高温噬菌体分子特征及热稳定麦芽糖基淀粉酶的性质
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摘要
海洋是人类最大也是最后一块尚未充分开发利用的生物资源宝库，在陆地资源开发已日趋饱和的今天，世界各国普遍意识和注意到海洋生物资源研究的重要性，纷纷将研究注意力转向海洋生物。海洋微生物，尤其是嗜热微生物已成为国际上的研究热点。现代理论和环境证据表明嗜热菌是地球上形成的第一类生命形式，研究它对探索生命起源具有重要意义，同时嗜热微生物及其嗜热酶在工业和分子生物学等方面有重要的用途。
近年来，感染嗜热微生物的高温病毒(高温嗜菌体)引起越来越多的科研工作者的关注。因为，高温嗜菌体可以作为一种模式系统来研究海洋微生物的生物化学及分子生物学特性，而且它们还影响生物地球化学和生态系统进化过程，包括营养循环、生物分类、微生物多样性和种群分布、遗传转换、生物进化等。高温嗜菌体的研究不仅可以丰富和发展对生命形式的认识，而且在构建嗜热菌表达系统的人工载体和开发热稳定的工业用酶以及分子生物学工具酶等方面，都有着广泛的应用前景。
本研究从太平洋深海热液区和厦门近海温泉分离到170株嗜热菌。为了使这些嗜热菌的鉴定工作更加简便，我们首先通过全菌体蛋白凝胶电泳(SDS-PAGE)对170株嗜热菌进行分析，结果显示存在四种不同的带型，说明170株嗜热菌可能属于四个种或属。9株代表菌DNA指纹多态性(RAPD)分析结果与SDS-PAGE结果完全一致。为了进一步鉴定9株代表菌，进行了16S rDNA序列分析，结果表明这9株代表菌属于三个属中的四个种，这与SDS-PAGE分析结果也一致。因此，我们认为全菌体蛋白SDS-PAGE凝胶电泳分析是一种简便、快速的菌株筛选方法，可以作为嗜热菌鉴定的第一个步骤。
在嗜热菌的分离过程中，我们从西太平洋深海热液区样品中分离到一株产淀粉酶的嗜热菌WPD616，根据16S rDNA序列，该嗜热菌属于Bacillus sp．WPD616。接着，从Bacillus sp．WPD616中克隆了一个编码588个氨基酸的麦芽糖基淀粉酶基因，并在Escherichia coli中进行表达。酶活性分析结果表明，在50℃，pH6.0条件下，重组麦芽糖基淀粉酶的酶活性最高。在pH6.0条件下，反应温度达到70℃时，该重组酶还有酶活。在50℃条件下，pH值在6.0-8.0之间时，重组酶保持稳定状态。进一步实验表明1mM或10mM的DTT，0.1％或1％Tween 20、Chaps和0.1％的Triton X-100对该重组酶的酶活性几乎没什么影响，但EDTA(1mM或10mM)、2-ME(1mM或10mM)、SDS(1mM)、PMSF(1mM)可以抑制大约18-55％的重组麦芽糖基淀粉酶活性，而10mM的PMSF或SDS可以完全抑制重组麦芽糖基淀粉酶活性。1mM或10mM的K~+和Li~+对酶活性无明显影响，1mM或10mM的Ba~(2+)，Mg~(2+)，Mn~(2+)，10mM的Ca~(2+)或1mM的Fe~(2+)可以抑制大约13-56.7％的重组麦芽糖基淀粉酶活性，1mM或10mM的Zn~(2+)，Fe~(3+)，Cu~(2+)和10mM的Fe~(2+)则可以完全抑制重组麦芽糖基淀粉酶活性。
在嗜热菌的培养过程中，我们从厦门近海温泉中分离到一株高温噬菌体Geobacillus sp．Virus 1 (GBSV1)，从太平洋深海热液区获得三株高温噬菌体Bacillus Virus W13(BVW13)、Geobacillus Vires E26323(GVE26323)和Geobacillus sp．Vires E1(GSVE1)。我们对GBSV1和GSVE1进行了深入研究。GBSV1分离自温泉嗜热菌6eobacillus sp．6K51。GBSV1是一个典型的Myoviridae噬菌体，包括一个直径为60nm的六角型的头，一条长为120-135nm的尾巴。根据PCR检测结果，说明噬菌体GBSV1可以感染Bacillus和Geobacillus属的5种嗜热菌。GBSV1的基因组是一个双链线型DNA，大小为34579bp，预测编码了55个阅读框(ORF)。其中有8个阅读框与人疾病有关的细菌的基因存在较高的同源性。这是高温噬菌体中首次发现的与人疾病相关的病源菌基因。根据GBSV1的形态及基因组特征，认为6BSV1是一株新的高温噬菌体。通过蛋白质组分析，GBSV1的5个主要蛋白被鉴定，其中VP425得到了进一步的分析。对噬菌体GBSV1功能基因组的研究，有利于更好的理解噬菌体与嗜热菌的互作机制。
在研究过程中，我们从东太平洋深海热液区嗜热菌Geobacillus sp．E263中纯化获得高温噬菌体GSVE1。GSVE1是个典型的Siphoviridae噬菌体，包含一个大小为40863bp的双链线型DNA，编码了62个阅读框(ORF)。其中也有6个阅读框序列与人类致病菌的噬菌体基因存在较高的同源性，2个阅读框与人类致病菌的蛋白同源性较高。芯片分析表明，74.2％的预测阅读框在GSVE1感染嗜热菌Geobacillus sp．E263后4小时得到了表达。通过质谱分析，GSVE1有6个主要蛋白带得到了鉴定，其中第四条蛋白带的VP371蛋白得到了进一步的分析。Western blot印迹杂交分析结果显示，GST-VP371的抗体与第四条蛋白带强烈反应。免疫电镜结果说明VP371蛋白是噬菌体GSVE1的一个主要的衣壳蛋白。这是第一次对深海热液区的高温噬菌体进行功能基因组学分析。GSVE1的分子生物学研究对阐明深海热液区的高温噬菌体的角色有很大的帮助。
The ocean is the most abundant and the last underutilized biology resources on earth. When the terrestrial resources have been developed fully, halobios have become new focuses for their importance. Marine microbes, especially the thermophiles have become a study hotspot. Current theory and circumstancial evidence suggest that the thermophiles are the first lifes on earth, which will be helpful for understanding the origin of life. Thermophiles and their enzymes are also the important resources in industry and biotechnology.
