基于全基因组测序和系统生物学分析的鸟苷工业生产菌分子育种研究
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摘要
本研究以一株鸟苷工业生产菌解淀粉芽孢杆菌XH7为出发菌株，为了提高育种效率、构建高产稳定的鸟苷基因工程菌，探索了将全基因组测序和系统生物学分析方法应用于XH7菌株分子育种的可行性，并获得了如下结果：
1.解淀粉芽孢杆菌XH7全基因组测序
采用Solexa高通量测序技术，对XH7菌株进行全基因组测序，共获得629Mb大小的原始数据，平均测序深度为160×。使用SOAPdenovo软件对测序产生的reads序列进行拼接和组装得到76个Contigs和23个Scaffolds。将Scaffolds的头尾序列与参考基因组序列进行比对，以确定每个Scaffold的相对位置，然后设计引物PCR扩增内洞和外洞并进行序列鉴定，最终得到XH7菌株的基因组完成图。基因组序列已提交至NCBI数据库，登录号为CP002927。解淀粉芽孢杆菌XH7基因组全长3,939,203bp，GC含量45.82%，共编码4204个蛋白、75个tRNA和7个rRNA操纵子。比较基因组学分析发现，有一段约1.26Mb大小的DNA片段发生了倒置，同时鉴定出多个基因缺失与XH7菌株高产鸟苷相关。
2.鸟苷生物合成的系统生物学分析
以枯草杆菌基因组尺度代谢网络模型iYO844为基础，以提高鸟苷合成水平为目标，对枯草杆菌鸟苷合成进行了系统生物学分析，包括最大理论产率分析，in silico菌种改造等。使用FDCA和PS-FDCA两套算法预测得到了一些可能提高鸟苷产率的关键基因改造位点，包括基因敲除位点、基因强化位点和基因弱化位点，为后续的分子育种改造工作提供了理论指导。
3.解淀粉芽孢杆菌遗传操作体系的建立及分子育种
建立了解淀粉芽孢杆菌XH7的电转感受态细胞制备和转化方法，并且将in silico菌种改造预测得到的基因强化位点prs、purF、guaB和透明颤菌血红蛋白基因vgb分别转化到XH7菌株中表达。四个转化子的鸟苷发酵实验结果表明：增强prs和purF基因表达后，鸟苷产量分别提高了10.8%和20.9%；增强guaB基因表达后，鸟苷产量不增反而略有下降，同时转化子的生长速度明显低于野生型；vgb基因的表达没有显著提高鸟苷产量，但是转化子的生长速度明显要比野生型菌株快，这有利于缩短发酵周期和降低能耗。
4.解淀粉芽孢杆菌基因敲除体系的建立及分子育种
基于温敏复制型质粒pKS1，建立了解淀粉芽孢杆菌XH7的基因敲除体系。根据insilico菌种改造预测得到的基因强化位点（purEKBCLQFMNHD）、弱化位点（ptsGHI）和敲除位点（deoD），分别构建了嘌呤操纵子多拷贝突变株、ptsGHI缺失突变株、deoD缺失突变株。由于嘌呤操纵子全长达12kb，难于直接对其进行分子克隆等操作。通过在嘌呤操纵子终止子末端插入一个氯霉素抗性基因和一段嘌呤操纵子启动子区域约1kb的DNA片段，然后通过不断提高培养基中氯霉素的浓度来诱导整个嘌呤操纵子在基因组上的倍增，qPCR鉴定最多达11个拷贝，并且鸟苷产量提高了25.5%。ptsG和ptsHI缺失突变株的发酵实验结果表明：敲除ptsG基因后，鸟苷产量提高了23.9%；而敲除ptsHI基因后，鸟苷产量降低了81.8%。这可能是因为敲除ptsG基因后，有利于提高葡萄糖进入磷酸戊糖途径的代谢通量，而敲除ptsHI基因后，彻底阻断了菌体对葡萄糖的吸收。deoD缺失突变株的鸟苷产量没有明显变化，表明deoD基因编码的酶基本不降解鸟苷。
本研究基于系统生物学分析得到的关键基因改造位点，对解淀粉芽孢杆菌XH7进行了分子育种改造。结果表明，该方法是可靠有效的，为后续的进一步分子育种提供了新的思路和研究方向。本文的研究平台具有良好的普适性，适合于其它各种类别产物的研究。随着系统生物学的发展，该平台也将得到逐步完善并趋于成熟。
Aguanosine industrial producer Bacillus amyloliquefaciens XH7was used as starting strain inthis work. In order to improve the efficiency of breeding and create high yielding stablegenetic engineering bacteria of guanosine, it was studied to improve guanosine productionwith whole genome sequencing and systems biology analysis. The main results were achievedand shown as follows:
(1) Whole-genome sequencing of Bacillus amyloliquefaciens XH7
Whole-genome sequencing of XH7was carried out by Solexa sequencing to produce629Mb filtered sequences, representing a160-fold coverage of the genome. The sequences wereassembled into76contigs and23scaffolds using the SOAPdenovo package. Scaffolds’relative position was identified by blasting with the published Bacillus amyloliquefaciensFZB42genome sequence. Then, special primers were designed to amplify the sequences ofinner gaps and outer gaps of the scaffolds. Finally, the identified PCR products and thescaffold make up of the whole genome sequence. The genome sequence of Bacillusamyloliquefaciens XH7was deposited in GenBank under the accession number CP002927.The complete genomic information of the Bacillus amyloliquefaciens XH7is contained on asingle circular chromosome of3,939,203bp with an average GC content of45.82%. Atotal of4,204protein coding genes,75tRNA genes, and7rRNA operons were identified.Comparative genomics analysis revealed that an approximately1.26Mb DNA fragment wasinverted, and multiple inactive gene realated with guanosine high-yield were identified.
(2) Systems biology analysis of guanosine biosynthesis
Based on Bacillus subtilis metabolic model iYO844, systems biology methods were usedto analyze the theoretical conversion yields of guanosine and in silico strain modification.Besides, two strategies including the flux distribution comparison analysis (FDCA) methodand product stress-flux distribution comparison analysis (PS-FDCA) method were employedto predict potential gene targets in order to improve the guanosine production. The resultswere reliable and could provide guidance for the follow-up strain modification.
(3) Genetic transformation system of Bacillus amyloliquefaciens and molecular breeding
A protocol for electroporation-competent cells preparation and transformation of XH7 strain was created. Based on the results of in silico strain improment for guanosine production,four genes (prs, purF, guaB, vgb) were transformed into XH7strain. The results of shakingflask fermentation showed that overexpression of prs and purF genes enhanced the guanosineproduction yield by10.8%and20.9%, while overexpression of guaB genes did not enhancethe guanosine production yield, but caused a slight decrease of guanosine production and asignificant decrease of growth rate. The expression of vgb caused no significant increase ofproduction yield, but vgb expression promoted cell growth, shortened fermentation period andreduced energy consumption.
(4) Gene-knockout technology of Bacillus amyloliquefaciens and molecular breeding
A gene-knockout technology based on temperature-sensitive plasmid pKS1wasestablished, and pur operon duplication mutants, phosphotransferase system and deoDdeficient mutants were constructed based on the results of in silico strain improment forguanosine production. As the total length of pur operon is12kb, it is very difficult to clone itdirectly. A chloramphenicol resistance gene and a pur operon promoter about1kbhomologous sequence were inserted into3’ end of pur operon terminator. By increasing theconcentration of chloramphenicol in the medium, the pur operon was induced doubling in thegenome. The max copy number of the pur operon was about11by qPCR. Meanwhile, theproduction yield was increased by25.5%. In guanosine fermentation experiments, theguanosine production yields of ptsG genetic defect strains was increased by23.9%, while thatof ptsHI genetic defect strain was decreased by81.8%. These results showed that ptsGdeletion was benefit to increase the carbon flux into the pentose phosphate pathway, whileptsHI deletion completely blocked the glucose use. The deoD genetic defect strain did notincrease the guanosine production yield, which suggested that the protein DeoD encoded bydeoD did not degradate the guanosine.
In this study, the molecular breeding of guanosine industrial producer XH7was carriedout based on systems biology. The results show that the method is reliable and effective, andcan provide new ideas and research directions for further follow-up molecular breeding. Theplatform constructed by this work is also suitable for other kinds of products research. Infuture, the platform will get well developed step-by-step with the development of systemsbiology.
1.解淀粉芽孢杆菌XH7全基因组测序
采用Solexa高通量测序技术，对XH7菌株进行全基因组测序，共获得629Mb大小的原始数据，平均测序深度为160×。使用SOAPdenovo软件对测序产生的reads序列进行拼接和组装得到76个Contigs和23个Scaffolds。将Scaffolds的头尾序列与参考基因组序列进行比对，以确定每个Scaffold的相对位置，然后设计引物PCR扩增内洞和外洞并进行序列鉴定，最终得到XH7菌株的基因组完成图。基因组序列已提交至NCBI数据库，登录号为CP002927。解淀粉芽孢杆菌XH7基因组全长3,939,203bp，GC含量45.82%，共编码4204个蛋白、75个tRNA和7个rRNA操纵子。比较基因组学分析发现，有一段约1.26Mb大小的DNA片段发生了倒置，同时鉴定出多个基因缺失与XH7菌株高产鸟苷相关。
2.鸟苷生物合成的系统生物学分析
以枯草杆菌基因组尺度代谢网络模型iYO844为基础，以提高鸟苷合成水平为目标，对枯草杆菌鸟苷合成进行了系统生物学分析，包括最大理论产率分析，in silico菌种改造等。使用FDCA和PS-FDCA两套算法预测得到了一些可能提高鸟苷产率的关键基因改造位点，包括基因敲除位点、基因强化位点和基因弱化位点，为后续的分子育种改造工作提供了理论指导。
3.解淀粉芽孢杆菌遗传操作体系的建立及分子育种
建立了解淀粉芽孢杆菌XH7的电转感受态细胞制备和转化方法，并且将in silico菌种改造预测得到的基因强化位点prs、purF、guaB和透明颤菌血红蛋白基因vgb分别转化到XH7菌株中表达。四个转化子的鸟苷发酵实验结果表明：增强prs和purF基因表达后，鸟苷产量分别提高了10.8%和20.9%；增强guaB基因表达后，鸟苷产量不增反而略有下降，同时转化子的生长速度明显低于野生型；vgb基因的表达没有显著提高鸟苷产量，但是转化子的生长速度明显要比野生型菌株快，这有利于缩短发酵周期和降低能耗。
4.解淀粉芽孢杆菌基因敲除体系的建立及分子育种
基于温敏复制型质粒pKS1，建立了解淀粉芽孢杆菌XH7的基因敲除体系。根据insilico菌种改造预测得到的基因强化位点（purEKBCLQFMNHD）、弱化位点（ptsGHI）和敲除位点（deoD），分别构建了嘌呤操纵子多拷贝突变株、ptsGHI缺失突变株、deoD缺失突变株。由于嘌呤操纵子全长达12kb，难于直接对其进行分子克隆等操作。通过在嘌呤操纵子终止子末端插入一个氯霉素抗性基因和一段嘌呤操纵子启动子区域约1kb的DNA片段，然后通过不断提高培养基中氯霉素的浓度来诱导整个嘌呤操纵子在基因组上的倍增，qPCR鉴定最多达11个拷贝，并且鸟苷产量提高了25.5%。ptsG和ptsHI缺失突变株的发酵实验结果表明：敲除ptsG基因后，鸟苷产量提高了23.9%；而敲除ptsHI基因后，鸟苷产量降低了81.8%。这可能是因为敲除ptsG基因后，有利于提高葡萄糖进入磷酸戊糖途径的代谢通量，而敲除ptsHI基因后，彻底阻断了菌体对葡萄糖的吸收。deoD缺失突变株的鸟苷产量没有明显变化，表明deoD基因编码的酶基本不降解鸟苷。
本研究基于系统生物学分析得到的关键基因改造位点，对解淀粉芽孢杆菌XH7进行了分子育种改造。结果表明，该方法是可靠有效的，为后续的进一步分子育种提供了新的思路和研究方向。本文的研究平台具有良好的普适性，适合于其它各种类别产物的研究。随着系统生物学的发展，该平台也将得到逐步完善并趋于成熟。
Aguanosine industrial producer Bacillus amyloliquefaciens XH7was used as starting strain inthis work. In order to improve the efficiency of breeding and create high yielding stablegenetic engineering bacteria of guanosine, it was studied to improve guanosine productionwith whole genome sequencing and systems biology analysis. The main results were achievedand shown as follows:
(1) Whole-genome sequencing of Bacillus amyloliquefaciens XH7
Whole-genome sequencing of XH7was carried out by Solexa sequencing to produce629Mb filtered sequences, representing a160-fold coverage of the genome. The sequences wereassembled into76contigs and23scaffolds using the SOAPdenovo package. Scaffolds’relative position was identified by blasting with the published Bacillus amyloliquefaciensFZB42genome sequence. Then, special primers were designed to amplify the sequences ofinner gaps and outer gaps of the scaffolds. Finally, the identified PCR products and thescaffold make up of the whole genome sequence. The genome sequence of Bacillusamyloliquefaciens XH7was deposited in GenBank under the accession number CP002927.The complete genomic information of the Bacillus amyloliquefaciens XH7is contained on asingle circular chromosome of3,939,203bp with an average GC content of45.82%. Atotal of4,204protein coding genes,75tRNA genes, and7rRNA operons were identified.Comparative genomics analysis revealed that an approximately1.26Mb DNA fragment wasinverted, and multiple inactive gene realated with guanosine high-yield were identified.
