多粘类芽孢杆菌（Paenibacillus polymyxa）SC2 fus基因簇的克隆与分析
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摘要
多粘类芽孢杆菌(Paenibacillus polymyxa)SC2是一株从辣椒根际分离筛选的根际促生细菌,该菌株抗菌谱广,对辣椒根腐病原菌( Fusarium solani)、黄瓜枯萎病原菌(Fusarium oxysporum f. sp. cucumerinum)、黄瓜霜霉病原菌(Pseudoperonospora cubensis)、芹菜灰霉病原菌(Botrytis cinerea Pers)以及西红柿灰霉病原菌(Botrytis cinerea)等具有良好的拮抗效果。
用已报道的检测非核糖体肽合成酶(non-ribosomal peptide synthetases, NRPSs)基因保守区的兼并引物TGD和LGG为引物,以多粘类芽孢杆菌(P. polymyxa )SC2的基因组DNA为模板进行PCR扩增,获得一段长度为497bp的NRPS基因保守区序列。采用热不对称交错PCR(TAIL-PCR)方法,以SC2菌株基因组DNA为模板,根据NRPS基因保守区序列,分别向两侧设计特异性引物,扩增该已知序列的两侧序列。随后,通过多次特异性引物设计,进行TAIL-PCR。同时,根据枯草芽孢杆菌(Bacillus subtilis)bamC、mycC、ituC和解淀粉芽孢杆菌(Bacillus amyloliquefaciens)FZB42 bmyC的同源序列,设计兼并引物进行PCR扩增,将得到的所有序列拼接,得到长度为19844bp的DNA序列。
经BLAST比对发现,此DNA序列与P. polymyxa PKB1中fus基因簇具有很高的相似性,因此,根据P. polymyxa PKB1中fusA基因簇与本试验获得的DNA序列的同源区域设计一系列兼并引物,进行特异性扩增,最终得到一条32680bp的DNA序列。
将得到的总长为32680bp的DNA序列提交GenBank,获得序列号为EU431181,该序列包含8个ORF,即fus基因簇,这8个ORF分别为fusG,fusF,fusE,fusD,fusC,fusB,fusA,fusTE,其核苷酸序列与多粘类芽孢杆菌(P. polymyxa) PKB1中对应的fusG,fusF,fusE,fusD,fusC,fusB,fusA,fusTE的相似性分别为90.61%,93.42%,91.75%,85.54%,83.29%,89.95%,88.97%,82.88%;其衍生氨基酸序列与多粘类芽孢杆菌(P. polymyxa)PKB1中对应的FusG,FusF,FusE,FusD,FusC,FusB,FusA,FusTE的相似性分别98.77%,99.15%,98.28%,90.64%,96.31%,97.78%,96.81%,和76.35%。另外,通过NCBI-BLAST,对fus基因簇的每个ORF进行了初步的功能分析。
fusA为一个完整的23727bp的ORF,编码7908个氨基酸,对其多肽序列进行结构域分析,结果表明,该多肽序列包含六个模块,分别为C-A-T、C-A-T-E、C-A-T、C-A-T-E、C-A-T-E和C-A-T;六个模块中的前五个模块的A结构域的特异性底物分别为L-Thr,D-Val,L-Tyr,D-Thr和D-Asn,但是第六个模块中特异性底物尚不能完全确定,通过构建系统发育树可以推测得到,多粘类芽孢杆菌(P. polymyxa)SC2的FusA-A6的结构域的特异性底物为D-Ala。预测的氨基酸残基组成、顺序与多粘芽孢杆菌(Bacillus polymyxa )KT-8产生的fusaricidin C和多粘芽孢杆菌(Bacillus polymyxa )L-1129产生的LI-F03a的第1、2、3、4、5、6位上氨基酸残基组成和顺序完全一致,因此,可以初步判断P. polymyxa SC2可能产生具有抗真菌活性的fusaricidin C。多粘类芽孢杆菌(P. polymyxa)SC2的FusA的六个A结构域的氨基酸序列与多粘类芽孢杆菌(P. poly- myxa)PKB1的FusA的A1、A2、A3、A4、A5和? A6结构域的相似性分别为94.13%、94.82%、91.52%、94.55%、95.34%和96.73%;其对应的核苷酸序列同源性分别为86.95%、89.00%、82.18%、89.38%、87.31%和89.49%。
Paenibacillus polymyxa SC2, a strain of plant growth-promoting rhizobacteria (PGPR) had significantly antagonistic to many soil-borne plant pathogenic fungi such as Phytophthora capsici. This has a broad-spectrum antimicrobial activity and can antagonize Fusarium solani, Fusarium oxysporum f. sp. cucumerinum, Pseudoperonospora cubensis, Botrytis cinerea Pers and Botrytis cinerea.
