摩氏摩根菌噬菌体MmP1生物学特性及其基因组学的研究
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摘要
摩氏摩根菌(亦称摩根摩根菌)归属肠杆菌科摩根菌属,仅有1个种,革兰染色阴性,其形态与变形杆菌相似。该菌广泛分布于自然界,人和动物粪便中,是引起医院感染重要病原菌之一,且当今发生感染的频率较过往有所增加。噬菌体作为细菌的病毒,是微生物中的非细胞形态的低级生命形式,它在自然界中广泛存在,是生物圈中数量最多的生命形式。有人估计,自然界中噬菌体的数量达1031之巨。而现实中人们对它的了解仍然很少,截止2008年4月底,目前已完成测序并登录GenBank的噬菌体基因组才484个,噬菌体的研究仍然需要更多积累。因噬菌体基因组较小,现有更多的噬菌体在被测序研究中,但是并没有一株摩氏摩根菌噬菌体。
噬菌体是细菌之间基因水平转移的重要载体,是除质粒之外的一股重要基因流,在细菌基因组的进化,细菌的致病性和耐药性中具有非常关键的作用。近年的研究表明,多价噬菌体和经人工改造形成的“广宿主谱”噬菌体在细菌感染性疾病的治疗上有着巨大的前景,对噬菌体展开广泛和深入的研究具有重要的基础意义和潜在的临床价值。摩氏摩根菌作为医院感染重要病原菌,临床耐药问题比较严重,研究其噬菌体并潜在地作为“治疗用药”就具有重要的意义。
本文以摩氏摩根菌的一株临床分离株作为宿主菌,从附属医院下水道污水中分离到1株噬菌体,命名为MmP1。首先对其生物学特性进行了重点研究;其次提取基因组送北京华大基因研究中心进行测序,并通过实验将“环状”的基因组鉴定为线性;进而,分离结构蛋白进行N-端测序并确定其编码基因;最后对基因组进行了初步注释,证实噬菌体MmP1属于T7噬菌体家族。研究内容及结果主要包括以下几个方面。
1.确定肠杆菌科细菌为摩氏摩根菌。肠杆菌科细菌由本校附属西南医院检验科自临床标本中分离得到,检验仪器只鉴定为肠杆菌科,未能进一步细化。在实验中,我们设计了一对扩增肠杆菌科细菌的16s rDNA保守引物,通过PCR扩增出一段序列长为1.5kb的条带,送上海英骏公司测序。测序结果在NCBI网站经BLAST比对,发现PCR扩增产物与多株摩氏摩根菌的16s rRNA序列100%相同,从而确定本株肠杆菌为摩氏摩根菌。
2.以摩氏摩根菌为宿主菌,从西南医院下水道污水中分离到1株具有半透明噬斑的溶原性噬菌体MmP1。噬菌体DNA经限制性内切酶HindⅢ酶切鉴定为dsDNA。其噬菌体滴度为2×1011,电镜观察发现有一个多面体立体对称的头部,直径约55nm,并有一个很短的尾巴,形态学上属于短尾噬菌体科。SDS-PAGE蛋白电泳分析发现,在中分子量蛋白质标准范围内,凝胶上至少出现了7条蛋白条带,表明噬菌体MmP1中至少含有7个结构蛋白。噬菌体MmP1感染其宿主菌摩氏摩根菌的最佳感染复数是0.1。根据一步生长曲线可知,噬菌体MmP1感染宿主菌的潜伏期约为10min,爆发期约为40min,爆发量约为105。
3.将噬菌体MmP1基因组DNA提取纯化后送北京华大基因研究中心进行全基因组测序。经BLAST比对检索,确定噬菌体MmP1为一全新噬菌体,是第一个被测序的摩氏摩根菌噬菌体。同时用PCR扩增的方法,鉴定了其末端序列的正确性。利用基因组的物理图谱和电子酶切图谱的比较,将测序的“环状”基因组鉴定为线性,同时推测它可能有5’-突出粘性末端序列存在。
4.噬菌体MmP1基因组的一般概况。①基因组测序表明该基因组全长为38,233bp,其碱基组成是:A = 27.98%,G = 25.30%,C = 21.24%,T =25.48%,G+C =46.54%,其G+C含量略低于T7噬菌体家族成员T7、phiA1122。②GC岛的分析表明噬菌体MmP1基因组上发现了20个大于200bp的GC岛。其中G+C含量偏离最大的两个基因,即基因35和基因42很可能是水平转移而来的外源基因。③基因表达全部位于正链上,且与噬菌体T7、T3类似,基因结构排列聚集成堆,分早中晚三个时期。