(2) Systems biology analysis of guanosine biosynthesis
Based on Bacillus subtilis metabolic model iYO844, systems biology methods were usedto analyze the theoretical conversion yields of guanosine and in silico strain modification.Besides, two strategies including the flux distribution comparison analysis (FDCA) methodand product stress-flux distribution comparison analysis (PS-FDCA) method were employedto predict potential gene targets in order to improve the guanosine production. The resultswere reliable and could provide guidance for the follow-up strain modification.
(3) Genetic transformation system of Bacillus amyloliquefaciens and molecular breeding
A protocol for electroporation-competent cells preparation and transformation of XH7 strain was created. Based on the results of in silico strain improment for guanosine production,four genes (prs, purF, guaB, vgb) were transformed into XH7strain. The results of shakingflask fermentation showed that overexpression of prs and purF genes enhanced the guanosineproduction yield by10.8%and20.9%, while overexpression of guaB genes did not enhancethe guanosine production yield, but caused a slight decrease of guanosine production and asignificant decrease of growth rate. The expression of vgb caused no significant increase ofproduction yield, but vgb expression promoted cell growth, shortened fermentation period andreduced energy consumption.
(4) Gene-knockout technology of Bacillus amyloliquefaciens and molecular breeding
A gene-knockout technology based on temperature-sensitive plasmid pKS1wasestablished, and pur operon duplication mutants, phosphotransferase system and deoDdeficient mutants were constructed based on the results of in silico strain improment forguanosine production. As the total length of pur operon is12kb, it is very difficult to clone itdirectly. A chloramphenicol resistance gene and a pur operon promoter about1kbhomologous sequence were inserted into3’ end of pur operon terminator. By increasing theconcentration of chloramphenicol in the medium, the pur operon was induced doubling in thegenome. The max copy number of the pur operon was about11by qPCR. Meanwhile, theproduction yield was increased by25.5%. In guanosine fermentation experiments, theguanosine production yields of ptsG genetic defect strains was increased by23.9%, while thatof ptsHI genetic defect strain was decreased by81.8%. These results showed that ptsGdeletion was benefit to increase the carbon flux into the pentose phosphate pathway, whileptsHI deletion completely blocked the glucose use. The deoD genetic defect strain did notincrease the guanosine production yield, which suggested that the protein DeoD encoded bydeoD did not degradate the guanosine.
In this study, the molecular breeding of guanosine industrial producer XH7was carriedout based on systems biology. The results show that the method is reliable and effective, andcan provide new ideas and research directions for further follow-up molecular breeding. Theplatform constructed by this work is also suitable for other kinds of products research. Infuture, the platform will get well developed step-by-step with the development of systemsbiology.
引文
[1] Yu X.F., Li Z.H., Yu M.H., et al. Yeast extract and method of producing the SAME [P]. US Patent20100303960A1,2010
[2] Kini G.D., Anderson J.D., Sanghvi Y.S., et al. Synthesis and antiviral activity of certain guanosineanalogues in the thiazolo[4,5-d]pyrimidine ring system [J]. J Med Chem,1991,34(10):3006-10
[3] Ray A.S., Yang Z., Chu C.K., et al. Novel use of a guanosine prodrug approach to convert2',3'-Didehydro-2',3'-Dideoxyguanosine into a viable antiviral agent [J]. Antimicrob Agents Ch,2002,46(3):887-91
[4] Sheremet A.S., Gronskiy S.V., Akhmadyshin R.A., et al. Enhancement of extracellular purine nucleosideaccumulation by Bacillus strains through genetic modifications of genes involved in nucleoside export [J]. JInd Microbiol Biotechnol,2011,38(1):65-70
[5] Zakataeva N.P., Gronskiy S.V., Sheremet A.S., et al. A new function for the Bacillus PbuE purine baseefflux pump: efflux of purine nucleosides [J]. Res Microbiol,2007,158(8-9):659-65
[6] Li H., Zhang G., Deng A., et al. De novo engineering and metabolic flux analysis of inosine biosynthesis inBacillus subtilis [J]. Biotechnol Lett,2011,33(8):1575-80
[7] Qian J., Cai X., Chu J., et al. Nucleotide mutations in purA gene and pur operon promoter discovered inguanosine-and inosine-producing Bacillus subtilis strains [J]. Biotechnol Lett,2006,28(12):937-41
[8] Chen S., Chu J., Zhuang Y., et al. Enhancement of inosine production by Bacillus subtilis throughsuppression of carbon overflow by sodium citrate [J]. Biotechnol Lett,2005,27(10):689-92
[9] Schallmey M., Singh A., Ward O.P. Developments in the use of Bacillus species for industrial production [J].Can J Microbiol,2004,50(1):1-17
[10] Shimaoka M., Takenaka Y., Kurahashi O., et al. Effect of amplification of desensitized purF and prs oninosine accumulation in Escherichia coli [J]. J Biosci Bioeng,2007,103(3):255-61
[11]张克旭,杜连祥.核酸发酵[M].轻工业出版社,1987
[12]王镜岩.生物化学[M].高等教育出版社,2002
[13] Ebbole D.J., Zalkin H. Cloning and characterization of a12-gene cluster from Bacillus subtilis encodingnine enzymes for de novo purinenucleotide synthesis [J]. J Biol Chem,1987,262(17):8274-87
[14] Kunst F., Ogasawara N., Moszer I., et al. The complete genome sequence of the gram-positive bacteriumBacillus subtilis [J]. Nature,1997,390(6657):249-56
[15] Aiba A., Mizobuchi K. Nucleotide sequence analysis of genes purH and purD involved in the de novopurine nucleotide biosynthesis of Escherichia coli [J]. J Biol Chem,1989,264(35):21239-46
[16] Saxild H.H., Nygaard P. Regulation of levels of purine biosynthetic enzymes in Bacillus subtilis: effects ofchanging purine nucleotide pools [J]. J Gen Microbiol,1991,137(10):2387-94
[17] Holt K.E., Parkhill J., Mazzoni C.J., et al. High-throughput sequencing provides insights into genomevariation and evolution in Salmonella Typhi [J]. Nat Genet,2008,40(8):987-93
[18] Rappu P., Shin B.S., Zalkin H., et al. A role for a highly conserved protein of unknown function inregulation of Bacillus subtilis purA by the purine repressor [J]. J Bacteriol,1999,181(12):3810-5
[19] Saxild H.H., Brunstedt K., Nielsen K.I., et al. Definition of the Bacillus subtilis PurR operator using geneticand bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD,and pbuO [J]. J Bacteriol,2001,183(21):6175-83
[20] Weng M., Nagy P.L., Zalkin H. Identification of the Bacillus subtilis pur operon repressor [J]. Proc NatlAcad Sci U S A,1995,92(16):7455-9
[21] Rappu P., Pullinen T., Mantsala P. In vivo effect of mutations at the PRPP binding site of the Bacillussubtilis purine repressor [J]. J Bacteriol,2003,185(22):6728-31
[22] Weng M., Zalkin H. Mutations in the Bacillus subtilis purine repressor that perturb PRPP effector functionin vitro and in vivo [J]. Curr Microbiol,2000,41(1):56-9
[23] Ebbole D.J., Zalkin H. Detection of pur operon-attenuated mRNA and accumulated degradationintermediates in Bacillus subtilis [J]. J Biol Chem,1988,263(22):10894-902
[24] Ebbole D.J., Zalkin H. Bacillus subtilis pur operon expression and regulation [J]. J Bacteriol,1989,171(4):2136-41
[25] Wu T.W., Scrimgeour K.G. Properties of inosinic acid dehydrogenase from Bacillus subtilis. II. Kineticproperties [J]. Can J Biochem,1973,51(10):1391-8
[26] Endo T., Uratani B., Freese E. Purine salvage pathways of Bacillus subtilis and effect of guanine on growthof GMPreductase mutants [J]. J Bacteriol,1983,155(1):169-79
[27] Asahara T., Mori Y., Zakataeva N.P., et al. Accumulation of gene-targeted Bacillus subtilis mutations thatenhance fermentative inosine production [J].Appl Microbiol Biotechnol,2010,87(6):2195-207
[28] Matsui H., Shimaoka M., Takenaka Y., et al. Gsk disruption leads to guanosine accumulation in Escherichiacoli [J]. Biosci Biotechnol Biochem,2001,65(5):1230-5
[29] Zakataeva N.P., Romanenkov D.V., Skripnikova V.S., et al. Wild-type and feedback-resistantphosphoribosyl pyrophosphate synthetases from Bacillus amyloliquefaciens: purification, characterization,and application to increase purine nucleoside production [J]. Appl Microbiol Biotechnol,2012,93(5):2023-33
[30] Livshits V.A., Zakataeva N.P., Aleshin V.V., et al. Identification and characterization of the new gene rhtAinvolved in threonine and homoserine efflux in Escherichia coli [J]. Res Microbiol,2003,154(2):123-35
[31] Diesveld R., Tietze N., Furst O., et al. Activity of exporters of Escherichia coli in Corynebacteriumglutamicum, and their use to increase L-threonine production [J]. J Mol Microbiol Biotechnol,2009,16(3-4):198-207
[32] Kruse D., Kramer R., Eggeling L., et al. Influence of threonine exporters on threonine production inEscherichia coli [J].Appl Microbiol Biotechnol,2002,59(2-3):205-10
[33] Venter J.C., Adams M.D., Myers E.W., et al. The sequence of the human genome [J]. Science,2001,291(5507):1304-51
[34] Li R., Fan W., Tian G., et al. The sequence and de novo assembly of the giant panda genome [J]. Nature,2010,463(7279):311-7
[35] Wilhelm B.T., Marguerat S., Watt S., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed atsingle-nucleotide resolution [J]. Nature,2008,453(7199):1239-43
[36] Nagalakshmi U., Wang Z., Waern K., et al. The transcriptional landscape of the yeast genome defined byRNAsequencing [J]. Science,2008,320(5881):1344-9
[37] Lefrancois P., Zheng W., Snyder M. ChIP-Seq using high-throughput DNA sequencing for genome-wideidentification of transcription factor binding sites [J]. Methods Enzymol,2010,470:77-104.