Recently years, viruses from thermophiles have attracted intensive investigation because they can serve as model systems to study the biochemistry and molecular biology of marine microbes, and they could influence many biogeochemical and ecological processes, including nutrient cycling, taxon of biology, bacterial biodiversity and species distribution, genetic transfer and evolution of biology. Therefore, thermophilic viruses are not only helpful for understanding the life, but also have great potential usese in industry and biotechnology.
In total, 170 strains of thermophilic bacteria were isolated from deep-sea hydrothermal fields in Pacific and a hot spring in Xiamen of China. To facilitate the identification of thermophilic strains, SDS-PAGE of whole-cell proteins of these strains was firstly performed. The results showed that there existed four different protein patterns, indicating that the 170 strains might belong to four species or genera. The RAPD (Random Amplified Polymorphic DNA) profiles of nine representative strains were consistent with those of SDS-PAGE. To further identify the species of the nine strains, their 16S rDNA sequences were analyzed. The results showed that the nine strains fell into four species of three genera, which was the same as revealed by SDS-PAGE. Therefore, SDS-PAGE of whole-cell proteins could be used as a rapid and simple method for the discrimination of thermophilic bacteria as the first step of species identification.
During the isolation of thermophiles, a maltogenic amylase-producing thermophilic strain WPD616, assigned to Bacillus sp. WPD616 based on 16S rRNA sequence, was isolated from a deep-sea hydrothermal field in west Pacific. Subsequently a maltogenic amylase gene encoding 588 amino acids from this isolate was cloned and expressed in Escherichia coli as a fusion protein with glutathione S-transferase (GST). The results showed that the recombinant maltogenic amylase had an activity optimum at 50℃and pH at 6．0．It was active up to 70℃at pH 6．0 and stable at pH ranging from 6．0 to 8．0．The recombinant enzyme was active when Chaps, DTT and Tween 20 (0．1% or 1%) were used. However, it can be partially inhibited by 1 mM of EDTA, PMSF or SDS, as well as 0．1% of Triton X-100 or 2-ME, and completely inhibited by 10 mM of PMSF and SDS (10mM). Its catalytic function was stable in the presence of Li~+ and K~+ (1mM or 10mM), but its activity decreased when Ba~(2+), Ca~(2+), Mg~(2+), Mn~(2+) (1mM or 10mM) and Fe~(2+) (1mM) were used. In the presence of Zn~(2+), Cu~2, Fe~(3+)(1mM and 10mM) and Fe~(2+) (10mM), no activity was detected.
