伤寒与甲型副伤寒沙门菌的全菌蛋白质组学比较分析
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摘要
伤寒是第三世界国家威胁人们健康的重要问题,每年导致近60万人死亡。近年来,甲型副伤寒迅速流行,在一些省份超过伤寒成为优势菌型。伤寒和甲型副伤寒都是以人为唯一宿主的疾病,二者临床症状难于区分。共有基因芯片杂交的结果发现伤寒沙门菌和甲型副伤寒沙门菌的亲缘关系比其他血清型的沙门菌近得多。本文进行了伤寒沙门菌CT18和甲型副伤寒沙门菌ATCC9150基因组的生物信息学比对,分别得到413和489个特有蛋白编码基因。而在本文分析所使用的培养条件下,CT18与9150的二维蛋白电泳图谱比对分别得到74和154个各自特异蛋白点。CT18菌株的特有蛋白编码基因只有STY3673在CT18全谱蛋白点中发现表达。9150菌株的特有蛋白编码基因只有SPA1555和SPA0985在9150全谱蛋白点中发现表达。说明两株菌蛋白谱比较得到的特异点主要是由两者的共有基因编码,而不是主要由特异基因编码。菌株CT18特异的蛋白点中,6个蛋白编码基因在9150基因组中不存在或者是假基因,10个未在9150全蛋白谱中找到,但其编码基因在9150基因组中存在,47个蛋白在9150全蛋白谱中亦有表达,只是处于不同的修饰状态;菌株9150的特异蛋白点中,3个蛋白编码基因在CT18中不存在或者是假基因,81个蛋白编码基因没有在CT18全蛋白谱中找到,但其编码基因在CT18基因组中存在,77个蛋白在CT18中有表达,只是处于不同的修饰状态。提示,两者的蛋白组学差异,主要是由共有基因产物的不同修饰造成,提示了蛋白表达、发挥功能遵循了经济的原则,同样的基因编码产物可能发挥不同的功能。两株菌的特异蛋白点中,部分蛋白编码基因在对方是假基因,这些假基因造成了某些酶的功能的失活,导致一些合成或分解代谢通路的差异,比如本文中发现的由于假基因造成两株菌0-抗原成分双脱氧己糖的差异,组氨酸分解代谢的差异,和维生素C代谢的差异。进一步证实这两株不同血清型的菌株某些功能或者代谢通路的差异是由两者共有基因部分失去功能造成,而不是基因组特有基因引起,基因组的使用很节约。
为了了解伤寒和甲型副伤寒沙门菌流行株之间的蛋白组学差异和进化关系,我们比较了四株伤寒之间和四株甲型副伤寒沙门菌之间的全菌蛋白二维电泳图谱。伤寒沙门菌CT18和国内三株分离于不同年代和地区的流行株的比较结果分别为,CT18与XJ19相比,各得到19和64个特异蛋白,CT18与906005相比,各得到28和54个特异蛋白,CT18与1321相比各得到27和36个特异蛋白。将菌株CT18的特异蛋白编码基因设计引物分别以其他三株流行菌株DNA为模板扩增结果发现,一个可能的DNA结合蛋白编码基因,在三株国内流行株扩增均为阴性,它位于CT18所包含的一个多耐药质粒PHCM1。提示这个质粒在这三个流行菌株可能不存在。四株伤寒沙门菌的比较发现,广西菌株1321与CT18的谱型相近,与XJ19和906005差距较大,由于广西和越南毗邻,二者在遗传上可能存在亲缘关系。
对于甲型副伤寒沙门菌,9150与98-53相比各得到15和17个差异蛋白,和YN77相比各得到26和11个差异蛋白,和9A05036相比各得到13和10个差异蛋白。将9150中的特异蛋白编码基因为靶标,以国内菌株DNA为模板进行PCR扩增,结果只有9A05036的501,663蛋白点编码基因扩增阴性,此外,国内菌株中都有表达、而9150中没有表达的蛋白yeaG,其编码基因在9150基因组中不存在。综合四株菌各自的特异蛋白发现,在一些与渗透压有关的摄取系统蛋白,可能的毒力因子,与转录有关的蛋白表达上,国内三株流行株很接近,与菌株9150存在明显差异。
另外,为筛选诊断用的伤寒和甲型副伤寒的外膜蛋白的特异抗原,将两者外膜蛋白进行了比较,谱型差异较大,但特异蛋白点的蛋白序列和基因序列比较发现这些特异蛋白点很少是由独有基因编码,大多由共有基因编码,虽然这亦有力证实基因组发挥功能遵循经济原则,但作为诊断用抗原,并不是最好选择。本文筛选到三株伤寒沙门菌都有表达、而在三株甲型副伤寒沙门菌均未见表达的一个脂蛋白,核酸和蛋白序列的blast比较发现它为伤寒沙门菌独有。对53株伤寒沙门菌和49株甲型副伤寒沙门菌的DNA进行该蛋白编码基因的PCR检测发现,伤寒沙门菌都扩增出目的条带,而甲型副伤寒沙门菌的扩增均为阴性。Western blot的结果显示它与伤寒病人的血清IgG显示了良好的反应,而与甲型副伤寒病人的血清反应微弱。提示它作为一个诊断用抗原是有希望的。
Typhoid fever was a major issue for public health in developing countries and caused about 600,000 people dead every year.Recently,paratyphoid fever became more severe than typhoid fever in some provinces in China and it is difficult to distinguish paratyphoid fever from typhoid fever only according to the symptoms caused by them.Micoarray data on shared genes indicated that S.paratyphi A and S.typhi are closely related.413 and 489 specific genes encoding different proteins were found respectively through the comparison of