[38] Schmidt D., Wilson M.D., Spyrou C., et al. ChIP-seq: Using high-throughput sequencing to discoverprotein-DNAinteractions [J]. Methods,2009,48(3):240-8
[39] Shohet J., Ludwig A., Chen Z.W., et al. High Throughput Sequencing And Chromatin Immunoprecipitation(Chip-Seq) Identifies Mycn-Regulated Micrornas As Tumor Suppressors And Oncogenes In Neuroblastoma[J]. Pediatr Blood&Cancer,2010,54(6):840-1
[40] Hesselberth J.R., Chen X., Zhang Z., et al. Global mapping of protein-DNA interactions in vivo by digitalgenomic footprinting [J]. Nat Methods,2009,6(4):283-9
[41] Serre D., Lee B.H., Ting A.H. MBD-isolated Genome Sequencing provides a high-throughput andcomprehensive survey of DNA methylation in the human genome [J]. Nucleic Acids Res,2010,38(2):391-9
[42] Mohn F., Weber M., Schubeler D., et al. Methylated DNA immunoprecipitation (MeDIP)[J]. Methods MolBiol,2009,507:55-64
[43] Wang J., Jiang H., Ji G., et al. High resolution profiling of human exon methylation by liquid hybridizationcapture-based bisulfite sequencing [J]. BMC Genomics,2011,12(1):597
[44] Haque N., Nishiguchi M. Bisulfite sequencing for cytosine-methylation analysis in plants [J]. Methods MolBiol,2011,744:187-97
[45] Yang H., Liao Y., Wang B., et al. Genome sequence of Escherichia coli XH140A, which producesL-threonine [J]. J Bacteriol,2011,193(21):6090-1
[46] Yang H., Liao Y., Wang B., et al. Draft genome sequence of Escherichia coli XH001, a producer ofL-threonine in industry [J]. J Bacteriol,2011,193(22):6406-7
[47]孙娟娟.普鲁兰酶在解淀粉芽孢杆菌中表达方法的探索[D].江南大学硕士学位论文,2011
[48] Welker N.E., Campbell L.L. Unrelatedness of Bacillus amyloliquefaciens and Bacillus subtilis [J]. JBacteriol,1967,94(4):1124-30
[49] Chen X.H., Koumoutsi A., Scholz R., et al. Comparative analysis of the complete genome sequence of theplant growth-promoting bacterium Bacillus amyloliquefaciens FZB42[J]. Nat Biotechnol,2007,25(9):1007-14
[50] Welker N.E., Campbell L.L. Crystallization and properties of alpha-amylase from five strains of Bacillusamyloliquefaciens [J]. Biochemistry,1967,6(12):3681-9
[51] Welker N.E., Campbell L.L. Comparison of the alpha-amylase of Bacillus subtilis and Bacillusamyloliquefaciens [J]. J Bacteriol,1967,94(4):1131-5
[52] Peng Y., Yang X.J., Xiao L., et al. Cloning and expression of a fibrinolytic enzyme (subtilisin DFE) genefrom Bacillus amyloliquefaciens DC-4in Bacillus subtilis [J]. Res Microbiol,2004,155(3):167-73
[53] Peng Y., Huang Q., Zhang R.H., et al. Purification and characterization of a fibrinolytic enzyme producedby Bacillus amyloliquefaciens DC-4screened from douchi, a traditional Chinese soybean food [J]. CompBiochem Physiol B Biochem Mol Biol,2003,134(1):45-52
[54] Wei X., Luo M., Xu L., et al. Production of fibrinolytic enzyme from Bacillus amyloliquefaciens byfermentation of chickpeas, with the evaluation of the anticoagulant and antioxidant properties of chickpeas[J]. JAgric Food Chem,2011,59(8):3957-63
[55] Kim P.I., Chung K.C. Production of an antifungal protein for control of Colletotrichum lagenarium byBacillus amyloliquefaciens MET0908[J]. FEMS Microbiol Lett,2004,234(1):177-83
[56] Zhang G., Deng A., Xu Q., et al. Complete genome sequence of Bacillus amyloliquefaciens TA208, a strainfor industrial production of guanosine and ribavirin [J]. J Bacteriol,2011,193(12):3142-3
[57] Yang H., Liao Y., Wang B., et al. Complete genome sequence of Bacillus amyloliquefaciens XH7, whichexhibits production of purine nucleosides [J]. J Bacteriol,2011,193(19):5593-4
[58] Geng W., Cao M., Song C., et al. Complete genome sequence of Bacillus amyloliquefaciens LL3, whichexhibits glutamic acid-independent production of poly-gamma-glutamic acid [J]. J Bacteriol,2011,193(13):3393-4
[59] Cao M., Geng W., Liu L., et al. Glutamic acid independent production of poly-gamma-glutamic acid byBacillus amyloliquefaciens LL3and cloning of pgsBCA genes [J]. Bioresour Technol,2011,102(5):4251-7
[60] Liu J., Ma X., Wang Y., et al. Depressed biofilm production in Bacillus amyloliquefaciens C06causesgamma-polyglutamic acid (gamma-PGA) overproduction [J]. Curr Microbiol,2011,62(1):235-41
[61] Romano A., Vitullo D., Di Pietro A., et al. Antifungal lipopeptides from Bacillus amyloliquefaciens strainBO7[J]. J Nat Prod,2011,74(2):145-51
[62] Katz E., Demain A.L. The peptide antibiotics of Bacillus: chemistry, biogenesis, and possible functions [J].Bacteriol Rev,1977,41(2):449-74
[63] Bonmatin J.M., Laprevote O., Peypoux F. Diversity among microbial cyclic lipopeptides: iturins andsurfactins. Activity-structure relationships to design new bioactive agents [J]. Comb Chem HighThroughput Screen,2003,6(6):541-56
[64] Ongena M., Jacques P. Bacillus lipopeptides: versatile weapons for plant disease biocontrol [J]. TrendsMicrobiol,2008,16(3):115-25
[65] Sutyak K.E., Wirawan R.E., Aroutcheva A.A., et al. Isolation of the Bacillus subtilis antimicrobial peptidesubtilosin from the dairy product-derived Bacillus amyloliquefaciens [J]. J Appl Microbiol,2008,104(4):1067-74
[66] Brooks J.E., Nathan P.D., Landry D., et al. Characterization of the cloned BamHI restriction modificationsystem: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts [J].NucleicAcids Res,1991,19(4):841-50
[67] Connaughton J.F., Vanek P.G., Lee-Lin S.Q., et al. Cloning of the BamHI methyl transferase gene fromBacillus amyloliquefaciens [J]. GeneAnal Tech,1988,5(6):116-24
[68] Paddon C.J., Hartley R.W. Expression of Bacillus amyloliquefaciens extracellular ribonuclease (barnase) inEscherichia coli following an inactivating mutation [J]. Gene,1987,53(1):11-9
[69] Fleischmann R.D., Adams M.D., White O., et al. Whole-genome random sequencing and assembly ofHaemophilus influenzae Rd [J]. Science,1995,269(5223):496-512
[70] Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs [J].Genome Res,2008,18(5):821-9
[71] Li R., Zhu H., Ruan J., et al. De novo assembly of human genomes with massively parallel short readsequencing [J]. Genome Res,2010,20(2):265-72
[72] Tyo K.E., Ajikumar P.K., Stephanopoulos G. Stabilized gene duplication enables long-term selection-freeheterologous pathway expression [J]. Nat Biotechnol,2009,27(8):760-5
[73] Horinouchi S., Weisblum B. Nucleotide sequence and functional map of pE194, a plasmid that specifiesinducible resistance to macrolide, lincosamide, and streptogramin type B antibodies [J]. J Bacteriol,1982,150(2):804-14
[74] Shatalin K.Y., Neyfakh A.A. Efficient gene inactivation in Bacillus anthracis [J]. FEMS Microbiol Lett,2005,245(2):315-9
[75] Horinouchi S., Weisblum B. Nucleotide sequence and functional map of pC194, a plasmid that specifiesinducible chloramphenicol resistance [J]. J Bacteriol,1982,150(2):815-25
[76] McKenzie T., Hoshino T., Tanaka T., et al. The nucleotide sequence of pUB110: some salient features inrelation to replication and its regulation [J]. Plasmid,1986,15(2):93-103
[77] Sullivan M.A., Yasbin R.E., Young F.E. New shuttle vectors for Bacillus subtilis and Escherichia coli whichallow rapid detection of inserted fragments [J]. Gene,1984,29(1-2):21-6
[78] Ferrari F.A., Nguyen A., Lang D., et al. Construction and properties of an integrable plasmid for Bacillussubtilis [J]. J Bacteriol,1983,154(3):1513-5
[79] Price C.W., Gitt M.A., Doi R.H. Isolation and physical mapping of the gene encoding the major sigmafactor of Bacillus subtilis RNApolymerase [J]. Proc NatlAcad Sci U S A,1983,80(13):4074-8
[80] Le Grice S.F., Beuck V., Mous J. Expression of biologically active human T-cell lymphotropic virus type IIIreverse transcriptase in Bacillus subtilis [J]. Gene,1987,55(1):95-103
[81] Yamagata H., Nakahama K., Suzuki Y., et al. Use of Bacillus brevis for efficient synthesis and secretion ofhuman epidermal growth factor [J]. Proceedings of the National Academy of Sciences,1989,86(10):3589-93
[82] Phan T.T., Nguyen H.D., Schumann W. Novel plasmid-based expression vectors for intra-and extracellularproduction of recombinant proteins in Bacillus subtilis [J]. Protein Expr Purif,2006,46(2):189-95
[83] Bron S., Bosma P., Van Belkum M., et al. Stability function in the Bacillus subtilis plasmid pTA1060[J].Plasmid,1987,18(1):8-15
[84] Jari V. Transformation of Bacillus amyloliquefaciens protoplasts with plasmid DNA [J]. FEMS MicrobiolLett,1988,49(1):101-5
[85] Borgmeier C., Voigt B., Hecker M., et al. Functional analysis of the response regulator DegU in Bacillusmegaterium DSM319and comparative secretome analysis of degSU mutants [J]. Appl MicrobiolBiotechnol,2011,91(3):699-711
[86] Gryczan T.J., Hahn J., Contente S., et al. Replication and incompatibility properties of plasmid pE194inBacillus subtilis [J]. J Bacteriol,1982,152(2):722-35
[87] Hofemeister J., Israeli-Reches M., Dubnau D. Integration of plasmid pE194at multiple sites on the Bacillussubtilis chromosome [J]. Mol Gen Genet,1983,189(1):58-68
[88] Zakataeva N.P., Nikitina O.V., Gronskiy S.V., et al. A simple method to introduce marker-free geneticmodifications into the chromosome of naturally nontransformable Bacillus amyloliquefaciens strains [J].Appl Microbiol Biotechnol,2010,85(4):1201-9
[89] Zhao D.L., Yu Z.C., Li P.Y., et al. Characterization of a cryptic plasmid pSM429and its application forheterologous expression in psychrophilic Pseudoalteromonas [J]. Microb Cell Fact,2011,10:30
[90] Qiao J.Q., Tian da W., Huo R., et al. Functional analysis and application of the cryptic plasmid pBSG3harboring the RapQ-PhrQ system in Bacillus amyloliquefaciens B3[J]. Plasmid,2011,65(2):141-9
[91] Yeng H.W., Shamsudin M.N., Rahim R.A. Construction of an expression vector for Lactococcus lactisbased on an indigenous cryptic plasmid [J]. Afr J Biotechnol,2009,8(21):5621-6
[92] ProzorovA.A. Competence pheromones in bacteria [J]. Mikrobiologiia,2001,70(1):5-14
[93] Sonenshein A.L., Hoch J.A., R. L. Bacillus subtilis and its closest relatives [J]. ASM Press,2002:453-71
[94] Mohan S., Aghion J., Guillen N., et al. Molecular cloning and characterization of comC, a late competencegene of Bacillus subtilis [J]. J Bacteriol,1989,171(11):6043-51
[95] Inamine G.S., Dubnau D. ComEA, a Bacillus subtilis integral membrane protein required for genetictransformation, is needed for both DNAbinding and transport [J]. J Bacteriol,1995,177(11):3045-51
[96] Provvedi R., Dubnau D. ComEA is a DNA receptor for transformation of competent Bacillus subtilis [J].Mol Microbiol,1999,31(1):271-80
[97] Londono-Vallejo J.A., Dubnau D. Mutation of the putative nucleotide binding site of the Bacillus subtilismembrane protein ComFA abolishes the uptake of DNA during transformation [J]. J Bacteriol,1994,176(15):4642-5
[98] Chung Y.S., Dubnau D. All seven comG open reading frames are required for DNA binding duringtransformation of competent Bacillus subtilis [J]. J Bacteriol,1998,180(1):41-5
[99] Zhang X.Z., Zhang Y.H. Simple, fast and high-efficiency transformation system for directed evolution ofcellulase in Bacillus subtilis [J]. Microb Biotechnol,2011,4(1):98-105
[100] Turgay K., Hahn J., Burghoorn J., et al. Competence in Bacillus subtilis is controlled by regulatedproteolysis of a transcription factor [J]. EMBO J,1998,17(22):6730-8
[101] van Sinderen D., Luttinger A., Kong L., et al. ComK encodes the competence transcription factor, the keyregulatory protein for competence development in Bacillus subtilis [J]. Mol Microbiol,1995,15(3):455-62
[102] Anagnostopoulos C., Spizizen J. Requirements for Transformation in Bacillus subtilis [J]. J Bacteriol,1961,81(5):741-6
[103] de Vos W.M., Venema G., Canosi U., et al. Plasmid transformation in Bacillus subtilis: fate of plasmidDNA[J]. Mol Gen Genet,1981,181(4):424-33
[104]陈乃用.电穿孔法在细菌质粒转化中的应用[J].微生物学通报,1991,18(2):97-103
[105] Brigidi P., De Rossi E., Bertarini M.L., et al. Genetic transformation of intact cells of Bacillus subtilis byelectroporation [J]. FEMS Microbiol Lett,1990,55(1-2):135-8