During the cultures of thermophiles, a thermophilic bacteriophage Geobacillus sp.Virus 1 (GBSV1) was obtained from an offshore hot spring in Xiamen of China, and three thermophilic bacteriophages Bacillus Virus W13 (BVW13)、Geobacillus Virus E26323 (GVE26323)和Geobacillus sp. Virus E1 (GSVE1) were isolated from a deep-sea hydrothermal field. The GBSV1 and GSVE1were further characterized. GBSV1 was isolated from a thermophilic bacterium Geobacillus sp. 6k51．GBSV1 was a typical Myoviridae phage with a hexagonal head (60 in diameter) and a tail (120-135 nm in length). As revealed by PCR detection, the GBSV1 could infect 5 species of Geobacillus or Bacillus thermophiles. The GBSV1 contained a double-stranded circular DNA of 34579 bp, which had the capacity encoding 55 open reading frames (ORFs). Surprisingly, eight of the 55 GBSV1 ORFs shared sequence similarities to genes from human disease-relevant bacteria. This was the first report that human disease-relevant bacterial genes were found in thermophilic phage. The different morphology and genome size from reported thermophilic viruses suggested that the GBSV1 was a novel thermophilic bacteriophage. Five proteins of the purified GBSV1 virions were identified by proteomic analysis. Among them, the vp425 gene was characterized to be a viral late gene. Determination of GBSV1 functional genomics would facilitate the better understanding of the mechanism for virus-thermophile interaction.
Bacteriophage GSVE1 infecting thermophilic Geobacillus sp. E263 was purified in this study. The results revealed that GSVE1 was a typical Siphoviridae phage containing a 40863-bp linear double-stranded genomic DNA with 62 presumptive open reading frames (ORFs). Surprisingly, 8 ORFs shared sequence similarities to genes from human disease-relevant bacteria and their bacteriophages. Microarray analysis indicated that 74．2% of the presumptive ORFs were expressed. The purified virions contained six protein bands, which were identified by mass spectrometric analysis. Of the newly retrieved proteins, VP371 (derived from band 4) was further characterized. Western blot analysis showed that the anti-GST-VP371 antibody reacted strongly with band 4．The immuno-electron microscopy indicated that VP371 protein was a component of the viral capsid. As the first characterized thermophlic bacteriophage from deep-sea hydrothermal field with functional genomics, the molecular characterizations of GSVE1 will be very helpful to elucidate the role of thermophilic virus in deep-sea hydrothermal vents.
近年来，感染嗜热微生物的高温病毒(高温嗜菌体)引起越来越多的科研工作者的关注。因为，高温嗜菌体可以作为一种模式系统来研究海洋微生物的生物化学及分子生物学特性，而且它们还影响生物地球化学和生态系统进化过程，包括营养循环、生物分类、微生物多样性和种群分布、遗传转换、生物进化等。高温嗜菌体的研究不仅可以丰富和发展对生命形式的认识，而且在构建嗜热菌表达系统的人工载体和开发热稳定的工业用酶以及分子生物学工具酶等方面，都有着广泛的应用前景。