5.基因组的生物信息学分析以及基因功能的探讨。在噬菌体MmP1基因组中具有152个大于100bp的ORFs,其中49个推定为编码基因,编码序列总长度为34359bp,基因的平均DNA长度为701bp。在整个基因组DNA中,平均每1000bp长度中有1.28个推定基因,基因组中碱基的使用率达到89.88%。在核苷酸水平,12个推定基因与目前已知的序列有同源性;在氨基酸水平,在公共数据库中共找到28个推定基因编码产物的同源蛋白质。综合分析,初步确定35个ORFs具有与噬菌体T7、phiA1122相似的功能。进而,利用CLUSTALX软件工具对搜索到的具有显著相似性的基因进行多重比对,通过phylip软件绘制系统发生树,用TreeView软件观察结果,分析其进化关系证实噬菌体MmP1属于T7噬菌体家族。
6.噬菌体结构蛋白及其编码基因的确定。本研究结果显示,噬菌体颗粒至少含有7个结构蛋白,其中,38kD蛋白是噬菌体的主要衣壳蛋白。将电泳分离的蛋白质转印至PVDF膜上进行N-端氨基酸测序。将N-端测序得到的氨基酸残基序列与所有推定基因编码产物的N-端氨基酸序列相比对,结合分子量大小,确定了ORF35是其编码基因。同时,根据噬菌体结构蛋白大小的唯一性,确定了69kD蛋白质是由ORF48编码的,150kD蛋白质是由ORF42编码的。
7.基因组的非编码序列分析表明在基因组上存在着37个长短不一的基因间区(1-1321bp),同时存在10个基因重叠区,16个基因的编码框相互之间发生了重叠。在基因组的5’-、3’-末端分别存在140和204bp的非编码序列。基因组中还存在大量反向重复序列、正向重复序列以及1个最长为61bp的串联重复序列。这些重复序列可能与转录调节、DNA重组以及基因组进化有关。在非编码序列还发现了5个可能的转录终止子,同时找到了5个可能的启动子。
噬菌体MmP1的全基因组序列已经在GenBank登录(No. EU652770)。
综上所述,通过本研究,明确了世界上第一株摩氏摩根菌噬菌体MmP1的基本生物学特性及其基因组组成序列,并对该基因组进行了初步注释。注释结果表明MmP1属于T7噬菌体家族成员,扩展了T7噬菌体家族宿主菌的范围(摩氏摩根菌未见报道为T7噬菌体家族宿主菌)。两类噬菌体(MmP1和T7)宿主菌分属不同的菌属,却拥有相同的基因结构和类似的基因,进一步揭示了噬菌体的生物多样性,为全面深入地认识噬菌体的遗传与变异、进化与分类、基因组织与调控以及寄生机制等生物学特性中的重大问题提供了新的数据。
Morganella morganii is a gram-negative rod commonly found in the environment and in the intestinal tracts of humans, mammals, and reptiles as normal flora. The genus Morganella belongs to the family Enterobacteriaceae. Despite its wide distribution, it is an uncommon cause of community-acquired infection and is most often encountered in postoperative and other nosocomial settings.