[106] McDonald I.R., Riley P.W., Sharp R.J., et al. Factors affecting the electroporation of Bacillus subtilis [J]. JAppl Bacteriol,1995,79(2):213-8
[107] Xue G.-P., Johnson J.S., Dalrymple B.P. High osmolarity improves the electro-transformation efficiency ofthe gram-positive bacteria Bacillus subtilis and Bacillus licheniformis [J]. J Microbiol Meth,1999,34(3):183-91
[108] Cao G., Zhang X., Zhong L., et al. A modified electro-transformation method for Bacillus subtilis and itsapplication in the production of antimicrobial lipopeptides [J]. Biotechnol Lett,2011,33(5):1047-51
[109] Chang S., Cohen S.N. High frequency transformation of Bacillus subtilis protoplasts by plasmid DNA [J].Mol Gen Genet,1979,168(1):111-5
[110] Levi-Meyrueis C., Fodor K., Schaeffer P. Polyethyleneglycol-induced transformation of Bacillus subtilisprotoplasts by bacterial chromosomal DNA [J]. Mol Gen Genet,1980,179(3):589-94
[111] de Vos W.M., Venema G. Fate of plasmid DNA in transformation of Bacillus subtilis protoplasts [J]. MolGen Genet,1981,182(1):39-43
[112] Jandova Z., Tichy P. Transformation of protoplasts of nontransformable Bacillus subtilis mutants byplasmid pUB110DNA[J]. Folia Microbiol (Praha),1982,27(6):465-7
[113] Romero D., Perez-Garcia A., Veening J.W., et al. Transformation of undomesticated strains of Bacillussubtilis by protoplast electroporation [J]. J Microbiol Meth,2006,66(3):556-9
[114] Zhang X.Z., Yan X., Cui Z.L., et al. MazF, a novel counter-selectable marker for unmarked chromosomalmanipulation in Bacillus subtilis [J]. NucleicAcids Res,2006,34(9): e71
[115] Morimoto T., Ara K., Ozaki K., et al. A simple method for introducing marker-free deletions in theBacillus subtilis genome [J]. Methods Mol Biol,2011,765:345-58
[116] Haima P., Bron S., Venema G. The effect of restriction on shotgun cloning and plasmid stability in Bacillussubtilis Marburg [J]. Mol Gen Genet,1987,209(2):335-42
[117] Ostroff G.R., Pene J.J. Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis. II. Transferof sequences propagated in Escherichia coli to B. subtilis [J]. Mol Gen Genet,1984,193(2):306-11
[118] de Vos W.M., de Vries S.C., Venema G. Cloning and expression of the Escherichia coli recA gene inBacillus subtilis [J]. Gene,1983,25(2-3):301-8
[119] Wu X.C., Lee W., Tran L., et al. Engineering a Bacillus subtilis expression-secretion system with a straindeficient in six extracellular proteases [J]. J Bacteriol,1991,173(16):4952-8
[120] Wu S.C., Yeung J.C., Duan Y., et al. Functional production and characterization of a fibrin-specificsingle-chain antibody fragment from Bacillus subtilis: effects of molecular chaperones and a wall-boundprotease on antibody fragment production [J].Appl Environ Microbiol,2002,68(7):3261-9
[121] Coukoulis H., Campbell L.L. Transformation in Bacillus amyloliquefaciens [J]. J Bacteriol,1971,105(1):319-22
[122] Jari V. Transformation of Bacillus amyloliquefaciens protoplasts with plasmid DNA [J]. FEMS MicrobiolLett,1988,49(1):101-5
[123] Vehmaanpera J. Transformation of Bacillus amyloliquefaciens by electroporation [J]. FEMS MicrobiolLett,1989,52(1-2):165-9
[124] Zhang G.Q., Bao P., Zhang Y., et al. Enhancing electro-transformation competency of recalcitrant Bacillusamyloliquefaciens by combining cell-wall weakening and cell-membrane fluidity disturbing [J]. AnalBiochem,2011,409(1):130-7
[125] Ideker T., Galitski T., Hood L. Anew approach to decoding life: systems biology [J]. Annu Rev GenomicsHum Genet,2001,2:343-72
[126] Hood L. Computing life: the challenge ahead [J]. IEEE Eng Med Biol Mag,2001,20(4):20
[127] Hood L., Perlmutter R.M. The impact of systems approaches on biological problems in drug discovery [J].Nat Biotechnol,2004,22(10):1215-7
[128] Kitano H. Systems biology: Systems biology: a brief overview [J]. Science,2002,295(5560):1662-4
[129] Hubner K., Sahle S., Kummer U. Applications and trends in systems biology in biochemistry [J]. FEBS J,2011,278(16):2767-857
[130]杨胜利.系统生物学研究进展[J].中国科学院院刊,2004,19(1):31-4
[131] Finney A., Hucka M. Systems biology markup language: Level2and beyond [J]. Biochem Soc Trans,2003,31(Pt6):1472-3
[132] Funahashi A. The ERATO Systems Biology Workbench and Systems Biology Markup Language: anintegrated environment and standardization for systems biology [J]. Tanpakushitsu Kakusan Koso,2003,48(7):810-6
[133] Hucka M., Finney A., Sauro H.M., et al. The systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models [J]. Bioinformatics,2003,19(4):524-31
[134] Wellock C., Chickarmane V., Sauro H.M. The SBW-MATLAB interface [J]. Bioinformatics,2005,21(6):823-4
[135] Savageau M.A. Biochemical systems analysis. II. The steady-state solutions for an n-pool system using apower-law approximation [J]. J Theor Biol,1969,25(3):370-9
[136] Michael A S. Biochemical systems analysis: I. Some mathematical properties of the rate law for thecomponent enzymatic reactions [J]. J Theor Biol,1969,25(3):365-9
[137] Savageau M.A. Finding multiple roots of nonlinear algebraic equations using S-system methodology [J].Appl Math Comput,1993,55(2-3):187-99
[138] Varma A., Palsson B.O. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursorsand cofactors [J]. J Theor Biol,1993,165(4):477-502
[139] Varma A., Palsson B.O. Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns [J]. J TheorBiol,1993,165(4):503-22
[140] Calik P., Akbay A. Mass flux balance-based model and metabolic flux analysis for collagen synthesis inthe fibrogenesis process of human liver [J]. Med Hypotheses,2000,55(1):5-14
[141] Edwards J.S., Palsson B.O. Metabolic flux balance analysis and the in silico analysis of Escherichia coliK-12gene deletions [J]. BMC Bioinformatics,2000,1:1
[142] Mahadevan R., Edwards J.S., Doyle F.J.,3rd. Dynamic flux balance analysis of diauxic growth inEscherichia coli [J]. Biophys J,2002,83(3):1331-40
[143] Segre D., Vitkup D., Church G.M. Analysis of optimality in natural and perturbed metabolic networks [J].Proc Natl Acad Sci U SA,2002,99(23):15112-7
[144] Shlomi T., Berkman O., Ruppin E. Regulatory on/off minimization of metabolic flux changes after geneticperturbations [J]. Proc Natl Acad Sci U SA,2005,102(21):7695-700
[145] Wiback S.J., Palsson B.O. Extreme pathway analysis of human red blood cell metabolism [J]. Biophys J,2002,83(2):808-18
[146] Kenanov D., Kaleta C., Petzold A., et al. Theoretical study of lipid biosynthesis in wild-type Escherichiacoli and in a protoplast-type L-form using elementary flux mode analysis [J]. FEBS J,2010,277(4):1023-34
[147] Kurata H., Zhao Q., Okuda R., et al. Integration of enzyme activities into metabolic flux distributions byelementary mode analysis [J]. BMC Syst Biol,2007,1:31
[148] Price N.D., Reed J.L., Papin J.A., et al. Analysis of metabolic capabilities using singular valuedecomposition of extreme pathway matrices [J]. Biophys J,2003,84(2Pt1):794-804
[149]蒙海林.基于系统-合成生物学的天然产物异源生物合成研究[D].华南理工大学博士学位论文,2011
[150] Brochado A.R., Matos C., Moller B.L., et al. Improved vanillin production in baker's yeast through insilico design [J]. Microb Cell Fact,2010,9:84
[151]陈琦,王卓,魏冬青.代谢网络流分析进展及应用[J].科学通报,2010,55(14):1302-9
[152] Klamt S., Stelling J., Ginkel M., et al. FluxAnalyzer: exploring structure, pathways, and flux distributionsin metabolic networks on interactive flux maps [J]. Bioinformatics,2003,19(2):261-9
[153] Garvey T.D., Lincoln P., Pedersen C.J., et al. BioSPICE: access to the most current computational tools forbiologists [J]. Omics,2003,7(4):411-20
[154] Becker S.A., Feist A.M., Mo M.L., et al. Quantitative prediction of cellular metabolism withconstraint-based models: the COBRAToolbox [J]. Nat Protoc,2007,2(3):727-38
[155] Schellenberger J., Que R., Fleming R.M., et al. Quantitative prediction of cellular metabolism withconstraint-based models: the COBRAToolbox v2.0[J]. Nat Protoc,2011,6(9):1290-307
[156] Luo R.Y., Liao S., Zeng S.Q., et al. FluxExplorer: A general platform for modeling and analyses ofmetabolic networks based on stoichiometry [J]. Chinese Science Bulletin,2006,51(6):689-96
[157] Lee S.Y., Lee D.Y., Hong S.H., et al. MetaFluxNet, a program package for metabolic pathway constructionand analysis, and its use in large-scale metabolic flux analysis of Escherichia coli [J]. Genome Inform,2003,14:23-33
[158] Karthik R., Nagasuma C. Pathwayanalyser: a systems biology tool for flux analysis of metabolic pathways[J]. Nature Precedings,2008, doi:10.1038/npre.2008.1868.1
[159] Feist A.M., Henry C.S., Reed J.L., et al. A genome-scale metabolic reconstruction for Escherichia coliK-12MG1655that accounts for1260ORFs and thermodynamic information [J]. Mol Syst Biol,2007,3:121
[160] Kim H.U., Kim T.Y., Lee S.Y. Genome-scale metabolic network analysis and drug targeting of multi-drugresistant pathogen Acinetobacter baumannii AYE [J]. Mol Biosyst,2010,6(2):339-48
[161] Durot M., Le Fevre F., de Berardinis V., et al. Iterative reconstruction of a global metabolic model ofAcinetobacter baylyi ADP1using high-throughput growth phenotype and gene essentiality data [J]. BMCSyst Biol,2008,2:85
[162] de Oliveira Dal'Molin C.G., Quek L.E., Palfreyman R.W., et al. AraGEM, a genome-scale reconstructionof the primary metabolic network in Arabidopsis [J]. Plant Physiol,2010,152(2):579-89
[163] David H., Hofmann G., Oliveira A.P., et al. Metabolic network driven analysis of genome-widetranscription data from Aspergillus nidulans [J]. Genome Biol,2006,7(11): R108
[164] Andersen M.R., Nielsen M.L., Nielsen J. Metabolic model integration of the bibliome, genome,metabolome and reactome of Aspergillus niger [J]. Mol Syst Biol,2008,4:178
[165] Vongsangnak W., Olsen P., Hansen K., et al. Improved annotation through genome-scale metabolicmodeling of Aspergillus oryzae [J]. BMC Genomics,2008,9(1):245
[166] Oh Y.K., Palsson B.O., Park S.M., et al. Genome-scale reconstruction of metabolic network in Bacillussubtilis based on high-throughput phenotyping and gene essentiality data [J]. J Biol Chem,2007,282(39):28791-9
[167] Henry C.S., Zinner J.F., Cohoon M.P., et al. iBsu1103: a new genome-scale metabolic model of Bacillussubtilis based on SEED annotations [J]. Genome Biol,2009,10(6): R69
[168] Thomas G.H., Zucker J., Macdonald S.J., et al. A fragile metabolic network adapted for cooperation in thesymbiotic bacterium Buchnera aphidicola [J]. BMC Syst Biol,2009,3:24
[169] Fang K., Zhao H., Sun C., et al. Exploring the metabolic network of the epidemic pathogen Burkholderiacenocepacia J2315via genome-scale reconstruction [J]. BMC Syst Biol,2011,5:83
[170] Chang R.L., Ghamsari L., Manichaikul A., et al. Metabolic network reconstruction of Chlamydomonasoffers insight into light-driven algal metabolism [J]. Mol Syst Biol,2011,7:518
[171] Ates O., Oner E.T., Arga K.Y. Genome-scale reconstruction of metabolic network for a halophilicextremophile, Chromohalobacter salexigens DSM3043[J]. BMC Syst Biol,2011,5:12
[172] Salimi F., Zhuang K., Mahadevan R. Genome-scale metabolic modeling of a clostridial co-culture forconsolidated bioprocessing [J]. Biotechnol J,2010,5(7):726-38
[173] Lee J., Yun H., Feist A.M., et al. Genome-scale reconstruction and in silico analysis of the ClostridiumacetobutylicumATCC824metabolic network [J]. Appl Microbiol Biotechnol,2008,80(5):849-62
[174] Milne C.B., Eddy J.A., Raju R., et al. Metabolic network reconstruction and genome-scale model ofbutanol-producing strain Clostridium beijerinckii NCIMB8052[J]. BMC Syst Biol,2011,5:130
[175] Roberts S.B., Gowen C.M., Brooks J.P., et al. Genome-scale metabolic analysis of Clostridiumthermocellum for bioethanol production [J]. BMC Syst Biol,2010,4:31
[176] Kjeldsen K.R., Nielsen J. In silico genome-scale reconstruction and validation of the Corynebacteriumglutamicum metabolic network [J]. Biotechnol Bioeng,2009,102(2):583-97
[177] Shinfuku Y., Sorpitiporn N., Sono M., et al. Development and experimental verification of a genome-scalemetabolic model for Corynebacterium glutamicum [J]. Microb Cell Fact,2009,8:43