本研究从太平洋深海热液区和厦门近海温泉分离到170株嗜热菌。为了使这些嗜热菌的鉴定工作更加简便，我们首先通过全菌体蛋白凝胶电泳(SDS-PAGE)对170株嗜热菌进行分析，结果显示存在四种不同的带型，说明170株嗜热菌可能属于四个种或属。9株代表菌DNA指纹多态性(RAPD)分析结果与SDS-PAGE结果完全一致。为了进一步鉴定9株代表菌，进行了16S rDNA序列分析，结果表明这9株代表菌属于三个属中的四个种，这与SDS-PAGE分析结果也一致。因此，我们认为全菌体蛋白SDS-PAGE凝胶电泳分析是一种简便、快速的菌株筛选方法，可以作为嗜热菌鉴定的第一个步骤。
在嗜热菌的分离过程中，我们从西太平洋深海热液区样品中分离到一株产淀粉酶的嗜热菌WPD616，根据16S rDNA序列，该嗜热菌属于Bacillus sp．WPD616。接着，从Bacillus sp．WPD616中克隆了一个编码588个氨基酸的麦芽糖基淀粉酶基因，并在Escherichia coli中进行表达。酶活性分析结果表明，在50℃，pH6.0条件下，重组麦芽糖基淀粉酶的酶活性最高。在pH6.0条件下，反应温度达到70℃时，该重组酶还有酶活。在50℃条件下，pH值在6.0-8.0之间时，重组酶保持稳定状态。进一步实验表明1mM或10mM的DTT，0.1％或1％Tween 20、Chaps和0.1％的Triton X-100对该重组酶的酶活性几乎没什么影响，但EDTA(1mM或10mM)、2-ME(1mM或10mM)、SDS(1mM)、PMSF(1mM)可以抑制大约18-55％的重组麦芽糖基淀粉酶活性，而10mM的PMSF或SDS可以完全抑制重组麦芽糖基淀粉酶活性。1mM或10mM的K~+和Li~+对酶活性无明显影响，1mM或10mM的Ba~(2+)，Mg~(2+)，Mn~(2+)，10mM的Ca~(2+)或1mM的Fe~(2+)可以抑制大约13-56.7％的重组麦芽糖基淀粉酶活性，1mM或10mM的Zn~(2+)，Fe~(3+)，Cu~(2+)和10mM的Fe~(2+)则可以完全抑制重组麦芽糖基淀粉酶活性。
在嗜热菌的培养过程中，我们从厦门近海温泉中分离到一株高温噬菌体Geobacillus sp．Virus 1 (GBSV1)，从太平洋深海热液区获得三株高温噬菌体Bacillus Virus W13(BVW13)、Geobacillus Vires E26323(GVE26323)和Geobacillus sp．Vires E1(GSVE1)。我们对GBSV1和GSVE1进行了深入研究。GBSV1分离自温泉嗜热菌6eobacillus sp．6K51。GBSV1是一个典型的Myoviridae噬菌体，包括一个直径为60nm的六角型的头，一条长为120-135nm的尾巴。根据PCR检测结果，说明噬菌体GBSV1可以感染Bacillus和Geobacillus属的5种嗜热菌。GBSV1的基因组是一个双链线型DNA，大小为34579bp，预测编码了55个阅读框(ORF)。其中有8个阅读框与人疾病有关的细菌的基因存在较高的同源性。这是高温噬菌体中首次发现的与人疾病相关的病源菌基因。根据GBSV1的形态及基因组特征，认为6BSV1是一株新的高温噬菌体。通过蛋白质组分析，GBSV1的5个主要蛋白被鉴定，其中VP425得到了进一步的分析。对噬菌体GBSV1功能基因组的研究，有利于更好的理解噬菌体与嗜热菌的互作机制。
在研究过程中，我们从东太平洋深海热液区嗜热菌Geobacillus sp．E263中纯化获得高温噬菌体GSVE1。GSVE1是个典型的Siphoviridae噬菌体，包含一个大小为40863bp的双链线型DNA，编码了62个阅读框(ORF)。其中也有6个阅读框序列与人类致病菌的噬菌体基因存在较高的同源性，2个阅读框与人类致病菌的蛋白同源性较高。芯片分析表明，74.2％的预测阅读框在GSVE1感染嗜热菌Geobacillus sp．E263后4小时得到了表达。通过质谱分析，GSVE1有6个主要蛋白带得到了鉴定，其中第四条蛋白带的VP371蛋白得到了进一步的分析。Western blot印迹杂交分析结果显示，GST-VP371的抗体与第四条蛋白带强烈反应。免疫电镜结果说明VP371蛋白是噬菌体GSVE1的一个主要的衣壳蛋白。这是第一次对深海热液区的高温噬菌体进行功能基因组学分析。GSVE1的分子生物学研究对阐明深海热液区的高温噬菌体的角色有很大的帮助。
The ocean is the most abundant and the last underutilized biology resources on earth. When the terrestrial resources have been developed fully, halobios have become new focuses for their importance. Marine microbes, especially the thermophiles have become a study hotspot. Current theory and circumstancial evidence suggest that the thermophiles are the first lifes on earth, which will be helpful for understanding the origin of life. Thermophiles and their enzymes are also the important resources in industry and biotechnology.
Recently years, viruses from thermophiles have attracted intensive investigation because they can serve as model systems to study the biochemistry and molecular biology of marine microbes, and they could influence many biogeochemical and ecological processes, including nutrient cycling, taxon of biology, bacterial biodiversity and species distribution, genetic transfer and evolution of biology. Therefore, thermophilic viruses are not only helpful for understanding the life, but also have great potential usese in industry and biotechnology.