Bacteriophages are viruses of bacteria. They are ubiquitous in nature, and are now recognized to be the most numerous entities in the biosphere. When the sensitive bacterium was infected by a phage, there will be two reactions, one is lytic reaction, the other is lysogenic reaction. The lysogenic bacteriophage can alter the biologic features of the host bacterium by its inheritance material, meanwhile, they can change host’s inheritance material constituent in the process of the DNA recombination, integration, transposition and excision in host genome, which result in the microbial genetic diversity. Lytic phages can lyse and kill the host bacteria, and lysogenic phages also have a lytic period. So that phages are in the hope to be developed as anti-bacteria pharmaceutics. Deep-looking insight into the genetic background of phage is very important for no matter investigating the interaction of phage and its host bacteria, and revealing the biological diversity mechanism resulting from gene horizontal transfer caused by phages, or engineering remodeling of phage and phage-therapy. Now the genomic era has re-focussed researchers’attention onto the importance of bacteriophages. To date, there are totally 484 completed bacteriophage genomes available in public databases. In this dissertation, we are focused on the whole genome sequence and annotation of Morganella morganii phage 1 ( MmP1 ). The results are as follows:
1. The biological characterization of MmP1. The phage MmP1 is a temperate phage of Morganella morganii. Electron microscopy revealed that the phage has an isometric head (about 55 nm in diameter) and a short tail, and it belongs to the Podoviridae family. The optimal multiplicity of infection (MOI) of MmP1 is about 0.1, and hosts infected by the phages with an MOI of 0.1 will produce highest phage titer at 3.5h after infection. One-step growth kinetics of the phage showed that the latent period is about 10 min, the rise period is about 40 min, and the average burst size is about 105 phage particles per an infected cell.
2. The general characterization of MmP1 genome. The complete nucleotide sequence of phage MmP1 is 38,233 bp, and includes terminal repeats of 61bp, which is highly similar to T7-like phage. The G+C content of the MmP1 genome averages 46.54%. There are two regions with significantly higher G+C content than the average, among which two genes, gene 35 and gene 42, having the highest G+C content, may be acquired genes by horizontal transfer. Genes are all transcribed from the same DNA strand and occupy almost 90% of the nucleotide sequence, the same value found for T7. This efficiency is presumably the result of evolutionary packaging of the maximum amount of useful information into a DNA molecule whose length is limited by a virion of fixed size.
3. The bioinformatics analysis of phage genome. 152 ORFs longer than 100bp are found out by ORF finder software at NCBI website. Predictions using the GeneMark and Softberry programs revealed that the phage genome has 49 predicted genes. No potential tRNA coding regions were found in the phage genome. The predicted genes are tightly organized with little space between them, and there are 10 overlapping gene regions with total 91 bp, ranging from 1 to 32 bp. At the DNA level, 12 of the phage-encoded putative proteins show homology to known proteins in the database using BLASTn program, and at the protein level, 28 of the phage-encoded putative proteins show homology to known proteins in the database using BLASTp program. The function of these 35 genes show homology to phage T7 and phage phiA1122. Thus , MmP1 is thought to be a member of the T7 group. Similar to the T3 and T7 genomes, MmP1 genes could be divided into three classes: I (early), II (middle) and III(late). Multiple sequence alignment was conducted among those homologous proteins using software CLUSTALX, and then the phylogenetic trees were drawn by phylip software.
4. The phage capsid proteins and their coding genes. Phage particles were purified with CsCl gradient centrifugation, then the total phage capsid proteins were separated at least 7 bands by SDS-PAGE, respectively with molecular weight 150, 95, 82, 69, 62, 44 and 38kD. After transferred to a PVDF filter, Most bands were excised from the membrane and were subjected to N-terminal sequence with Edman degradation method. Only 38kD proteins could be sequenced and the N-terminal sequences were figured out. By comparative analysis of the N-terminal amino acid sequences of the proteins to the products coded by all the predicted genes, we got to know that gene 35 coded the 38kD proteins.