[178] Vanee N., Roberts S.B., Fong S.S., et al. Agenome-scale metabolic model of Cryptosporidium hominis [J].Chem Biodivers,2010,7(5):1026-39
[179] Islam M.A., Edwards E.A., Mahadevan R. Characterizing the Metabolism of Dehalococcoides with aconstraint-Based Model [J]. PLoS Comput Biol,2010,6(8): e1000887
[180] Reed J.L., Vo T.D., Schilling C.H., et al. An expanded genome-scale model of Escherichia coli K-12(iJR904GSM/GPR)[J]. Genome Biol,2003,4(9): R54
[181] Orth J.D., Conrad T.M., Na J., et al. A comprehensive genome-scale reconstruction of Escherichia colimetabolism--2011[J]. Mol Syst Biol,2011,7:535
[182] Sun J., Sayyar B., Butler J.E., et al. Genome-scale constraint-based modeling of Geobactermetallireducens [J]. BMC Syst Biol,2009,3:15
[183] Mahadevan R., Bond D.R., Butler J.E., et al. Characterization of metabolism in the Fe(III)-reducingorganism Geobacter sulfurreducens by constraint-based modeling [J]. Appl Environ Microbiol,2006,72(2):1558-68
[184] Schilling C.H., Palsson B.O. Assessment of the metabolic capabilities of Haemophilus influenzae Rdthrough a genome-scale pathway analysis [J]. J Theor Biol,2000,203(3):249-83
[185] Gonzalez O., Gronau S., Falb M., et al. Reconstruction, modeling&analysis of Halobacterium salinarumR-1metabolism [J]. Mol Biosyst,2008,4(2):148-59
[186] Thiele I., Vo T.D., Price N.D., et al. Expanded metabolic reconstruction of Helicobacter pylori (iIT341GSM/GPR): an in silico genome-scale characterization of single-and double-deletion mutants [J]. JBacteriol,2005,187(16):5818-30
[187] Duarte N.C., Becker S.A., Jamshidi N., et al. Global reconstruction of the human metabolic network basedon genomic and bibliomic data [J]. Proc Natl Acad Sci U S A,2007,104(6):1777-82
[188] Liao Y.C., Huang T.W., Chen F.C., et al. An experimentally validated genome-scale metabolicreconstruction of Klebsiella pneumoniae MGH78578, iYL1228[J]. J Bacteriol,2011,193(7):1710-7
[189] Teusink B., Wiersma A., Molenaar D., et al. Analysis of growth of Lactobacillus plantarum WCFS1on acomplex medium using a genome-scale metabolic model [J]. J Biol Chem,2006,281(52):40041-8
[190] Verouden M.P.H., Notebaart R.A., Westerhuis J.A., et al. Multi-way analysis of flux distributions acrossmultiple conditions [J]. J Chemometr,2009,23(7-8):406-20
[191] Chavali A.K., Whittemore J.D., Eddy J.A., et al. Systems analysis of metabolism in the pathogenictrypanosomatid Leishmania major [J]. Mol Syst Biol,2008,4:177
[192] Kim T.Y., Kim H.U., Park J.M., et al. Genome-scale analysis of Mannheimia succiniciproducensmetabolism [J]. Biotechnol Bioeng,2007,97(4):657-71
[193] Tsoka S., Simon D., Ouzounis C.A. Automated metabolic reconstruction for Methanococcus jannaschii [J].Archaea,2004,1(4):223-9
[194] Satish Kumar V., Ferry J.G., Maranas C.D. Metabolic reconstruction of the archaeon methanogenMethanosarcina Acetivorans [J]. BMC Syst Biol,2011,5:28
[195] Feist A.M., Scholten J.C., Palsson B.O., et al. Modeling methanogenesis with a genome-scale metabolicreconstruction of Methanosarcina barkeri [J]. Mol Syst Biol,2006,2:2006.0004
[196] Rokem J.S., Vongsangnak W., Nielsen J. Comparative metabolic capabilities for Micrococcus luteusNCTC2665, the "Fleming" strain, and actinobacteria [J]. Biotechnol Bioeng,2011,108(11):2770-5
[197] Sigurdsson M.I., Jamshidi N., Steingrimsson E., et al. A detailed genome-wide reconstruction of mousemetabolism based on human Recon1[J]. BMC Syst Biol,2010,4:140
[198] Jamshidi N., Palsson B.O. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rvusing the in silico strain iNJ661and proposing alternative drug targets [J]. BMC Syst Biol,2007,1:26
[199] Suthers P.F., Dasika M.S., Kumar V.S., et al. A genome-scale metabolic reconstruction of Mycoplasmagenitalium, iPS189[J]. PLoS Comput Biol,2009,5(2): e1000285
[200] Gonzalez O., Oberwinkler T., Mansueto L., et al. Characterization of growth and metabolism of thehaloalkaliphile Natronomonas pharaonis [J]. PLoS Comput Biol,2010,6(6): e1000799
[201] Baart G.J., Zomer B., de Haan A., et al. Modeling Neisseria meningitidis metabolism: from genome tometabolic fluxes [J]. Genome Biol,2007,8(7): R136
[202] Sun J., Haveman S.A., Bui O., et al. Constraint-based modeling analysis of the metabolism of twoPelobacter species [J]. BMC Syst Biol,2010,4:174
[203] Sohn S.B., Graf A.B., Kim T.Y., et al. Genome-scale metabolic model of methylotrophic yeast Pichiapastoris and its use for in silico analysis of heterologous protein production [J]. Biotechnol J,2010,5(7):705-15
[204] Chung B.K., Selvarasu S., Andrea C., et al. Genome-scale metabolic reconstruction and in silico analysisof methylotrophic yeast Pichia pastoris for strain improvement [J]. Microb Cell Fact,2010,9:50
[205] Plata G., Hsiao T.L., Olszewski K.L., et al. Reconstruction and flux-balance analysis of the Plasmodiumfalciparum metabolic network [J]. Mol Syst Biol,2010,6:408
[206] Huthmacher C., Hoppe A., Bulik S., et al. Antimalarial drug targets in Plasmodium falciparum predictedby stage-specific metabolic network analysis [J]. BMC Syst Biol,2010,4:120
[207] Mazumdar V., Snitkin E.S., Amar S., et al. Metabolic network model of a human oral pathogen [J]. JBacteriol,2009,191(1):74-90
[208] Oberhardt M.A., Puchalka J., Fryer K.E., et al. Genome-scale metabolic network analysis of theopportunistic pathogen Pseudomonas aeruginosa PAO1[J]. J Bacteriol,2008,190(8):2790-803
[209] Sohn S.B., Kim T.Y., Park J.M., et al. In silico genome-scale metabolic analysis of Pseudomonas putidaKT2440for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival [J].Biotechnol J,2010,5(7):739-50
[210] Park J.M., Kim T.Y., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Ralstonia eutrophaH16for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and2-methyl citric acid production [J].BMC Syst Biol,2011,5:101
[211] Resendis-Antonio O., Hernandez M., Salazar E., et al. Systems biology of bacterial nitrogen fixation:high-throughput technology and its integrative description with constraint-based modeling [J]. BMC SystBiol,2011,5:120
[212] Imam S., Yilmaz S., Sohmen U., et al. iRsp1095: a genome-scale reconstruction of the Rhodobactersphaeroides metabolic network [J]. BMC Syst Biol,2011,5:116
[213] Aggarwal S., Karimi I.A., Lee D.Y. Reconstruction of a genome-scale metabolic network of Rhodococcuserythropolis for desulfurization studies [J]. Mol Biosyst,2011,7(11):3122-31
[214] Risso C., Sun J., Zhuang K., et al. Genome-scale comparison and constraint-based metabolicreconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens [J]. BMC Genomics,2009,10:447
[215] Nookaew I., Jewett M.C., Meechai A., et al. The genome-scale metabolic model iIN800of Saccharomycescerevisiae and its validation: a scaffold to query lipid metabolism [J]. BMC Syst Biol,2008,2:71
[216] Mo M.L., Palsson B.O., Herrgard M.J. Connecting extracellular metabolomic measurements tointracellular flux states in yeast [J]. BMC Syst Biol,2009,3:37
[217] Dobson P.D., Smallbone K., Jameson D., et al. Further developments towards a genome-scale metabolicmodel of yeast [J]. BMC Syst Biol,2010,4:145
[218] Raghunathan A., Reed J., Shin S., et al. Constraint-based analysis of metabolic capacity of Salmonellatyphimurium during host-pathogen interaction [J]. BMC Syst Biol,2009,3:38
[219] AbuOun M., Suthers P.F., Jones G.I., et al. Genome scale reconstruction of a Salmonella metabolic model:comparison of similarity and differences with a commensal Escherichia coli strain [J]. J Biol Chem,2009,284(43):29480-8
[220] Thiele I., Hyduke D.R., Steeb B., et al. A community effort towards a knowledge-base and mathematicalmodel of the human pathogen Salmonella Typhimurium LT2[J]. BMC Syst Biol,2011,5:8
[221] Pinchuk G.E., Hill E.A., Geydebrekht O.V., et al. Constraint-based model of Shewanella oneidensis MR-1metabolism: a tool for data analysis and hypothesis generation [J]. PLoS Comput Biol,2010,6(6):e1000822
[222] Lee D.S., Burd H., Liu J., et al. Comparative genome-scale metabolic reconstruction and flux balanceanalysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets [J]. JBacteriol,2009,191(12):4015-24
[223] Pastink M.I., Teusink B., Hols P., et al. Genome-scale model of Streptococcus thermophilus LMG18311for metabolic comparison of lactic acid bacteria [J].Appl Environ Microbiol,2009,75(11):3627-33
[224] Alam M.T., Merlo M.E., Hodgson D.A., et al. Metabolic modeling and analysis of the metabolic switch inStreptomyces coelicolor [J]. BMC Genomics,2010,11:202
[225] Zhang Y., Thiele I., Weekes D., et al. Three-dimensional structural view of the central metabolic networkof Thermotoga maritima [J]. Science,2009,325(5947):1544-9
[226] Kim H.U., Kim S.Y., Jeong H., et al. Integrative genome-scale metabolic analysis of Vibrio vulnificus fordrug targeting and discovery [J]. Mol Syst Biol,2011,7:460
[227] Charusanti P., Chauhan S., McAteer K., et al. An experimentally-supported genome-scale metabolicnetwork reconstruction for Yersinia pestis CO92[J]. BMC Syst Biol,2011,5:163
[228] Widiastuti H., Kim J.Y., Selvarasu S., et al. Genome-scale modeling and in silico analysis of ethanologenicbacteria Zymomonas mobilis [J]. Biotechnol Bioeng,2011,108(3):655-65
[229] Hyduke D.R., Palsson B.O. Towards genome-scale signalling network reconstructions [J]. Nat Rev Genet,2010,11(4):297-307
[230] Jensen P.A., Lutz K.A., Papin J.A. TIGER: Toolbox for integrating genome-scale metabolic models,expression data, and transcriptional regulatory networks [J]. BMC Syst Biol,2011,5:147
[231] Thiele I., Jamshidi N., Fleming R.M., et al. Genome-scale reconstruction of Escherichia coli'stranscriptional and translational machinery: a knowledge base, its mathematical formulation, and itsfunctional characterization [J]. PLoS Comput Biol,2009,5(3): e1000312
[232] Thiele I., Palsson B.O. Aprotocol for generating a high-quality genome-scale metabolic reconstruction [J].Nat Protoc,2010,5(1):93-121
[233] Zelle R.M., de Hulster E., van Winden W.A., et al. Malic acid production by Saccharomyces cerevisiae:engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export [J]. Appl EnvironMicrobiol,2008,74(9):2766-77
[234] Lee S.Y., Kim J.M., Song H., et al. From genome sequence to integrated bioprocess for succinic acidproduction by Mannheimia succiniciproducens [J].Appl Microbiol Biotechnol,2008,79(1):11-22
[235] Alper H., Jin Y.S., Moxley J.F., et al. Identifying gene targets for the metabolic engineering of lycopenebiosynthesis in Escherichia coli [J]. Metab Eng,2005,7(3):155-64
[236] Choi H.S., Lee S.Y., Kim T.Y., et al. In silico identification of gene amplification targets for improvementof lycopene production [J]. Appl Environ Microbiol,2010,76(10):3097-105
[237] Driouch H., Melzer G., Wittmann C. Integration of in vivo and in silico metabolic fluxes for improvementof recombinant protein production [J]. Metab Eng,2012,14(1):47-58
[238] Wilson K. Preparation of genomic DNA from bacteria [J]. Curr Protoc Mol Biol,2001, Chapter2: Unit24
[239] Delcher A.L., Harmon D., Kasif S., et al. Improved microbial gene identification with GLIMMER [J].NucleicAcids Res,1999,27(23):4636-41
[240] Salzberg S.L., Delcher A.L., Kasif S., et al. Microbial gene identification using interpolated Markovmodels [J]. NucleicAcids Res,1998,26(2):544-8
[241] Tatusov R.L., Galperin M.Y., Natale D.A., et al. The COG database: a tool for genome-scale analysis ofprotein functions and evolution [J]. Nucleic Acids Res,2000,28(1):33-6
[242] Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNAgenes in genomicsequence [J]. NucleicAcids Res,1997,25(5):955-64
[243] Lagesen K., Hallin P., Rodland E.A., et al. RNAmmer: consistent and rapid annotation of ribosomal RNAgenes [J]. Nucleic Acids Res,2007,35(9):3100-8
[244] Kurtz S., Phillippy A., Delcher A.L., et al. Versatile and open software for comparing large genomes [J].Genome Biol,2004,5(2): R12