the genomes of S.typhi CT18 with S.paratyphi A ATCC9150.74 and 154 specific protein spots were identified with the comparison of their proteomics displayed on 2-D gels.Among the specific genes identified by genome analysis,only STY3673 gene was found expressing in proteomic spectrum of strain CT18,and SPA1555,SPA0985 expressed in strain ATCC 9150,suggesting that different protein expressing spectrum was mainly produced by modification of proteins but not specific genes contained in each genome.Within CT18 specific protein coding genes,6 genes were psuedogenes or absent in the genome of ATCC 9150,10 proteins did not express in ATCC 9150 strain but their ORFs were found present in the chromosome of ATCC 9150,47 proteins expressed in both strains were differently modified.For ATCC 9150 specific protein spots,3 were psedogenes or absent in CT18,81 proteins did not express in CT18 but their ORFs located in the chromosome DNA,77 proteins expressed both in CT18 and ATCC 9150 strains were differently modified.It is suggested that the proteomics difference between CT18 and ATCC 9150 was mainly due to different translational modification of different common genes during gene expression process indicating a economic usage of chromosome DNA in bacteria.One gene encoded different proteins with different functions.Among the specific protein spots some psuedogenes while present as active genes in the other strain caused the inactivation of the gene product,making the related metabolic pathway different.For example some genes related to the synthesis of O-antigen,catabolism of histidine and ascorbate were psuedogenes.
To understand the genetic relationship of S.typhi and paratyphi A,Proteomics analysis of reference strain CT18 and 3 isolates in China was applied.19 and 64 specific protein spots were obtained between the CT18 and XJ19,28 and 54 specific spots were found between CT18 and 906005,27 and 36 specific proteins between CT18 and 1321, respectively.Primers were designed according to the sequence of the specific protein coding genes of CT18 and PCR was developed to identify these genes in China strains.As a result,one gene coding putative DNA binding protein present on the plasmid PHCM1 was not found in chromosome DNA of all China strains.It is showed the proteomics pattern of GX1321 were similar with that of CT18,while significant difference between XJ19 and 906005,indicating the close relationship in genetics between GX1321 strain and CT18 strain.