5. The non-coding sequences of the genome. There are 37 intergenic regions ranging from 1 to 1321 bps. There are non-coding sequences with length of 140 bps and 204 bps respectively on the 5’-and 3’-terminus of the phage genome. 17 inverted repeats (palindrome sequence) and 1 long tandem repeats(61bp) are found in the genome. These repeat sequences are related to the transcription, recombination of DNA and genomic evolution. 5 possible terminators are found in the intergenic regions, and 5 possible promoter was predicted at the genomic positive strand.
The genome data of phage MmP1 has been deposited in GenBank under the accession No. EU652770.
噬菌体是细菌之间基因水平转移的重要载体,是除质粒之外的一股重要基因流,在细菌基因组的进化,细菌的致病性和耐药性中具有非常关键的作用。近年的研究表明,多价噬菌体和经人工改造形成的“广宿主谱”噬菌体在细菌感染性疾病的治疗上有着巨大的前景,对噬菌体展开广泛和深入的研究具有重要的基础意义和潜在的临床价值。摩氏摩根菌作为医院感染重要病原菌,临床耐药问题比较严重,研究其噬菌体并潜在地作为“治疗用药”就具有重要的意义。
本文以摩氏摩根菌的一株临床分离株作为宿主菌,从附属医院下水道污水中分离到1株噬菌体,命名为MmP1。首先对其生物学特性进行了重点研究;其次提取基因组送北京华大基因研究中心进行测序,并通过实验将“环状”的基因组鉴定为线性;进而,分离结构蛋白进行N-端测序并确定其编码基因;最后对基因组进行了初步注释,证实噬菌体MmP1属于T7噬菌体家族。研究内容及结果主要包括以下几个方面。
1.确定肠杆菌科细菌为摩氏摩根菌。肠杆菌科细菌由本校附属西南医院检验科自临床标本中分离得到,检验仪器只鉴定为肠杆菌科,未能进一步细化。在实验中,我们设计了一对扩增肠杆菌科细菌的16s rDNA保守引物,通过PCR扩增出一段序列长为1.5kb的条带,送上海英骏公司测序。测序结果在NCBI网站经BLAST比对,发现PCR扩增产物与多株摩氏摩根菌的16s rRNA序列100%相同,从而确定本株肠杆菌为摩氏摩根菌。
2.以摩氏摩根菌为宿主菌,从西南医院下水道污水中分离到1株具有半透明噬斑的溶原性噬菌体MmP1。噬菌体DNA经限制性内切酶HindⅢ酶切鉴定为dsDNA。其噬菌体滴度为2×1011,电镜观察发现有一个多面体立体对称的头部,直径约55nm,并有一个很短的尾巴,形态学上属于短尾噬菌体科。SDS-PAGE蛋白电泳分析发现,在中分子量蛋白质标准范围内,凝胶上至少出现了7条蛋白条带,表明噬菌体MmP1中至少含有7个结构蛋白。噬菌体MmP1感染其宿主菌摩氏摩根菌的最佳感染复数是0.1。根据一步生长曲线可知,噬菌体MmP1感染宿主菌的潜伏期约为10min,爆发期约为40min,爆发量约为105。
3.将噬菌体MmP1基因组DNA提取纯化后送北京华大基因研究中心进行全基因组测序。经BLAST比对检索,确定噬菌体MmP1为一全新噬菌体,是第一个被测序的摩氏摩根菌噬菌体。同时用PCR扩增的方法,鉴定了其末端序列的正确性。利用基因组的物理图谱和电子酶切图谱的比较,将测序的“环状”基因组鉴定为线性,同时推测它可能有5’-突出粘性末端序列存在。