In the present study, We obtained a 497bp conserved DNA fragment of NRPSs gene, with the primers TGD and LGG detecting non-ribosomal peptide synthetases concerved domain, with genomic DNA of P. polymyxa SC2 as template. According to the conserved DNA sequence, we designed specific primers of TAIL-PCR, amplified the DNA sequences flanking on the conserved DNA fragment by the method of TAIL-PCR with genomic DNA of P. polymyxa SC2 as template. Subsequently, the TAIL-PCR of upstream or downstream DNA sequences of the last amplified DNA fragments were continually carried out for several times. Alternatively, depending on the identity of the NRPS gene to bamC, mycC, ituC sequences of Bacillus subtilis strains and bmyC of Bacillus amyloliquefaciens FZB42, degenerate primers were designed to amplify the aimed DNA fragments. Then, we obtained a resulting DNA sequence with the length of 19844bp by assembling all amplified DNA fragments.
BLAST analysis revealed the ORF is identical to the homologous fus gene cluster sequence of P. polymyxa PKB1, so, depending on the identity of the DNA fragments has obtained to fus gene cluster of P. polymyxa PKB1, degenerate primers were designed to amplify the aimed DNA fragments. Finally, we obtained a resulting DNA sequence with the length of 32680bp by assembling all amplified DNA fragments.
Finally, the fus gene cluster was cloned and sequenced (the accession number of GenBank is EU431181), and it spans 32680 bp, including 8 open reading frames (the fus gene cluster), they are fusG, fusF, fusE, fusD, fusC, fusB, fusA, fusTE. Similarity of the 8 ORFs in the fusaricidin biosynthetic gene cluster of P. polymyxa SC2 to the corresponding gene fusG, fusF, fusE, fusD, fusC, fusB, fusA, fusTE of the P. polymyxa PKB1 is 90.61%, 93.42%, 91.75%, 85.54%, 83.29%, 89.95%, 88.97%, 82.88%, and similarity of the deduced amino acid sequences to FusG, FusF, FusE, FusD, FusC, FusB, FusA, FusTE of the strain P. polymyxa PKB1 is 98.77%, 99.15%, 98.28%, 90.64%, 96.31%, 97.78%, 96.81%, and 76.35%, respectively. Then,wo do the primary analysis to the fus gene cluster by NCBI-BLAST.
The fusA is 23727 bp, encoding a six-module nonribosomal peptide synthetase. The domain organization for these six modules are C-A-T, C-A-T-E, C-A-T, C-A-T-E, C-A-T-E and C-A-T-TE, respectively. The predicted substrate specificities of the top five A domains within FusA were consistent with the five amino acids, L-Thr, D-Val, L-Tyr, D-Thr and D-Asn. The amino acid substrate for FusA-A6 could not be predicted because its signature sequence shows no similarity to A domains with assigned specificities, including those activating L- and D-Ala. We have build up the phylogenetic tree of FusA-A6 of the P. polymyxa SC2 using the MEGA4 software. Finally, we have predicted that the amino acid substrate for FusA-A6 may be D-Ala. The predicted amino acid composition and sequence of the P. polymyxa SC2 was exactly consistent with the fusaricidin C produced by Bacillus polymyxa KT-8 and LI-F03a produced by Bacillus polymyxa L-1129. Accordingly, P. polymyxa SC2 may be responsible for the synthesis of fusaricidin C (LI-F03a) which has the antifungal activity. Similarity of the six A domains to the corresponding domain A1, A2, A3, A4, A5 and A6 of FusA of P. polymyxa PKB1 are 94.13%, 94.82%, 91.52%, 94.55%, 95.34% and 96.73%, respectively. Accordingly, identity of their DNA sequences are 86.95%, 89.00%, 82.18%, 89.38%, 87.31% and 89.49%. We deduce that fusA is a key gene involved in biosynthesis of nonribosomal peptide fusaricidin C from P. polymyxa SC2.