With the analysis of proteomics between S.paratyphi A strain 9150 and China strains we found 15 and 17 specific proteins between 9150 and 98-53,26 and 11 proteins between 9150 and YN77,13 and 10 proteins between 9150 and 9A05036,respectively.Primers were designed according to the sequences of specific protein coding genes of 9150 and PCR was developed to check whether these genes present in China strains or not.As a result,spot number 501 and 663 were PCR amplification negative in 9A05036.Additional, a protein named yeaG,whose coding gene was not found in chromosome of 9150.
Although it showed large diversity with comparing identified outer membrane proteins between S.typhi and S.paratyphi A,sequences of specific protein coding gene were conserved and only one specific protein of S.typhi was identified,named 90-38. Primers were designed according to its gene sequence,53 S.typhi strains and 49 S. paratyphi A strains were detected with PCR amplification,all S.typhi strains were positive except two,which can not agglutinate with 09 antiserum.All S.paratyphi A strains were negative.The protein was expressed in E.coli and purified.Western blot was carried out and it is showed a strong reaction with several sera from patients with typhoid fever and a weak reaction with people who had paratyphoid fever,which indicates that this protein is a potential candidate for developing diagnostic antigens in typhoid fever diagnosis.
为了了解伤寒和甲型副伤寒沙门菌流行株之间的蛋白组学差异和进化关系,我们比较了四株伤寒之间和四株甲型副伤寒沙门菌之间的全菌蛋白二维电泳图谱。伤寒沙门菌CT18和国内三株分离于不同年代和地区的流行株的比较结果分别为,CT18与XJ19相比,各得到19和64个特异蛋白,CT18与906005相比,各得到28和54个特异蛋白,CT18与1321相比各得到27和36个特异蛋白。将菌株CT18的特异蛋白编码基因设计引物分别以其他三株流行菌株DNA为模板扩增结果发现,一个可能的DNA结合蛋白编码基因,在三株国内流行株扩增均为阴性,它位于CT18所包含的一个多耐药质粒PHCM1。提示这个质粒在这三个流行菌株可能不存在。四株伤寒沙门菌的比较发现,广西菌株1321与CT18的谱型相近,与XJ19和906005差距较大,由于广西和越南毗邻,二者在遗传上可能存在亲缘关系。
对于甲型副伤寒沙门菌,9150与98-53相比各得到15和17个差异蛋白,和YN77相比各得到26和11个差异蛋白,和9A05036相比各得到13和10个差异蛋白。将9150中的特异蛋白编码基因为靶标,以国内菌株DNA为模板进行PCR扩增,结果只有9A05036的501,663蛋白点编码基因扩增阴性,此外,国内菌株中都有表达、而9150中没有表达的蛋白yeaG,其编码基因在9150基因组中不存在。综合四株菌各自的特异蛋白发现,在一些与渗透压有关的摄取系统蛋白,可能的毒力因子,与转录有关的蛋白表达上,国内三株流行株很接近,与菌株9150存在明显差异。
另外,为筛选诊断用的伤寒和甲型副伤寒的外膜蛋白的特异抗原,将两者外膜蛋白进行了比较,谱型差异较大,但特异蛋白点的蛋白序列和基因序列比较发现这些特异蛋白点很少是由独有基因编码,大多由共有基因编码,虽然这亦有力证实基因组发挥功能遵循经济原则,但作为诊断用抗原,并不是最好选择。本文筛选到三株伤寒沙门菌都有表达、而在三株甲型副伤寒沙门菌均未见表达的一个脂蛋白,核酸和蛋白序列的blast比较发现它为伤寒沙门菌独有。对53株伤寒沙门菌和49株甲型副伤寒沙门菌的DNA进行该蛋白编码基因的PCR检测发现,伤寒沙门菌都扩增出目的条带,而甲型副伤寒沙门菌的扩增均为阴性。Western blot的结果显示它与伤寒病人的血清IgG显示了良好的反应,而与甲型副伤寒病人的血清反应微弱。提示它作为一个诊断用抗原是有希望的。
Typhoid fever was a major issue for public health in developing countries and caused about 600,000 people dead every year.Recently,paratyphoid fever became more severe than typhoid fever in some provinces in China and it is difficult to distinguish paratyphoid fever from typhoid fever only according to the symptoms caused by them.Micoarray data on shared genes indicated that S.paratyphi A and S.typhi are closely related.413 and 489 specific genes encoding different proteins were found respectively through the comparison of the genomes of S.typhi CT18 with S.paratyphi A ATCC9150.74 and 154 specific protein spots were identified with the comparison of their proteomics displayed on 2-D gels.Among the specific genes identified by genome analysis,only STY3673 gene was found expressing in proteomic spectrum of strain CT18,and SPA1555,SPA0985 expressed in strain ATCC 9150,suggesting that different protein expressing spectrum was mainly produced by modification of proteins but not specific genes contained in each genome.Within