4.噬菌体MmP1基因组的一般概况。①基因组测序表明该基因组全长为38,233bp,其碱基组成是:A = 27.98%,G = 25.30%,C = 21.24%,T =25.48%,G+C =46.54%,其G+C含量略低于T7噬菌体家族成员T7、phiA1122。②GC岛的分析表明噬菌体MmP1基因组上发现了20个大于200bp的GC岛。其中G+C含量偏离最大的两个基因,即基因35和基因42很可能是水平转移而来的外源基因。③基因表达全部位于正链上,且与噬菌体T7、T3类似,基因结构排列聚集成堆,分早中晚三个时期。
5.基因组的生物信息学分析以及基因功能的探讨。在噬菌体MmP1基因组中具有152个大于100bp的ORFs,其中49个推定为编码基因,编码序列总长度为34359bp,基因的平均DNA长度为701bp。在整个基因组DNA中,平均每1000bp长度中有1.28个推定基因,基因组中碱基的使用率达到89.88%。在核苷酸水平,12个推定基因与目前已知的序列有同源性;在氨基酸水平,在公共数据库中共找到28个推定基因编码产物的同源蛋白质。综合分析,初步确定35个ORFs具有与噬菌体T7、phiA1122相似的功能。进而,利用CLUSTALX软件工具对搜索到的具有显著相似性的基因进行多重比对,通过phylip软件绘制系统发生树,用TreeView软件观察结果,分析其进化关系证实噬菌体MmP1属于T7噬菌体家族。
6.噬菌体结构蛋白及其编码基因的确定。本研究结果显示,噬菌体颗粒至少含有7个结构蛋白,其中,38kD蛋白是噬菌体的主要衣壳蛋白。将电泳分离的蛋白质转印至PVDF膜上进行N-端氨基酸测序。将N-端测序得到的氨基酸残基序列与所有推定基因编码产物的N-端氨基酸序列相比对,结合分子量大小,确定了ORF35是其编码基因。同时,根据噬菌体结构蛋白大小的唯一性,确定了69kD蛋白质是由ORF48编码的,150kD蛋白质是由ORF42编码的。
7.基因组的非编码序列分析表明在基因组上存在着37个长短不一的基因间区(1-1321bp),同时存在10个基因重叠区,16个基因的编码框相互之间发生了重叠。在基因组的5’-、3’-末端分别存在140和204bp的非编码序列。基因组中还存在大量反向重复序列、正向重复序列以及1个最长为61bp的串联重复序列。这些重复序列可能与转录调节、DNA重组以及基因组进化有关。在非编码序列还发现了5个可能的转录终止子,同时找到了5个可能的启动子。
噬菌体MmP1的全基因组序列已经在GenBank登录(No. EU652770)。
综上所述,通过本研究,明确了世界上第一株摩氏摩根菌噬菌体MmP1的基本生物学特性及其基因组组成序列,并对该基因组进行了初步注释。注释结果表明MmP1属于T7噬菌体家族成员,扩展了T7噬菌体家族宿主菌的范围(摩氏摩根菌未见报道为T7噬菌体家族宿主菌)。两类噬菌体(MmP1和T7)宿主菌分属不同的菌属,却拥有相同的基因结构和类似的基因,进一步揭示了噬菌体的生物多样性,为全面深入地认识噬菌体的遗传与变异、进化与分类、基因组织与调控以及寄生机制等生物学特性中的重大问题提供了新的数据。
Morganella morganii is a gram-negative rod commonly found in the environment and in the intestinal tracts of humans, mammals, and reptiles as normal flora. The genus Morganella belongs to the family Enterobacteriaceae. Despite its wide distribution, it is an uncommon cause of community-acquired infection and is most often encountered in postoperative and other nosocomial settings.
