萘降解菌株Pseudomonas putida ND6中水杨醛脱氢酶NahV的生物学功能和转录调控
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摘要
萘降解菌株Pseudomonas putida ND6分离自天津市南排污河,是一株高效降解萘的菌株,能在48h内降解培养基中98%的萘(2g/L)。同大部分萘降解细菌一样,P. putida ND6的萘降解基因位于一个10,1858bp的大质粒pND6-1上,此质粒已被测序和注释。序列分析表明P. putida ND6的萘降解基因排列及降解途径都与其它经典的萘降解菌株相似,上游操纵子(nah操纵子)包括nahAaAbAcAdBFCED,编码将萘转变为水杨酸所需的酶；下游操纵子(sal操纵子)包括nahGTHINLOMKJY,编码水杨酸经由儿茶酚间位裂解途径生成乙酰乙醛和丙酮酸所需的酶。
P. putida ND6的独特之处在于在经典的萘降解操纵子之外有两个额外的萘降解基因,既水杨醛脱氢酶基因nahF的同工基因nahv和水杨酸羟化酶基因nahG的同工基因nahU。本论文主要研究了其中水杨醛脱氢酶同工酶NahV的生物学功能和转录调控方式。
质粒拷贝数(Plasmid copy number, PCN)是指每个细菌细胞中所含质粒的个数。P. putida ND6的萘降解基因位于大质粒pND6-1上。应用实时定量PCR(quantitative real-time PCR, qPCR)方法测定了萘降解菌株P. putida ND6中萘降解质粒pND6-1的拷贝数为2。
通过自杀载体基因敲除的方法,分别构建了nahF和nahv基因突变株ND6-△△F和ND6-△△V。对比了野生型ND6与基因敲除菌株ND6-△△F和ND6-△△V在生长和萘降解速率方面的不同,发现不论ND6-△△F还是ND6-△△V的萘降解速率与野生型ND6相比都有所降低；在mRNA和蛋白表达水平上,在nahF(或nahV)基因突变株ND6-△△F(或ND6-△△V)中,另一基因nahv(或nahF)的表达量都比野生型高；在水杨醛脱氢酶活性方面,无论以何种碳源培养,野生型ND6的水杨醛脱氢酶活性都比基因突变株高。以上结果表明,虽然NahF的水杨醛脱氢酶活性比NahV高,但萘降解菌株P. putida ND6中额外的水杨醛脱氢酶NahV的存在增加了细胞中水杨醛脱氢酶的剂量,从而加快了萘降解的速率；NahV能作为经典水杨醛脱氢酶NahF的后备和补充,当经典水杨醛脱氢酶基因nahF在细菌的进化过程中发生突变或缺失后,NahV能部分取代NahF的作用,行使水杨醛脱氢酶的功能,使得突变株能继续生存。
构建了nahR基因突变株ND6-△△R,对比了突变株与野生株中NahF和NahV在mRNA及酶活性水平的差异。无论以何种碳源培养,诱导物水杨酸钠是否存在时,P. putida ND6中的nahR基因都有一定量的本底表达,当加入诱导物水杨酸钠时,nahR基因的表达量增加；P. putida ND6菌株中的水杨醛脱氢酶基因nahF和nahv都不是组成型表达(以葡萄糖为唯一碳源时,检测不到它们的表达)。只有当诱导物水杨酸钠和调节蛋白NahR同时存在,水杨酸钠与NahR相结合,才能使RNA聚合酶Ⅰ结合于启动子的正确位置,起始水杨醛脱氢酶基因nahF和nahv的转录。
Pseudomonas putida ND6, which was isolated from Tianjin southern effluents, can degrade naphthalene of2g/L in minimal medium by98%in48hours. As most other naphthalene-degrading strains, the naphthalene-degrading genes of P. putida ND6are located on the large10,1858base pair (bp) pND6-1plasmid which has been sequenced and annotated. Sequence analysis indicated that P. putida ND6-mediated naphthalene degradation occurred via mechanisms similar to those described for other naphthalene-degrading strains. The naphthalene-degrading genes in these strains are organized in two operons:the upper pathway operon (nahAaAbAcAdBFCED) encoding enzymes involved in the conversion of naphthalene to salicylate and the lower pathway operon (nahGTHINLOMKJ) encoding enzymes necessary for the conversion of salicylate to tricarboxylic acid cycle intermediates via the meta-cleavage pathway.