CT18 specific protein coding genes,6 genes were psuedogenes or absent in the genome of ATCC 9150,10 proteins did not express in ATCC 9150 strain but their ORFs were found present in the chromosome of ATCC 9150,47 proteins expressed in both strains were differently modified.For ATCC 9150 specific protein spots,3 were psedogenes or absent in CT18,81 proteins did not express in CT18 but their ORFs located in the chromosome DNA,77 proteins expressed both in CT18 and ATCC 9150 strains were differently modified.It is suggested that the proteomics difference between CT18 and ATCC 9150 was mainly due to different translational modification of different common genes during gene expression process indicating a economic usage of chromosome DNA in bacteria.One gene encoded different proteins with different functions.Among the specific protein spots some psuedogenes while present as active genes in the other strain caused the inactivation of the gene product,making the related metabolic pathway different.For example some genes related to the synthesis of O-antigen,catabolism of histidine and ascorbate were psuedogenes.
To understand the genetic relationship of S.typhi and paratyphi A,Proteomics analysis of reference strain CT18 and 3 isolates in China was applied.19 and 64 specific protein spots were obtained between the CT18 and XJ19,28 and 54 specific spots were found between CT18 and 906005,27 and 36 specific proteins between CT18 and 1321, respectively.Primers were designed according to the sequence of the specific protein coding genes of CT18 and PCR was developed to identify these genes in China strains.As a result,one gene coding putative DNA binding protein present on the plasmid PHCM1 was not found in chromosome DNA of all China strains.It is showed the proteomics pattern of GX1321 were similar with that of CT18,while significant difference between XJ19 and 906005,indicating the close relationship in genetics between GX1321 strain and CT18 strain.
With the analysis of proteomics between S.paratyphi A strain 9150 and China strains we found 15 and 17 specific proteins between 9150 and 98-53,26 and 11 proteins between 9150 and YN77,13 and 10 proteins between 9150 and 9A05036,respectively.Primers were designed according to the sequences of specific protein coding genes of 9150 and PCR was developed to check whether these genes present in China strains or not.As a result,spot number 501 and 663 were PCR amplification negative in 9A05036.Additional, a protein named yeaG,whose coding gene was not found in chromosome of 9150.
Although it showed large diversity with comparing identified outer membrane proteins between S.typhi and S.paratyphi A,sequences of specific protein coding gene were conserved and only one specific protein of S.typhi was identified,named 90-38. Primers were designed according to its gene sequence,53 S.typhi strains and 49 S. paratyphi A strains were detected with PCR amplification,all S.typhi strains were positive except two,which can not agglutinate with 09 antiserum.All S.paratyphi A strains were negative.The protein was expressed in E.coli and purified.Western blot was carried out and it is showed a strong reaction with several sera from patients with typhoid fever and a weak reaction with people who had paratyphoid fever,which indicates that this protein is a potential candidate for developing diagnostic antigens in typhoid fever diagnosis.
引文
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