用已报道的检测非核糖体肽合成酶(non-ribosomal peptide synthetases, NRPSs)基因保守区的兼并引物TGD和LGG为引物,以多粘类芽孢杆菌(P. polymyxa )SC2的基因组DNA为模板进行PCR扩增,获得一段长度为497bp的NRPS基因保守区序列。采用热不对称交错PCR(TAIL-PCR)方法,以SC2菌株基因组DNA为模板,根据NRPS基因保守区序列,分别向两侧设计特异性引物,扩增该已知序列的两侧序列。随后,通过多次特异性引物设计,进行TAIL-PCR。同时,根据枯草芽孢杆菌(Bacillus subtilis)bamC、mycC、ituC和解淀粉芽孢杆菌(Bacillus amyloliquefaciens)FZB42 bmyC的同源序列,设计兼并引物进行PCR扩增,将得到的所有序列拼接,得到长度为19844bp的DNA序列。
经BLAST比对发现,此DNA序列与P. polymyxa PKB1中fus基因簇具有很高的相似性,因此,根据P. polymyxa PKB1中fusA基因簇与本试验获得的DNA序列的同源区域设计一系列兼并引物,进行特异性扩增,最终得到一条32680bp的DNA序列。
将得到的总长为32680bp的DNA序列提交GenBank,获得序列号为EU431181,该序列包含8个ORF,即fus基因簇,这8个ORF分别为fusG,fusF,fusE,fusD,fusC,fusB,fusA,fusTE,其核苷酸序列与多粘类芽孢杆菌(P. polymyxa) PKB1中对应的fusG,fusF,fusE,fusD,fusC,fusB,fusA,fusTE的相似性分别为90.61%,93.42%,91.75%,85.54%,83.29%,89.95%,88.97%,82.88%;其衍生氨基酸序列与多粘类芽孢杆菌(P. polymyxa)PKB1中对应的FusG,FusF,FusE,FusD,FusC,FusB,FusA,FusTE的相似性分别98.77%,99.15%,98.28%,90.64%,96.31%,97.78%,96.81%,和76.35%。另外,通过NCBI-BLAST,对fus基因簇的每个ORF进行了初步的功能分析。
fusA为一个完整的23727bp的ORF,编码7908个氨基酸,对其多肽序列进行结构域分析,结果表明,该多肽序列包含六个模块,分别为C-A-T、C-A-T-E、C-A-T、C-A-T-E、C-A-T-E和C-A-T;六个模块中的前五个模块的A结构域的特异性底物分别为L-Thr,D-Val,L-Tyr,D-Thr和D-Asn,但是第六个模块中特异性底物尚不能完全确定,通过构建系统发育树可以推测得到,多粘类芽孢杆菌(P. polymyxa)SC2的FusA-A6的结构域的特异性底物为D-Ala。预测的氨基酸残基组成、顺序与多粘芽孢杆菌(Bacillus polymyxa )KT-8产生的fusaricidin C和多粘芽孢杆菌(Bacillus polymyxa )L-1129产生的LI-F03a的第1、2、3、4、5、6位上氨基酸残基组成和顺序完全一致,因此,可以初步判断P. polymyxa SC2可能产生具有抗真菌活性的fusaricidin C。多粘类芽孢杆菌(P. polymyxa)SC2的FusA的六个A结构域的氨基酸序列与多粘类芽孢杆菌(P. poly- myxa)PKB1的FusA的A1、A2、A3、A4、A5和? A6结构域的相似性分别为94.13%、94.82%、91.52%、94.55%、95.34%和96.73%;其对应的核苷酸序列同源性分别为86.95%、89.00%、82.18%、89.38%、87.31%和89.49%。
Paenibacillus polymyxa SC2, a strain of plant growth-promoting rhizobacteria (PGPR) had significantly antagonistic to many soil-borne plant pathogenic fungi such as Phytophthora capsici. This has a broad-spectrum antimicrobial activity and can antagonize Fusarium solani, Fusarium oxysporum f. sp. cucumerinum, Pseudoperonospora cubensis, Botrytis cinerea Pers and Botrytis cinerea.