[245] Carver T., Thomson N., Bleasby A., et al. DNAPlotter: circular and linear interactive genome visualization[J]. Bioinformatics,2009,25(1):119-20
[246] Meng H., Wang Y., Hua Q., et al. In silico Analysis and Experimental Improvement of TaxadieneHeterologous Biosynthesis in Escherichia coli [J]. Biotechnol Bioproc E,2011,16(2):205-15
[247] Meng H., Lu Z., Wang Y., et al. In silico improvement of heterologous biosynthesis of erythromycinprecursor6-deoxyerythronolide B in Escherichia coli [J]. Biotechnol Bioproc E,2011,16(3):445-56
[248] Dauner M., Sauer U. Stoichiometric growth model for riboflavin-producing Bacillus subtilis [J].Biotechnol Bioeng,2001,76(2):132-43
[249]王健,周昌平,张蓓,等.鸟苷产生菌的代谢途径分析[J].生物加工过程,2004,2(2):74-48
[250] Wei X.X., Chen G.Q. Applications of the VHb gene vgb for improved microbial fermentation processes [J].Methods Enzymol,2008,436:273-87
[251] Zhu H., Sun S., Zhang S. Enhanced production of total flavones and exopolysaccharides viaVitreoscillahemoglobin biosynthesis in Phellinus igniarius [J]. Bioresour Technol,2011,102(2):1747-51
[252] Wu J.M., Fu W.C. Intracellular co-expression of Vitreoscilla hemoglobin enhances cell performance andbeta-galactosidase production in Pichia pastoris [J]. J Biosci Bioeng,2012,113(3):332-7
[253] Luo W.H., Guo Y., Han S.Y. High-level expression of douchi fibrinolytic enzyme (DFE) in Bacillussubtilis WB800[J]. Chin J Appl Environ Biol,2007,13(4):565-9
[254] McInerney J.O. GCUA: general codon usage analysis [J]. Bioinformatics,1998,14(4):372-3
[255] Puigbo P., Guzman E., Romeu A., et al. OPTIMIZER: a web server for optimizing the codon usage ofDNAsequences [J]. NucleicAcids Res,2007,35(Web Server issue): W126-31
[256] Puigbo P., Romeu A., Garcia-Vallve S. HEG-DB: a database of predicted highly expressed genes inprokaryotic complete genomes under translational selection [J]. Nucleic Acids Res,2008,36(Databaseissue): D524-7
[257] Dikshit K.L., Webster D.A. Cloning, characterization and expression of the bacterial globin gene fromVitreoscilla in Escherichia coli [J]. Gene,1988,70(2):377-86
[258]刘清术.透明颤菌血红蛋白基因在解淀粉芽孢杆菌FZB42中的重组表达及其功能研究[D].湖南师范大学硕士学位论文,2009
[259]鲍朋,陈宁,温廷益.修饰的谷氨酰胺磷酸核糖焦磷酸转酰胺酶对鸟苷产量的影响[J].安徽农业科学,2011,39(17):10097-8
[260]周军智,邹永康,戴红梅,等.大肠杆菌ptsHIcrr操纵子的快速敲除及敲除菌生长性能测定[J].微生物学通报,2010,37(8):1146-52
[261]韩聪,张惟材,游松,等.大肠杆菌ptsG基因敲除及其缺陷株生长特性研究[J].生物工程学报,2004,20(1):16-20
[262] Kilstrup M., Martinussen J. Atranscriptional activator, homologous to the Bacillus subtilis PurR repressor,is required for expression of purine biosynthetic genes in Lactococcus lactis [J]. J Bacteriol,1998,180(15):3907-16
[2] Kini G.D., Anderson J.D., Sanghvi Y.S., et al. Synthesis and antiviral activity of certain guanosineanalogues in the thiazolo[4,5-d]pyrimidine ring system [J]. J Med Chem,1991,34(10):3006-10
[3] Ray A.S., Yang Z., Chu C.K., et al. Novel use of a guanosine prodrug approach to convert2',3'-Didehydro-2',3'-Dideoxyguanosine into a viable antiviral agent [J]. Antimicrob Agents Ch,2002,46(3):887-91
[4] Sheremet A.S., Gronskiy S.V., Akhmadyshin R.A., et al. Enhancement of extracellular purine nucleosideaccumulation by Bacillus strains through genetic modifications of genes involved in nucleoside export [J]. JInd Microbiol Biotechnol,2011,38(1):65-70
[5] Zakataeva N.P., Gronskiy S.V., Sheremet A.S., et al. A new function for the Bacillus PbuE purine baseefflux pump: efflux of purine nucleosides [J]. Res Microbiol,2007,158(8-9):659-65
[6] Li H., Zhang G., Deng A., et al. De novo engineering and metabolic flux analysis of inosine biosynthesis inBacillus subtilis [J]. Biotechnol Lett,2011,33(8):1575-80
[7] Qian J., Cai X., Chu J., et al. Nucleotide mutations in purA gene and pur operon promoter discovered inguanosine-and inosine-producing Bacillus subtilis strains [J]. Biotechnol Lett,2006,28(12):937-41
[8] Chen S., Chu J., Zhuang Y., et al. Enhancement of inosine production by Bacillus subtilis throughsuppression of carbon overflow by sodium citrate [J]. Biotechnol Lett,2005,27(10):689-92
[9] Schallmey M., Singh A., Ward O.P. Developments in the use of Bacillus species for industrial production [J].Can J Microbiol,2004,50(1):1-17
[10] Shimaoka M., Takenaka Y., Kurahashi O., et al. Effect of amplification of desensitized purF and prs oninosine accumulation in Escherichia coli [J]. J Biosci Bioeng,2007,103(3):255-61
[11]张克旭,杜连祥.核酸发酵[M].轻工业出版社,1987
[12]王镜岩.生物化学[M].高等教育出版社,2002
[13] Ebbole D.J., Zalkin H. Cloning and characterization of a12-gene cluster from Bacillus subtilis encodingnine enzymes for de novo purinenucleotide synthesis [J]. J Biol Chem,1987,262(17):8274-87
[14] Kunst F., Ogasawara N., Moszer I., et al. The complete genome sequence of the gram-positive bacteriumBacillus subtilis [J]. Nature,1997,390(6657):249-56
[15] Aiba A., Mizobuchi K. Nucleotide sequence analysis of genes purH and purD involved in the de novopurine nucleotide biosynthesis of Escherichia coli [J]. J Biol Chem,1989,264(35):21239-46
[16] Saxild H.H., Nygaard P. Regulation of levels of purine biosynthetic enzymes in Bacillus subtilis: effects ofchanging purine nucleotide pools [J]. J Gen Microbiol,1991,137(10):2387-94
[17] Holt K.E., Parkhill J., Mazzoni C.J., et al. High-throughput sequencing provides insights into genomevariation and evolution in Salmonella Typhi [J]. Nat Genet,2008,40(8):987-93
[18] Rappu P., Shin B.S., Zalkin H., et al. A role for a highly conserved protein of unknown function inregulation of Bacillus subtilis purA by the purine repressor [J]. J Bacteriol,1999,181(12):3810-5
[19] Saxild H.H., Brunstedt K., Nielsen K.I., et al. Definition of the Bacillus subtilis PurR operator using geneticand bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD,and pbuO [J]. J Bacteriol,2001,183(21):6175-83
[20] Weng M., Nagy P.L., Zalkin H. Identification of the Bacillus subtilis pur operon repressor [J]. Proc NatlAcad Sci U S A,1995,92(16):7455-9
[21] Rappu P., Pullinen T., Mantsala P. In vivo effect of mutations at the PRPP binding site of the Bacillussubtilis purine repressor [J]. J Bacteriol,2003,185(22):6728-31
[22] Weng M., Zalkin H. Mutations in the Bacillus subtilis purine repressor that perturb PRPP effector functionin vitro and in vivo [J]. Curr Microbiol,2000,41(1):56-9
[23] Ebbole D.J., Zalkin H. Detection of pur operon-attenuated mRNA and accumulated degradationintermediates in Bacillus subtilis [J]. J Biol Chem,1988,263(22):10894-902
[24] Ebbole D.J., Zalkin H. Bacillus subtilis pur operon expression and regulation [J]. J Bacteriol,1989,171(4):2136-41
[25] Wu T.W., Scrimgeour K.G. Properties of inosinic acid dehydrogenase from Bacillus subtilis. II. Kineticproperties [J]. Can J Biochem,1973,51(10):1391-8
[26] Endo T., Uratani B., Freese E. Purine salvage pathways of Bacillus subtilis and effect of guanine on growthof GMPreductase mutants [J]. J Bacteriol,1983,155(1):169-79
[27] Asahara T., Mori Y., Zakataeva N.P., et al. Accumulation of gene-targeted Bacillus subtilis mutations thatenhance fermentative inosine production [J].Appl Microbiol Biotechnol,2010,87(6):2195-207
[28] Matsui H., Shimaoka M., Takenaka Y., et al. Gsk disruption leads to guanosine accumulation in Escherichiacoli [J]. Biosci Biotechnol Biochem,2001,65(5):1230-5
[29] Zakataeva N.P., Romanenkov D.V., Skripnikova V.S., et al. Wild-type and feedback-resistantphosphoribosyl pyrophosphate synthetases from Bacillus amyloliquefaciens: purification, characterization,and application to increase purine nucleoside production [J]. Appl Microbiol Biotechnol,2012,93(5):2023-33
[30] Livshits V.A., Zakataeva N.P., Aleshin V.V., et al. Identification and characterization of the new gene rhtAinvolved in threonine and homoserine efflux in Escherichia coli [J]. Res Microbiol,2003,154(2):123-35
[31] Diesveld R., Tietze N., Furst O., et al. Activity of exporters of Escherichia coli in Corynebacteriumglutamicum, and their use to increase L-threonine production [J]. J Mol Microbiol Biotechnol,2009,16(3-4):198-207
[32] Kruse D., Kramer R., Eggeling L., et al. Influence of threonine exporters on threonine production inEscherichia coli [J].Appl Microbiol Biotechnol,2002,59(2-3):205-10
[33] Venter J.C., Adams M.D., Myers E.W., et al. The sequence of the human genome [J]. Science,2001,291(5507):1304-51
[34] Li R., Fan W., Tian G., et al. The sequence and de novo assembly of the giant panda genome [J]. Nature,2010,463(7279):311-7
[35] Wilhelm B.T., Marguerat S., Watt S., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed atsingle-nucleotide resolution [J]. Nature,2008,453(7199):1239-43
[36] Nagalakshmi U., Wang Z., Waern K., et al. The transcriptional landscape of the yeast genome defined byRNAsequencing [J]. Science,2008,320(5881):1344-9
[37] Lefrancois P., Zheng W., Snyder M. ChIP-Seq using high-throughput DNA sequencing for genome-wideidentification of transcription factor binding sites [J]. Methods Enzymol,2010,470:77-104.
[38] Schmidt D., Wilson M.D., Spyrou C., et al. ChIP-seq: Using high-throughput sequencing to discoverprotein-DNAinteractions [J]. Methods,2009,48(3):240-8
[39] Shohet J., Ludwig A., Chen Z.W., et al. High Throughput Sequencing And Chromatin Immunoprecipitation(Chip-Seq) Identifies Mycn-Regulated Micrornas As Tumor Suppressors And Oncogenes In Neuroblastoma[J]. Pediatr Blood&Cancer,2010,54(6):840-1
[40] Hesselberth J.R., Chen X., Zhang Z., et al. Global mapping of protein-DNA interactions in vivo by digitalgenomic footprinting [J]. Nat Methods,2009,6(4):283-9
[41] Serre D., Lee B.H., Ting A.H. MBD-isolated Genome Sequencing provides a high-throughput andcomprehensive survey of DNA methylation in the human genome [J]. Nucleic Acids Res,2010,38(2):391-9
[42] Mohn F., Weber M., Schubeler D., et al. Methylated DNA immunoprecipitation (MeDIP)[J]. Methods MolBiol,2009,507:55-64
[43] Wang J., Jiang H., Ji G., et al. High resolution profiling of human exon methylation by liquid hybridizationcapture-based bisulfite sequencing [J]. BMC Genomics,2011,12(1):597
[44] Haque N., Nishiguchi M. Bisulfite sequencing for cytosine-methylation analysis in plants [J]. Methods MolBiol,2011,744:187-97
[45] Yang H., Liao Y., Wang B., et al. Genome sequence of Escherichia coli XH140A, which producesL-threonine [J]. J Bacteriol,2011,193(21):6090-1
[46] Yang H., Liao Y., Wang B., et al. Draft genome sequence of Escherichia coli XH001, a producer ofL-threonine in industry [J]. J Bacteriol,2011,193(22):6406-7
[47]孙娟娟.普鲁兰酶在解淀粉芽孢杆菌中表达方法的探索[D].江南大学硕士学位论文,2011
[48] Welker N.E., Campbell L.L. Unrelatedness of Bacillus amyloliquefaciens and Bacillus subtilis [J]. JBacteriol,1967,94(4):1124-30
[49] Chen X.H., Koumoutsi A., Scholz R., et al. Comparative analysis of the complete genome sequence of theplant growth-promoting bacterium Bacillus amyloliquefaciens FZB42[J]. Nat Biotechnol,2007,25(9):1007-14
[50] Welker N.E., Campbell L.L. Crystallization and properties of alpha-amylase from five strains of Bacillusamyloliquefaciens [J]. Biochemistry,1967,6(12):3681-9
[51] Welker N.E., Campbell L.L. Comparison of the alpha-amylase of Bacillus subtilis and Bacillusamyloliquefaciens [J]. J Bacteriol,1967,94(4):1131-5
[52] Peng Y., Yang X.J., Xiao L., et al. Cloning and expression of a fibrinolytic enzyme (subtilisin DFE) genefrom Bacillus amyloliquefaciens DC-4in Bacillus subtilis [J]. Res Microbiol,2004,155(3):167-73
[53] Peng Y., Huang Q., Zhang R.H., et al. Purification and characterization of a fibrinolytic enzyme producedby Bacillus amyloliquefaciens DC-4screened from douchi, a traditional Chinese soybean food [J]. CompBiochem Physiol B Biochem Mol Biol,2003,134(1):45-52
[54] Wei X., Luo M., Xu L., et al. Production of fibrinolytic enzyme from Bacillus amyloliquefaciens byfermentation of chickpeas, with the evaluation of the anticoagulant and antioxidant properties of chickpeas[J]. JAgric Food Chem,2011,59(8):3957-63
