基于RAST的离子束重组菌DOB981的代谢网络研究
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摘要
为进一步深入理解低能离子注入对DOB的生理代谢产生的生物学意义,本研究基于DOB全基因组De novo测序数据,应用生物信息学方法对离子束重组菌DOB981及其原始菌株进行基因组结构和功能注释,构建基因尺度的代谢网络,并用Cytoscape对其进行可视化分析。研究表明,离子束重组菌株DOB981的基因组大小比原始菌株减少了223 268 bp,ORF减少了204个,功能基因减少了136个,生化反应的数量减少了10个,而生物反应的反应底物比原始菌株增加了3个;离子束重组菌株DOB981独有19个生化反应,比原始菌株减少了10个。Cytoscape可视化分析表明,离子束重组菌DOB981代谢网络中包含1 604个节点和3 733条连线,虽然比原始菌株减少了1个节点,但连线却增加了68条。基因尺度代谢网络拓扑属性分析表明,离子束重组菌DOB981与原始菌株的代谢网络均为无标度网络,具有小世界网络(SWN)特性,但重组菌DOB981的代谢网络的特征路径长度大于原始菌株,其总体结构相对松散,且密度低。本研究不仅对DOB的环境适应性机制的研究具有重要意义,也为DOB基因组代谢网络模拟构建提供了理论基础。
In order to further understand the biological significance of low-energy ion beam implantation on the physiological metabolism of DOB, the genomic structure and functional annotation of ion beam recombinant becteria DOB981 and its original strain were analyzed by bioinformatics methods based on the de novo sequencing of DOB genome in this paper. The metabolic network of gene scale was constructed and visualized by Cytoscape.The results showed that the genome size of the recombinant DOB981 was 223 268 bp lower than that of the original strain, the ORF and the functional gene were reduced by 204 and 136, respectively, and also the number of biochemical reaction was reduced by 10, but the substrates of the biological response were increased by 3. The recombinant DOB981 had 19 biochemical reactions, which was reduced by 10 compared with the original strain.The analysis results of Cytoscape visualization indicated that the metabolic network of the recombinant DOB981 included 1 604 nodes and 3 733 lines. Although it had 1 node less than the original strain, the lines were increased by 68. The analysis results of gene scale metabolic network topology suggested that the metabolic networks of recombinant DOB981 and original strain were scale-free network with small world network(SWN), while the characteristics path length of DOB981 metabolic network was longer than the original strain, and the overall structure of DOB981 was relatively loose, and the density was low. This study not only had an important significance for the research on the mechanism of environmental adaptation of DOB, but also laid the foundation for the construction of DOB genome metabolic network.
In order to further understand the biological significance of low-energy ion beam implantation on the physiological metabolism of DOB, the genomic structure and functional annotation of ion beam recombinant becteria DOB981 and its original strain were analyzed by bioinformatics methods based on the de novo sequencing of DOB genome in this paper. The metabolic network of gene scale was constructed and visualized by Cytoscape.The results showed that the genome size of the recombinant DOB981 was 223 268 bp lower than that of the original strain, the ORF and the functional gene were reduced by 204 and 136, respectively, and also the number of biochemical reaction was reduced by 10, but the substrates of the biological response were increased by 3. The recombinant DOB981 had 19 biochemical reactions, which was reduced by 10 compared with the original strain.The analysis results of Cytoscape visualization indicated that the metabolic network of the recombinant DOB981 included 1 604 nodes and 3 733 lines. Although it had 1 node less than the original strain, the lines were increased by 68. The analysis results of gene scale metabolic network topology suggested that the metabolic networks of recombinant DOB981 and original strain were scale-free network with small world network(SWN), while the characteristics path length of DOB981 metabolic network was longer than the original strain, and the overall structure of DOB981 was relatively loose, and the density was low. This study not only had an important significance for the research on the mechanism of environmental adaptation of DOB, but also laid the foundation for the construction of DOB genome metabolic network.