In the present study, We obtained a 497bp conserved DNA fragment of NRPSs gene, with the primers TGD and LGG detecting non-ribosomal peptide synthetases concerved domain, with genomic DNA of P. polymyxa SC2 as template. According to the conserved DNA sequence, we designed specific primers of TAIL-PCR, amplified the DNA sequences flanking on the conserved DNA fragment by the method of TAIL-PCR with genomic DNA of P. polymyxa SC2 as template. Subsequently, the TAIL-PCR of upstream or downstream DNA sequences of the last amplified DNA fragments were continually carried out for several times. Alternatively, depending on the identity of the NRPS gene to bamC, mycC, ituC sequences of Bacillus subtilis strains and bmyC of Bacillus amyloliquefaciens FZB42, degenerate primers were designed to amplify the aimed DNA fragments. Then, we obtained a resulting DNA sequence with the length of 19844bp by assembling all amplified DNA fragments.
BLAST analysis revealed the ORF is identical to the homologous fus gene cluster sequence of P. polymyxa PKB1, so, depending on the identity of the DNA fragments has obtained to fus gene cluster of P. polymyxa PKB1, degenerate primers were designed to amplify the aimed DNA fragments. Finally, we obtained a resulting DNA sequence with the length of 32680bp by assembling all amplified DNA fragments.
Finally, the fus gene cluster was cloned and sequenced (the accession number of GenBank is EU431181), and it spans 32680 bp, including 8 open reading frames (the fus gene cluster), they are fusG, fusF, fusE, fusD, fusC, fusB, fusA, fusTE. Similarity of the 8 ORFs in the fusaricidin biosynthetic gene cluster of P. polymyxa SC2 to the corresponding gene fusG, fusF, fusE, fusD, fusC, fusB, fusA, fusTE of the P. polymyxa PKB1 is 90.61%, 93.42%, 91.75%, 85.54%, 83.29%, 89.95%, 88.97%, 82.88%, and similarity of the deduced amino acid sequences to FusG, FusF, FusE, FusD, FusC, FusB, FusA, FusTE of the strain P. polymyxa PKB1 is 98.77%, 99.15%, 98.28%, 90.64%, 96.31%, 97.78%, 96.81%, and 76.35%, respectively. Then,wo do the primary analysis to the fus gene cluster by NCBI-BLAST.
The fusA is 23727 bp, encoding a six-module nonribosomal peptide synthetase. The domain organization for these six modules are C-A-T, C-A-T-E, C-A-T, C-A-T-E, C-A-T-E and C-A-T-TE, respectively. The predicted substrate specificities of the top five A domains within FusA were consistent with the five amino acids, L-Thr, D-Val, L-Tyr, D-Thr and D-Asn. The amino acid substrate for FusA-A6 could not be predicted because its signature sequence shows no similarity to A domains with assigned specificities, including those activating L- and D-Ala. We have build up the phylogenetic tree of FusA-A6 of the P. polymyxa SC2 using the MEGA4 software. Finally, we have predicted that the amino acid substrate for FusA-A6 may be D-Ala. The predicted amino acid composition and sequence of the P. polymyxa SC2 was exactly consistent with the fusaricidin C produced by Bacillus polymyxa KT-8 and LI-F03a produced by Bacillus polymyxa L-1129. Accordingly, P. polymyxa SC2 may be responsible for the synthesis of fusaricidin C (LI-F03a) which has the antifungal activity. Similarity of the six A domains to the corresponding domain A1, A2, A3, A4, A5 and A6 of FusA of P. polymyxa PKB1 are 94.13%, 94.82%, 91.52%, 94.55%, 95.34% and 96.73%, respectively. Accordingly, identity of their DNA sequences are 86.95%, 89.00%, 82.18%, 89.38%, 87.31% and 89.49%. We deduce that fusA is a key gene involved in biosynthesis of nonribosomal peptide fusaricidin C from P. polymyxa SC2.
引文
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