate and is the sixth baseplate protein whose structure has been determined. A 2.0A resolution X-ray structure of gp8 shows that the two-domain protein forms a dimer, in which each monomer consists of a three-layered beta-sandwich with two loops, each containing an alpha-helix at the opposite sides of the sandwich. The crystals of gp8 were produced in the presence of concentrated chloride and bromide ions, resulting in at least 11 halide-binding sites per monomer. Five halide sites, situated at the N termini of alpha-helices, have a protein environment observed in other halide-containing protein crystal structures. The computer programs EMfit and SITUS were used to determine the positions of six gp8 dimers within the 12A resolution cryo-electron microscopy image reconstruction of the baseplate-tail tube complex. The gp8 dimers were found to be located in the upper part of the baseplate outer rim. About 20% of the gp8 surface is involved in contacts with other baseplate proteins, presumed to be gp6, gp7, and gp10. With the structure determination of gp8, a total of 53% of the volume of the baseplate has now been interpreted in terms of its atomic structure.     

Chaperonin-mediated folding of bacteriophage T4 major capsid protein. II. Production of gene product 23 deletion mutants

Folding of bacteriophage T4 major capsid protein, gene product 23 (534 a.a.), is aided by two proteins: E. coli GroEL chaperonin and viral gp31 co-chaperonin. In the present work a set of mutants with extensive deletions inside gene 23 using controlled digestion with Bal31 nuclease has been constructed. Proteins with deletions were co-expressed from plasmid vectors with phage gp31 co-chaperonin. Deletions from 8 to 33 a.a. in the N-terminal region of the gp23 molecule covering the protein proteolytic cleavage site during capsid maturation have no influence on the mutants' ability to produce in E. coli cells proteins which form regular structures—polyheads. Deletions in other regions of the polypeptide chain (187-203 and 367-476 a.a.) disturb the correct folding and subsequent assembly of gp23 into polyheads.