In total, 170 strains of thermophilic bacteria were isolated from deep-sea hydrothermal fields in Pacific and a hot spring in Xiamen of China. To facilitate the identification of thermophilic strains, SDS-PAGE of whole-cell proteins of these strains was firstly performed. The results showed that there existed four different protein patterns, indicating that the 170 strains might belong to four species or genera. The RAPD (Random Amplified Polymorphic DNA) profiles of nine representative strains were consistent with those of SDS-PAGE. To further identify the species of the nine strains, their 16S rDNA sequences were analyzed. The results showed that the nine strains fell into four species of three genera, which was the same as revealed by SDS-PAGE. Therefore, SDS-PAGE of whole-cell proteins could be used as a rapid and simple method for the discrimination of thermophilic bacteria as the first step of species identification.
During the isolation of thermophiles, a maltogenic amylase-producing thermophilic strain WPD616, assigned to Bacillus sp. WPD616 based on 16S rRNA sequence, was isolated from a deep-sea hydrothermal field in west Pacific. Subsequently a maltogenic amylase gene encoding 588 amino acids from this isolate was cloned and expressed in Escherichia coli as a fusion protein with glutathione S-transferase (GST). The results showed that the recombinant maltogenic amylase had an activity optimum at 50℃and pH at 6．0．It was active up to 70℃at pH 6．0 and stable at pH ranging from 6．0 to 8．0．The recombinant enzyme was active when Chaps, DTT and Tween 20 (0．1% or 1%) were used. However, it can be partially inhibited by 1 mM of EDTA, PMSF or SDS, as well as 0．1% of Triton X-100 or 2-ME, and completely inhibited by 10 mM of PMSF and SDS (10mM). Its catalytic function was stable in the presence of Li~+ and K~+ (1mM or 10mM), but its activity decreased when Ba~(2+), Ca~(2+), Mg~(2+), Mn~(2+) (1mM or 10mM) and Fe~(2+) (1mM) were used. In the presence of Zn~(2+), Cu~2, Fe~(3+)(1mM and 10mM) and Fe~(2+) (10mM), no activity was detected.
During the cultures of thermophiles, a thermophilic bacteriophage Geobacillus sp.Virus 1 (GBSV1) was obtained from an offshore hot spring in Xiamen of China, and three thermophilic bacteriophages Bacillus Virus W13 (BVW13)、Geobacillus Virus E26323 (GVE26323)和Geobacillus sp. Virus E1 (GSVE1) were isolated from a deep-sea hydrothermal field. The GBSV1 and GSVE1were further characterized. GBSV1 was isolated from a thermophilic bacterium Geobacillus sp. 6k51．GBSV1 was a typical Myoviridae phage with a hexagonal head (60 in diameter) and a tail (120-135 nm in length). As revealed by PCR detection, the GBSV1 could infect 5 species of Geobacillus or Bacillus thermophiles. The GBSV1 contained a double-stranded circular DNA of 34579 bp, which had the capacity encoding 55 open reading frames (ORFs). Surprisingly, eight of the 55 GBSV1 ORFs shared sequence similarities to genes from human disease-relevant bacteria. This was the first report that human disease-relevant bacterial genes were found in thermophilic phage. The different morphology and genome size from reported thermophilic viruses suggested that the GBSV1 was a novel thermophilic bacteriophage. Five proteins of the purified GBSV1 virions were identified by proteomic analysis. Among them, the vp425 gene was characterized to be a viral late gene. Determination of GBSV1 functional genomics would facilitate the better understanding of the mechanism for virus-thermophile interaction.
Bacteriophage GSVE1 infecting thermophilic Geobacillus sp. E263 was purified in this study. The results revealed that GSVE1 was a typical Siphoviridae phage containing a 40863-bp linear double-stranded genomic DNA with 62 presumptive open reading frames (ORFs). Surprisingly, 8 ORFs shared sequence similarities to genes from human disease-relevant bacteria and their bacteriophages. Microarray analysis indicated that 74．2% of the presumptive ORFs were expressed. The purified virions contained six protein bands, which were identified by mass spectrometric analysis. Of the newly retrieved proteins, VP371 (derived from band 4) was further characterized. Western blot analysis showed that the anti-GST-VP371 antibody reacted strongly with band 4．The immuno-electron microscopy indicated that VP371 protein was a component of the viral capsid. As the first characterized thermophlic bacteriophage from deep-sea hydrothermal field with functional genomics, the molecular characterizations of GSVE1 will be very helpful to elucidate the role of thermophilic virus in deep-sea hydrothermal vents.
引文
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