[55] Kim P.I., Chung K.C. Production of an antifungal protein for control of Colletotrichum lagenarium byBacillus amyloliquefaciens MET0908[J]. FEMS Microbiol Lett,2004,234(1):177-83
[56] Zhang G., Deng A., Xu Q., et al. Complete genome sequence of Bacillus amyloliquefaciens TA208, a strainfor industrial production of guanosine and ribavirin [J]. J Bacteriol,2011,193(12):3142-3
[57] Yang H., Liao Y., Wang B., et al. Complete genome sequence of Bacillus amyloliquefaciens XH7, whichexhibits production of purine nucleosides [J]. J Bacteriol,2011,193(19):5593-4
[58] Geng W., Cao M., Song C., et al. Complete genome sequence of Bacillus amyloliquefaciens LL3, whichexhibits glutamic acid-independent production of poly-gamma-glutamic acid [J]. J Bacteriol,2011,193(13):3393-4
[59] Cao M., Geng W., Liu L., et al. Glutamic acid independent production of poly-gamma-glutamic acid byBacillus amyloliquefaciens LL3and cloning of pgsBCA genes [J]. Bioresour Technol,2011,102(5):4251-7
[60] Liu J., Ma X., Wang Y., et al. Depressed biofilm production in Bacillus amyloliquefaciens C06causesgamma-polyglutamic acid (gamma-PGA) overproduction [J]. Curr Microbiol,2011,62(1):235-41
[61] Romano A., Vitullo D., Di Pietro A., et al. Antifungal lipopeptides from Bacillus amyloliquefaciens strainBO7[J]. J Nat Prod,2011,74(2):145-51
[62] Katz E., Demain A.L. The peptide antibiotics of Bacillus: chemistry, biogenesis, and possible functions [J].Bacteriol Rev,1977,41(2):449-74
[63] Bonmatin J.M., Laprevote O., Peypoux F. Diversity among microbial cyclic lipopeptides: iturins andsurfactins. Activity-structure relationships to design new bioactive agents [J]. Comb Chem HighThroughput Screen,2003,6(6):541-56
[64] Ongena M., Jacques P. Bacillus lipopeptides: versatile weapons for plant disease biocontrol [J]. TrendsMicrobiol,2008,16(3):115-25
[65] Sutyak K.E., Wirawan R.E., Aroutcheva A.A., et al. Isolation of the Bacillus subtilis antimicrobial peptidesubtilosin from the dairy product-derived Bacillus amyloliquefaciens [J]. J Appl Microbiol,2008,104(4):1067-74
[66] Brooks J.E., Nathan P.D., Landry D., et al. Characterization of the cloned BamHI restriction modificationsystem: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts [J].NucleicAcids Res,1991,19(4):841-50
[67] Connaughton J.F., Vanek P.G., Lee-Lin S.Q., et al. Cloning of the BamHI methyl transferase gene fromBacillus amyloliquefaciens [J]. GeneAnal Tech,1988,5(6):116-24
[68] Paddon C.J., Hartley R.W. Expression of Bacillus amyloliquefaciens extracellular ribonuclease (barnase) inEscherichia coli following an inactivating mutation [J]. Gene,1987,53(1):11-9
[69] Fleischmann R.D., Adams M.D., White O., et al. Whole-genome random sequencing and assembly ofHaemophilus influenzae Rd [J]. Science,1995,269(5223):496-512
[70] Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs [J].Genome Res,2008,18(5):821-9
[71] Li R., Zhu H., Ruan J., et al. De novo assembly of human genomes with massively parallel short readsequencing [J]. Genome Res,2010,20(2):265-72
[72] Tyo K.E., Ajikumar P.K., Stephanopoulos G. Stabilized gene duplication enables long-term selection-freeheterologous pathway expression [J]. Nat Biotechnol,2009,27(8):760-5
[73] Horinouchi S., Weisblum B. Nucleotide sequence and functional map of pE194, a plasmid that specifiesinducible resistance to macrolide, lincosamide, and streptogramin type B antibodies [J]. J Bacteriol,1982,150(2):804-14
[74] Shatalin K.Y., Neyfakh A.A. Efficient gene inactivation in Bacillus anthracis [J]. FEMS Microbiol Lett,2005,245(2):315-9
[75] Horinouchi S., Weisblum B. Nucleotide sequence and functional map of pC194, a plasmid that specifiesinducible chloramphenicol resistance [J]. J Bacteriol,1982,150(2):815-25
[76] McKenzie T., Hoshino T., Tanaka T., et al. The nucleotide sequence of pUB110: some salient features inrelation to replication and its regulation [J]. Plasmid,1986,15(2):93-103
[77] Sullivan M.A., Yasbin R.E., Young F.E. New shuttle vectors for Bacillus subtilis and Escherichia coli whichallow rapid detection of inserted fragments [J]. Gene,1984,29(1-2):21-6
[78] Ferrari F.A., Nguyen A., Lang D., et al. Construction and properties of an integrable plasmid for Bacillussubtilis [J]. J Bacteriol,1983,154(3):1513-5
[79] Price C.W., Gitt M.A., Doi R.H. Isolation and physical mapping of the gene encoding the major sigmafactor of Bacillus subtilis RNApolymerase [J]. Proc NatlAcad Sci U S A,1983,80(13):4074-8
[80] Le Grice S.F., Beuck V., Mous J. Expression of biologically active human T-cell lymphotropic virus type IIIreverse transcriptase in Bacillus subtilis [J]. Gene,1987,55(1):95-103
[81] Yamagata H., Nakahama K., Suzuki Y., et al. Use of Bacillus brevis for efficient synthesis and secretion ofhuman epidermal growth factor [J]. Proceedings of the National Academy of Sciences,1989,86(10):3589-93
[82] Phan T.T., Nguyen H.D., Schumann W. Novel plasmid-based expression vectors for intra-and extracellularproduction of recombinant proteins in Bacillus subtilis [J]. Protein Expr Purif,2006,46(2):189-95
[83] Bron S., Bosma P., Van Belkum M., et al. Stability function in the Bacillus subtilis plasmid pTA1060[J].Plasmid,1987,18(1):8-15
[84] Jari V. Transformation of Bacillus amyloliquefaciens protoplasts with plasmid DNA [J]. FEMS MicrobiolLett,1988,49(1):101-5
[85] Borgmeier C., Voigt B., Hecker M., et al. Functional analysis of the response regulator DegU in Bacillusmegaterium DSM319and comparative secretome analysis of degSU mutants [J]. Appl MicrobiolBiotechnol,2011,91(3):699-711
[86] Gryczan T.J., Hahn J., Contente S., et al. Replication and incompatibility properties of plasmid pE194inBacillus subtilis [J]. J Bacteriol,1982,152(2):722-35
[87] Hofemeister J., Israeli-Reches M., Dubnau D. Integration of plasmid pE194at multiple sites on the Bacillussubtilis chromosome [J]. Mol Gen Genet,1983,189(1):58-68
[88] Zakataeva N.P., Nikitina O.V., Gronskiy S.V., et al. A simple method to introduce marker-free geneticmodifications into the chromosome of naturally nontransformable Bacillus amyloliquefaciens strains [J].Appl Microbiol Biotechnol,2010,85(4):1201-9
[89] Zhao D.L., Yu Z.C., Li P.Y., et al. Characterization of a cryptic plasmid pSM429and its application forheterologous expression in psychrophilic Pseudoalteromonas [J]. Microb Cell Fact,2011,10:30
[90] Qiao J.Q., Tian da W., Huo R., et al. Functional analysis and application of the cryptic plasmid pBSG3harboring the RapQ-PhrQ system in Bacillus amyloliquefaciens B3[J]. Plasmid,2011,65(2):141-9
[91] Yeng H.W., Shamsudin M.N., Rahim R.A. Construction of an expression vector for Lactococcus lactisbased on an indigenous cryptic plasmid [J]. Afr J Biotechnol,2009,8(21):5621-6
[92] ProzorovA.A. Competence pheromones in bacteria [J]. Mikrobiologiia,2001,70(1):5-14
[93] Sonenshein A.L., Hoch J.A., R. L. Bacillus subtilis and its closest relatives [J]. ASM Press,2002:453-71
[94] Mohan S., Aghion J., Guillen N., et al. Molecular cloning and characterization of comC, a late competencegene of Bacillus subtilis [J]. J Bacteriol,1989,171(11):6043-51
[95] Inamine G.S., Dubnau D. ComEA, a Bacillus subtilis integral membrane protein required for genetictransformation, is needed for both DNAbinding and transport [J]. J Bacteriol,1995,177(11):3045-51
[96] Provvedi R., Dubnau D. ComEA is a DNA receptor for transformation of competent Bacillus subtilis [J].Mol Microbiol,1999,31(1):271-80
[97] Londono-Vallejo J.A., Dubnau D. Mutation of the putative nucleotide binding site of the Bacillus subtilismembrane protein ComFA abolishes the uptake of DNA during transformation [J]. J Bacteriol,1994,176(15):4642-5
[98] Chung Y.S., Dubnau D. All seven comG open reading frames are required for DNA binding duringtransformation of competent Bacillus subtilis [J]. J Bacteriol,1998,180(1):41-5
[99] Zhang X.Z., Zhang Y.H. Simple, fast and high-efficiency transformation system for directed evolution ofcellulase in Bacillus subtilis [J]. Microb Biotechnol,2011,4(1):98-105
[100] Turgay K., Hahn J., Burghoorn J., et al. Competence in Bacillus subtilis is controlled by regulatedproteolysis of a transcription factor [J]. EMBO J,1998,17(22):6730-8
[101] van Sinderen D., Luttinger A., Kong L., et al. ComK encodes the competence transcription factor, the keyregulatory protein for competence development in Bacillus subtilis [J]. Mol Microbiol,1995,15(3):455-62
[102] Anagnostopoulos C., Spizizen J. Requirements for Transformation in Bacillus subtilis [J]. J Bacteriol,1961,81(5):741-6
[103] de Vos W.M., Venema G., Canosi U., et al. Plasmid transformation in Bacillus subtilis: fate of plasmidDNA[J]. Mol Gen Genet,1981,181(4):424-33
[104]陈乃用.电穿孔法在细菌质粒转化中的应用[J].微生物学通报,1991,18(2):97-103
[105] Brigidi P., De Rossi E., Bertarini M.L., et al. Genetic transformation of intact cells of Bacillus subtilis byelectroporation [J]. FEMS Microbiol Lett,1990,55(1-2):135-8
[106] McDonald I.R., Riley P.W., Sharp R.J., et al. Factors affecting the electroporation of Bacillus subtilis [J]. JAppl Bacteriol,1995,79(2):213-8
[107] Xue G.-P., Johnson J.S., Dalrymple B.P. High osmolarity improves the electro-transformation efficiency ofthe gram-positive bacteria Bacillus subtilis and Bacillus licheniformis [J]. J Microbiol Meth,1999,34(3):183-91
[108] Cao G., Zhang X., Zhong L., et al. A modified electro-transformation method for Bacillus subtilis and itsapplication in the production of antimicrobial lipopeptides [J]. Biotechnol Lett,2011,33(5):1047-51
[109] Chang S., Cohen S.N. High frequency transformation of Bacillus subtilis protoplasts by plasmid DNA [J].Mol Gen Genet,1979,168(1):111-5
[110] Levi-Meyrueis C., Fodor K., Schaeffer P. Polyethyleneglycol-induced transformation of Bacillus subtilisprotoplasts by bacterial chromosomal DNA [J]. Mol Gen Genet,1980,179(3):589-94
[111] de Vos W.M., Venema G. Fate of plasmid DNA in transformation of Bacillus subtilis protoplasts [J]. MolGen Genet,1981,182(1):39-43
[112] Jandova Z., Tichy P. Transformation of protoplasts of nontransformable Bacillus subtilis mutants byplasmid pUB110DNA[J]. Folia Microbiol (Praha),1982,27(6):465-7
[113] Romero D., Perez-Garcia A., Veening J.W., et al. Transformation of undomesticated strains of Bacillussubtilis by protoplast electroporation [J]. J Microbiol Meth,2006,66(3):556-9
[114] Zhang X.Z., Yan X., Cui Z.L., et al. MazF, a novel counter-selectable marker for unmarked chromosomalmanipulation in Bacillus subtilis [J]. NucleicAcids Res,2006,34(9): e71
[115] Morimoto T., Ara K., Ozaki K., et al. A simple method for introducing marker-free deletions in theBacillus subtilis genome [J]. Methods Mol Biol,2011,765:345-58
[116] Haima P., Bron S., Venema G. The effect of restriction on shotgun cloning and plasmid stability in Bacillussubtilis Marburg [J]. Mol Gen Genet,1987,209(2):335-42
[117] Ostroff G.R., Pene J.J. Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis. II. Transferof sequences propagated in Escherichia coli to B. subtilis [J]. Mol Gen Genet,1984,193(2):306-11
[118] de Vos W.M., de Vries S.C., Venema G. Cloning and expression of the Escherichia coli recA gene inBacillus subtilis [J]. Gene,1983,25(2-3):301-8
[119] Wu X.C., Lee W., Tran L., et al. Engineering a Bacillus subtilis expression-secretion system with a straindeficient in six extracellular proteases [J]. J Bacteriol,1991,173(16):4952-8
[120] Wu S.C., Yeung J.C., Duan Y., et al. Functional production and characterization of a fibrin-specificsingle-chain antibody fragment from Bacillus subtilis: effects of molecular chaperones and a wall-boundprotease on antibody fragment production [J].Appl Environ Microbiol,2002,68(7):3261-9
[121] Coukoulis H., Campbell L.L. Transformation in Bacillus amyloliquefaciens [J]. J Bacteriol,1971,105(1):319-22
[122] Jari V. Transformation of Bacillus amyloliquefaciens protoplasts with plasmid DNA [J]. FEMS MicrobiolLett,1988,49(1):101-5