P. putida ND6is unique in that it possesses two isofunctional salicylaldehyde dehydrogenase genes nahF and nahV in addition to two isofunctional salicylate hydroxylase genes nahG and nahU. In this study, the biological function and regulation model of NahV in P. putida ND6were studied.
Plasmid copy number (PCN) is the number of the plasmid copy included in one strain. The PCN of plasmid pND6-1in P. putida ND6is two determined by quantitative real-time PCR. This is the first report of copy number of plasmid that the size is more than100kb.
Using homologous recombination method, nahF-mutated strain P. putida ND6-AAF and nahv-mutated strain P. putida ND6-△△V were constructed, respectively.By comparing the respective mutants to the parental strain with respect to growth and naphthalene-degrading rates, we found that the naphthalene-degrading rates differed between the wild-type and mutant strains, that is, naphthalene-degrading rates was considerably lower in both the ND6-△△F and ND6-AAV than that in wild-type ND6. At the mRNA and protein level, the nahF or nah V expression levels in the ND6-△△V or ND6-△△F mutant were higher compared to levels observed in the wild-type strain. Furthermore, the salicylaldehyde dehydrogenase activities were considerably lower in both the nah V and nahF mutants compared to wild-type ND6when cultured with naphthalene or salicylate as the sole carbon source. In conclusion, the presence of the additional salicylaldehyde dehydroxylase NahV may be physiologically advantageous to the host strain ND6, which facilitates degradation of naphthalene through increasing the salicylaldehyde transformation efficiency, prevents salicylaldehyde toxic effect and reduces lethality when deletion mutations happened in the classical salicylaldehyde dehydroxylase NahF.
nahR-mutated strain P. putida ND6-△△R was also constructed to compare the differences between mutant and wild-type strain at mRNA and salicylaldehyde dehydrogenase activities level. We can detect the expression of nahR in P. putida ND6, whenever cultured with any carbon source, and the expression of nahR increased with the addition of inducer salicylate. Neither nahF nor nahV gene expressed constitutively. NahR binds to the promoter first. In the presence of inducer salicylate, NahR shifts its conformation to interact with RNA polymerase and help it bind to the promoter to initiate transcription.
P. putida ND6的独特之处在于在经典的萘降解操纵子之外有两个额外的萘降解基因,既水杨醛脱氢酶基因nahF的同工基因nahv和水杨酸羟化酶基因nahG的同工基因nahU。本论文主要研究了其中水杨醛脱氢酶同工酶NahV的生物学功能和转录调控方式。
质粒拷贝数(Plasmid copy number, PCN)是指每个细菌细胞中所含质粒的个数。P. putida ND6的萘降解基因位于大质粒pND6-1上。应用实时定量PCR(quantitative real-time PCR, qPCR)方法测定了萘降解菌株P. putida ND6中萘降解质粒pND6-1的拷贝数为2。
通过自杀载体基因敲除的方法,分别构建了nahF和nahv基因突变株ND6-△△F和ND6-△△V。对比了野生型ND6与基因敲除菌株ND6-△△F和ND6-△△V在生长和萘降解速率方面的不同,发现不论ND6-△△F还是ND6-△△V的萘降解速率与野生型ND6相比都有所降低；在mRNA和蛋白表达水平上,在nahF(或nahV)基因突变株ND6-△△F(或ND6-△△V)中,另一基因nahv(或nahF)的表达量都比野生型高；在水杨醛脱氢酶活性方面,无论以何种碳源培养,野生型ND6的水杨醛脱氢酶活性都比基因突变株高。以上结果表明,虽然NahF的水杨醛脱氢酶活性比NahV高,但萘降解菌株P. putida ND6中额外的水杨醛脱氢酶NahV的存在增加了细胞中水杨醛脱氢酶的剂量,从而加快了萘降解的速率；NahV能作为经典水杨醛脱氢酶NahF的后备和补充,当经典水杨醛脱氢酶基因nahF在细菌的进化过程中发生突变或缺失后,NahV能部分取代NahF的作用,行使水杨醛脱氢酶的功能,使得突变株能继续生存。
构建了nahR基因突变株ND6-△△R,对比了突变株与野生株中NahF和NahV在mRNA及酶活性水平的差异。无论以何种碳源培养,诱导物水杨酸钠是否存在时,P. putida ND6中的nahR基因都有一定量的本底表达,当加入诱导物水杨酸钠时,nahR基因的表达量增加；P. putida ND6菌株中的水杨醛脱氢酶基因nahF和nahv都不是组成型表达(以葡萄糖为唯一碳源时,检测不到它们的表达)。只有当诱导物水杨酸钠和调节蛋白NahR同时存在,水杨酸钠与NahR相结合,才能使RNA聚合酶Ⅰ结合于启动子的正确位置,起始水杨醛脱氢酶基因nahF和nahv的转录。