Bacteriophages are viruses of bacteria. They are ubiquitous in nature, and are now recognized to be the most numerous entities in the biosphere. When the sensitive bacterium was infected by a phage, there will be two reactions, one is lytic reaction, the other is lysogenic reaction. The lysogenic bacteriophage can alter the biologic features of the host bacterium by its inheritance material, meanwhile, they can change host’s inheritance material constituent in the process of the DNA recombination, integration, transposition and excision in host genome, which result in the microbial genetic diversity. Lytic phages can lyse and kill the host bacteria, and lysogenic phages also have a lytic period. So that phages are in the hope to be developed as anti-bacteria pharmaceutics. Deep-looking insight into the genetic background of phage is very important for no matter investigating the interaction of phage and its host bacteria, and revealing the biological diversity mechanism resulting from gene horizontal transfer caused by phages, or engineering remodeling of phage and phage-therapy. Now the genomic era has re-focussed researchers’attention onto the importance of bacteriophages. To date, there are totally 484 completed bacteriophage genomes available in public databases. In this dissertation, we are focused on the whole genome sequence and annotation of Morganella morganii phage 1 ( MmP1 ). The results are as follows:
1. The biological characterization of MmP1. The phage MmP1 is a temperate phage of Morganella morganii. Electron microscopy revealed that the phage has an isometric head (about 55 nm in diameter) and a short tail, and it belongs to the Podoviridae family. The optimal multiplicity of infection (MOI) of MmP1 is about 0.1, and hosts infected by the phages with an MOI of 0.1 will produce highest phage titer at 3.5h after infection. One-step growth kinetics of the phage showed that the latent period is about 10 min, the rise period is about 40 min, and the average burst size is about 105 phage particles per an infected cell.
2. The general characterization of MmP1 genome. The complete nucleotide sequence of phage MmP1 is 38,233 bp, and includes terminal repeats of 61bp, which is highly similar to T7-like phage. The G+C content of the MmP1 genome averages 46.54%. There are two regions with significantly higher G+C content than the average, among which two genes, gene 35 and gene 42, having the highest G+C content, may be acquired genes by horizontal transfer. Genes are all transcribed from the same DNA strand and occupy almost 90% of the nucleotide sequence, the same value found for T7. This efficiency is presumably the result of evolutionary packaging of the maximum amount of useful information into a DNA molecule whose length is limited by a virion of fixed size.
3. The bioinformatics analysis of phage genome. 152 ORFs longer than 100bp are found out by ORF finder software at NCBI website. Predictions using the GeneMark and Softberry programs revealed that the phage genome has 49 predicted genes. No potential tRNA coding regions were found in the phage genome. The predicted genes are tightly organized with little space between them, and there are 10 overlapping gene regions with total 91 bp, ranging from 1 to 32 bp. At the DNA level, 12 of the phage-encoded putative proteins show homology to known proteins in the database using BLASTn program, and at the protein level, 28 of the phage-encoded putative proteins show homology to known proteins in the database using BLASTp program. The function of these 35 genes show homology to phage T7 and phage phiA1122. Thus , MmP1 is thought to be a member of the T7 group. Similar to the T3 and T7 genomes, MmP1 genes could be divided into three classes: I (early), II (middle) and III(late). Multiple sequence alignment was conducted among those homologous proteins using software CLUSTALX, and then the phylogenetic trees were drawn by phylip software.
4. The phage capsid proteins and their coding genes. Phage particles were purified with CsCl gradient centrifugation, then the total phage capsid proteins were separated at least 7 bands by SDS-PAGE, respectively with molecular weight 150, 95, 82, 69, 62, 44 and 38kD. After transferred to a PVDF filter, Most bands were excised from the membrane and were subjected to N-terminal sequence with Edman degradation method. Only 38kD proteins could be sequenced and the N-terminal sequences were figured out. By comparative analysis of the N-terminal amino acid sequences of the proteins to the products coded by all the predicted genes, we got to know that gene 35 coded the 38kD proteins.
5. The non-coding sequences of the genome. There are 37 intergenic regions ranging from 1 to 1321 bps. There are non-coding sequences with length of 140 bps and 204 bps respectively on the 5’-and 3’-terminus of the phage genome. 17 inverted repeats (palindrome sequence) and 1 long tandem repeats(61bp) are found in the genome. These repeat sequences are related to the transcription, recombination of DNA and genomic evolution. 5 possible terminators are found in the intergenic regions, and 5 possible promoter was predicted at the genomic positive strand.
The genome data of phage MmP1 has been deposited in GenBank under the accession No. EU652770.
引文
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