引文
Aziz R.K.,Bartels D.,Best A.A.,De Jongh M.,Disz T.,Edwards R.A.,Formsma K.,Gerdes S.,Glass E.M.,Kubal M.,Meyer F.,Olsen G.J.,Olson R.,Osterman A.L.,Overbeek R.A.,Mc Neil L.K.,Paarmann D.,Paczian T.,Parrello B.,Pusch G.D.,Reich C.,Stevens R.,Vassieva O.,Vonstein V.,Wilke A.,and Zagnitko O.,2008,The RAST Server:Rapid annotations using subsystems technology,BMC Genomics,9(1):75-89
Bao S.S.,and Mao P.H.,2017,Study on 16S r RNA gene of desert oligotrophic bacteria recombined by ion beam based on De novo sequencing,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(1):277-280(包珊珊,毛培宏,2017,基于基因组De novo测序的离子束重组沙漠寡营养细菌的16S r RNA基因研究,基因组学与应用生物学,36(1):277-280)
Edwards J.S.,and Palsson B.O.,1999,Systems properties of the Haemophilus influenzae Rd metabolic genotype,Journal of Biological Chemistry,274(25):17410-17416
Kim T.Y.,Sohn S.B.,Kim Y.B.,Kim W.J.,and Lee S.Y.,2012,Recent advances in reconstruction and applications of genome-scale metabolic models,Current Opinion in Biotechnology,23(4):617-623
Li L.,and Mao P.H.,2016,Study on single nucleotide polymorphisms in genomes of desert oligotrophic bacteria by low-energy N+implantation,35(12):3425-3429(李黎,毛培宏,2016,低能N+注入介导的沙漠寡营养细菌基因组SNP研究,基因组学与应用生物学,35(12):3425-3429)
Overbeek R.,Olson R.,Pusch G.D.,Olsen G.J.,Davis J.J.,Disz T.,Edwards R.A.,Gerdes S.,Parrello B.,Shukla M.,Vonstein V.,Wattam A.R.,Xia F.F.,and Stevens R.,2014,The SEED and the rapid annotation of microbial genomes using subsystems technology(RAST),Nucleic Acids Research,42:D206-D214
Tang Y.,and Mao P.H.,2017,The analyse of nif H gene mutation in genomes of desert oligotrophic bacteria by low-energy N+implantation,Jiyi nzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(1):281-286(唐亚,毛培宏,2017,低能N+注入介导的沙漠寡营养细菌的nif H基因突变研究,基因组学与应用生物学,36(1):281-286)
Bao S.S.,and Mao P.H.,2017,Study on 16S r RNA gene of desert oligotrophic bacteria recombined by ion beam based on De novo sequencing,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(1):277-280(包珊珊,毛培宏,2017,基于基因组De novo测序的离子束重组沙漠寡营养细菌的16S r RNA基因研究,基因组学与应用生物学,36(1):277-280)
Edwards J.S.,and Palsson B.O.,1999,Systems properties of the Haemophilus influenzae Rd metabolic genotype,Journal of Biological Chemistry,274(25):17410-17416
Kim T.Y.,Sohn S.B.,Kim Y.B.,Kim W.J.,and Lee S.Y.,2012,Recent advances in reconstruction and applications of genome-scale metabolic models,Current Opinion in Biotechnology,23(4):617-623
Li L.,and Mao P.H.,2016,Study on single nucleotide polymorphisms in genomes of desert oligotrophic bacteria by low-energy N+implantation,35(12):3425-3429(李黎,毛培宏,2016,低能N+注入介导的沙漠寡营养细菌基因组SNP研究,基因组学与应用生物学,35(12):3425-3429)
Overbeek R.,Olson R.,Pusch G.D.,Olsen G.J.,Davis J.J.,Disz T.,Edwards R.A.,Gerdes S.,Parrello B.,Shukla M.,Vonstein V.,Wattam A.R.,Xia F.F.,and Stevens R.,2014,The SEED and the rapid annotation of microbial genomes using subsystems technology(RAST),Nucleic Acids Research,42:D206-D214
Tang Y.,and Mao P.H.,2017,The analyse of nif H gene mutation in genomes of desert oligotrophic bacteria by low-energy N+implantation,Jiyi nzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(1):281-286(唐亚,毛培宏,2017,低能N+注入介导的沙漠寡营养细菌的nif H基因突变研究,基因组学与应用生物学,36(1):281-286)