Pseudomonas putida ND6, which was isolated from Tianjin southern effluents, can degrade naphthalene of2g/L in minimal medium by98%in48hours. As most other naphthalene-degrading strains, the naphthalene-degrading genes of P. putida ND6are located on the large10,1858base pair (bp) pND6-1plasmid which has been sequenced and annotated. Sequence analysis indicated that P. putida ND6-mediated naphthalene degradation occurred via mechanisms similar to those described for other naphthalene-degrading strains. The naphthalene-degrading genes in these strains are organized in two operons:the upper pathway operon (nahAaAbAcAdBFCED) encoding enzymes involved in the conversion of naphthalene to salicylate and the lower pathway operon (nahGTHINLOMKJ) encoding enzymes necessary for the conversion of salicylate to tricarboxylic acid cycle intermediates via the meta-cleavage pathway.
P. putida ND6is unique in that it possesses two isofunctional salicylaldehyde dehydrogenase genes nahF and nahV in addition to two isofunctional salicylate hydroxylase genes nahG and nahU. In this study, the biological function and regulation model of NahV in P. putida ND6were studied.
Plasmid copy number (PCN) is the number of the plasmid copy included in one strain. The PCN of plasmid pND6-1in P. putida ND6is two determined by quantitative real-time PCR. This is the first report of copy number of plasmid that the size is more than100kb.
Using homologous recombination method, nahF-mutated strain P. putida ND6-AAF and nahv-mutated strain P. putida ND6-△△V were constructed, respectively.By comparing the respective mutants to the parental strain with respect to growth and naphthalene-degrading rates, we found that the naphthalene-degrading rates differed between the wild-type and mutant strains, that is, naphthalene-degrading rates was considerably lower in both the ND6-△△F and ND6-AAV than that in wild-type ND6. At the mRNA and protein level, the nahF or nah V expression levels in the ND6-△△V or ND6-△△F mutant were higher compared to levels observed in the wild-type strain. Furthermore, the salicylaldehyde dehydrogenase activities were considerably lower in both the nah V and nahF mutants compared to wild-type ND6when cultured with naphthalene or salicylate as the sole carbon source. In conclusion, the presence of the additional salicylaldehyde dehydroxylase NahV may be physiologically advantageous to the host strain ND6, which facilitates degradation of naphthalene through increasing the salicylaldehyde transformation efficiency, prevents salicylaldehyde toxic effect and reduces lethality when deletion mutations happened in the classical salicylaldehyde dehydroxylase NahF.
nahR-mutated strain P. putida ND6-△△R was also constructed to compare the differences between mutant and wild-type strain at mRNA and salicylaldehyde dehydrogenase activities level. We can detect the expression of nahR in P. putida ND6, whenever cultured with any carbon source, and the expression of nahR increased with the addition of inducer salicylate. Neither nahF nor nahV gene expressed constitutively. NahR binds to the promoter first. In the presence of inducer salicylate, NahR shifts its conformation to interact with RNA polymerase and help it bind to the promoter to initiate transcription.
引文
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