[123] Vehmaanpera J. Transformation of Bacillus amyloliquefaciens by electroporation [J]. FEMS MicrobiolLett,1989,52(1-2):165-9
[124] Zhang G.Q., Bao P., Zhang Y., et al. Enhancing electro-transformation competency of recalcitrant Bacillusamyloliquefaciens by combining cell-wall weakening and cell-membrane fluidity disturbing [J]. AnalBiochem,2011,409(1):130-7
[125] Ideker T., Galitski T., Hood L. Anew approach to decoding life: systems biology [J]. Annu Rev GenomicsHum Genet,2001,2:343-72
[126] Hood L. Computing life: the challenge ahead [J]. IEEE Eng Med Biol Mag,2001,20(4):20
[127] Hood L., Perlmutter R.M. The impact of systems approaches on biological problems in drug discovery [J].Nat Biotechnol,2004,22(10):1215-7
[128] Kitano H. Systems biology: Systems biology: a brief overview [J]. Science,2002,295(5560):1662-4
[129] Hubner K., Sahle S., Kummer U. Applications and trends in systems biology in biochemistry [J]. FEBS J,2011,278(16):2767-857
[130]杨胜利.系统生物学研究进展[J].中国科学院院刊,2004,19(1):31-4
[131] Finney A., Hucka M. Systems biology markup language: Level2and beyond [J]. Biochem Soc Trans,2003,31(Pt6):1472-3
[132] Funahashi A. The ERATO Systems Biology Workbench and Systems Biology Markup Language: anintegrated environment and standardization for systems biology [J]. Tanpakushitsu Kakusan Koso,2003,48(7):810-6
[133] Hucka M., Finney A., Sauro H.M., et al. The systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models [J]. Bioinformatics,2003,19(4):524-31
[134] Wellock C., Chickarmane V., Sauro H.M. The SBW-MATLAB interface [J]. Bioinformatics,2005,21(6):823-4
[135] Savageau M.A. Biochemical systems analysis. II. The steady-state solutions for an n-pool system using apower-law approximation [J]. J Theor Biol,1969,25(3):370-9
[136] Michael A S. Biochemical systems analysis: I. Some mathematical properties of the rate law for thecomponent enzymatic reactions [J]. J Theor Biol,1969,25(3):365-9
[137] Savageau M.A. Finding multiple roots of nonlinear algebraic equations using S-system methodology [J].Appl Math Comput,1993,55(2-3):187-99
[138] Varma A., Palsson B.O. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursorsand cofactors [J]. J Theor Biol,1993,165(4):477-502
[139] Varma A., Palsson B.O. Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns [J]. J TheorBiol,1993,165(4):503-22
[140] Calik P., Akbay A. Mass flux balance-based model and metabolic flux analysis for collagen synthesis inthe fibrogenesis process of human liver [J]. Med Hypotheses,2000,55(1):5-14
[141] Edwards J.S., Palsson B.O. Metabolic flux balance analysis and the in silico analysis of Escherichia coliK-12gene deletions [J]. BMC Bioinformatics,2000,1:1
[142] Mahadevan R., Edwards J.S., Doyle F.J.,3rd. Dynamic flux balance analysis of diauxic growth inEscherichia coli [J]. Biophys J,2002,83(3):1331-40
[143] Segre D., Vitkup D., Church G.M. Analysis of optimality in natural and perturbed metabolic networks [J].Proc Natl Acad Sci U SA,2002,99(23):15112-7
[144] Shlomi T., Berkman O., Ruppin E. Regulatory on/off minimization of metabolic flux changes after geneticperturbations [J]. Proc Natl Acad Sci U SA,2005,102(21):7695-700
[145] Wiback S.J., Palsson B.O. Extreme pathway analysis of human red blood cell metabolism [J]. Biophys J,2002,83(2):808-18
[146] Kenanov D., Kaleta C., Petzold A., et al. Theoretical study of lipid biosynthesis in wild-type Escherichiacoli and in a protoplast-type L-form using elementary flux mode analysis [J]. FEBS J,2010,277(4):1023-34
[147] Kurata H., Zhao Q., Okuda R., et al. Integration of enzyme activities into metabolic flux distributions byelementary mode analysis [J]. BMC Syst Biol,2007,1:31
[148] Price N.D., Reed J.L., Papin J.A., et al. Analysis of metabolic capabilities using singular valuedecomposition of extreme pathway matrices [J]. Biophys J,2003,84(2Pt1):794-804
[149]蒙海林.基于系统-合成生物学的天然产物异源生物合成研究[D].华南理工大学博士学位论文,2011
[150] Brochado A.R., Matos C., Moller B.L., et al. Improved vanillin production in baker's yeast through insilico design [J]. Microb Cell Fact,2010,9:84
[151]陈琦,王卓,魏冬青.代谢网络流分析进展及应用[J].科学通报,2010,55(14):1302-9
[152] Klamt S., Stelling J., Ginkel M., et al. FluxAnalyzer: exploring structure, pathways, and flux distributionsin metabolic networks on interactive flux maps [J]. Bioinformatics,2003,19(2):261-9
[153] Garvey T.D., Lincoln P., Pedersen C.J., et al. BioSPICE: access to the most current computational tools forbiologists [J]. Omics,2003,7(4):411-20
[154] Becker S.A., Feist A.M., Mo M.L., et al. Quantitative prediction of cellular metabolism withconstraint-based models: the COBRAToolbox [J]. Nat Protoc,2007,2(3):727-38
[155] Schellenberger J., Que R., Fleming R.M., et al. Quantitative prediction of cellular metabolism withconstraint-based models: the COBRAToolbox v2.0[J]. Nat Protoc,2011,6(9):1290-307
[156] Luo R.Y., Liao S., Zeng S.Q., et al. FluxExplorer: A general platform for modeling and analyses ofmetabolic networks based on stoichiometry [J]. Chinese Science Bulletin,2006,51(6):689-96
[157] Lee S.Y., Lee D.Y., Hong S.H., et al. MetaFluxNet, a program package for metabolic pathway constructionand analysis, and its use in large-scale metabolic flux analysis of Escherichia coli [J]. Genome Inform,2003,14:23-33
[158] Karthik R., Nagasuma C. Pathwayanalyser: a systems biology tool for flux analysis of metabolic pathways[J]. Nature Precedings,2008, doi:10.1038/npre.2008.1868.1
[159] Feist A.M., Henry C.S., Reed J.L., et al. A genome-scale metabolic reconstruction for Escherichia coliK-12MG1655that accounts for1260ORFs and thermodynamic information [J]. Mol Syst Biol,2007,3:121
[160] Kim H.U., Kim T.Y., Lee S.Y. Genome-scale metabolic network analysis and drug targeting of multi-drugresistant pathogen Acinetobacter baumannii AYE [J]. Mol Biosyst,2010,6(2):339-48
[161] Durot M., Le Fevre F., de Berardinis V., et al. Iterative reconstruction of a global metabolic model ofAcinetobacter baylyi ADP1using high-throughput growth phenotype and gene essentiality data [J]. BMCSyst Biol,2008,2:85
[162] de Oliveira Dal'Molin C.G., Quek L.E., Palfreyman R.W., et al. AraGEM, a genome-scale reconstructionof the primary metabolic network in Arabidopsis [J]. Plant Physiol,2010,152(2):579-89
[163] David H., Hofmann G., Oliveira A.P., et al. Metabolic network driven analysis of genome-widetranscription data from Aspergillus nidulans [J]. Genome Biol,2006,7(11): R108
[164] Andersen M.R., Nielsen M.L., Nielsen J. Metabolic model integration of the bibliome, genome,metabolome and reactome of Aspergillus niger [J]. Mol Syst Biol,2008,4:178
[165] Vongsangnak W., Olsen P., Hansen K., et al. Improved annotation through genome-scale metabolicmodeling of Aspergillus oryzae [J]. BMC Genomics,2008,9(1):245
[166] Oh Y.K., Palsson B.O., Park S.M., et al. Genome-scale reconstruction of metabolic network in Bacillussubtilis based on high-throughput phenotyping and gene essentiality data [J]. J Biol Chem,2007,282(39):28791-9
[167] Henry C.S., Zinner J.F., Cohoon M.P., et al. iBsu1103: a new genome-scale metabolic model of Bacillussubtilis based on SEED annotations [J]. Genome Biol,2009,10(6): R69
[168] Thomas G.H., Zucker J., Macdonald S.J., et al. A fragile metabolic network adapted for cooperation in thesymbiotic bacterium Buchnera aphidicola [J]. BMC Syst Biol,2009,3:24
[169] Fang K., Zhao H., Sun C., et al. Exploring the metabolic network of the epidemic pathogen Burkholderiacenocepacia J2315via genome-scale reconstruction [J]. BMC Syst Biol,2011,5:83
[170] Chang R.L., Ghamsari L., Manichaikul A., et al. Metabolic network reconstruction of Chlamydomonasoffers insight into light-driven algal metabolism [J]. Mol Syst Biol,2011,7:518
[171] Ates O., Oner E.T., Arga K.Y. Genome-scale reconstruction of metabolic network for a halophilicextremophile, Chromohalobacter salexigens DSM3043[J]. BMC Syst Biol,2011,5:12
[172] Salimi F., Zhuang K., Mahadevan R. Genome-scale metabolic modeling of a clostridial co-culture forconsolidated bioprocessing [J]. Biotechnol J,2010,5(7):726-38
[173] Lee J., Yun H., Feist A.M., et al. Genome-scale reconstruction and in silico analysis of the ClostridiumacetobutylicumATCC824metabolic network [J]. Appl Microbiol Biotechnol,2008,80(5):849-62
[174] Milne C.B., Eddy J.A., Raju R., et al. Metabolic network reconstruction and genome-scale model ofbutanol-producing strain Clostridium beijerinckii NCIMB8052[J]. BMC Syst Biol,2011,5:130
[175] Roberts S.B., Gowen C.M., Brooks J.P., et al. Genome-scale metabolic analysis of Clostridiumthermocellum for bioethanol production [J]. BMC Syst Biol,2010,4:31
[176] Kjeldsen K.R., Nielsen J. In silico genome-scale reconstruction and validation of the Corynebacteriumglutamicum metabolic network [J]. Biotechnol Bioeng,2009,102(2):583-97
[177] Shinfuku Y., Sorpitiporn N., Sono M., et al. Development and experimental verification of a genome-scalemetabolic model for Corynebacterium glutamicum [J]. Microb Cell Fact,2009,8:43
[178] Vanee N., Roberts S.B., Fong S.S., et al. Agenome-scale metabolic model of Cryptosporidium hominis [J].Chem Biodivers,2010,7(5):1026-39
[179] Islam M.A., Edwards E.A., Mahadevan R. Characterizing the Metabolism of Dehalococcoides with aconstraint-Based Model [J]. PLoS Comput Biol,2010,6(8): e1000887
[180] Reed J.L., Vo T.D., Schilling C.H., et al. An expanded genome-scale model of Escherichia coli K-12(iJR904GSM/GPR)[J]. Genome Biol,2003,4(9): R54
[181] Orth J.D., Conrad T.M., Na J., et al. A comprehensive genome-scale reconstruction of Escherichia colimetabolism--2011[J]. Mol Syst Biol,2011,7:535
[182] Sun J., Sayyar B., Butler J.E., et al. Genome-scale constraint-based modeling of Geobactermetallireducens [J]. BMC Syst Biol,2009,3:15
[183] Mahadevan R., Bond D.R., Butler J.E., et al. Characterization of metabolism in the Fe(III)-reducingorganism Geobacter sulfurreducens by constraint-based modeling [J]. Appl Environ Microbiol,2006,72(2):1558-68
[184] Schilling C.H., Palsson B.O. Assessment of the metabolic capabilities of Haemophilus influenzae Rdthrough a genome-scale pathway analysis [J]. J Theor Biol,2000,203(3):249-83
[185] Gonzalez O., Gronau S., Falb M., et al. Reconstruction, modeling&analysis of Halobacterium salinarumR-1metabolism [J]. Mol Biosyst,2008,4(2):148-59
[186] Thiele I., Vo T.D., Price N.D., et al. Expanded metabolic reconstruction of Helicobacter pylori (iIT341GSM/GPR): an in silico genome-scale characterization of single-and double-deletion mutants [J]. JBacteriol,2005,187(16):5818-30
[187] Duarte N.C., Becker S.A., Jamshidi N., et al. Global reconstruction of the human metabolic network basedon genomic and bibliomic data [J]. Proc Natl Acad Sci U S A,2007,104(6):1777-82
[188] Liao Y.C., Huang T.W., Chen F.C., et al. An experimentally validated genome-scale metabolicreconstruction of Klebsiella pneumoniae MGH78578, iYL1228[J]. J Bacteriol,2011,193(7):1710-7
[189] Teusink B., Wiersma A., Molenaar D., et al. Analysis of growth of Lactobacillus plantarum WCFS1on acomplex medium using a genome-scale metabolic model [J]. J Biol Chem,2006,281(52):40041-8
[190] Verouden M.P.H., Notebaart R.A., Westerhuis J.A., et al. Multi-way analysis of flux distributions acrossmultiple conditions [J]. J Chemometr,2009,23(7-8):406-20
[191] Chavali A.K., Whittemore J.D., Eddy J.A., et al. Systems analysis of metabolism in the pathogenictrypanosomatid Leishmania major [J]. Mol Syst Biol,2008,4:177
[192] Kim T.Y., Kim H.U., Park J.M., et al. Genome-scale analysis of Mannheimia succiniciproducensmetabolism [J]. Biotechnol Bioeng,2007,97(4):657-71
[193] Tsoka S., Simon D., Ouzounis C.A. Automated metabolic reconstruction for Methanococcus jannaschii [J].Archaea,2004,1(4):223-9
[194] Satish Kumar V., Ferry J.G., Maranas C.D. Metabolic reconstruction of the archaeon methanogenMethanosarcina Acetivorans [J]. BMC Syst Biol,2011,5:28
[195] Feist A.M., Scholten J.C., Palsson B.O., et al. Modeling methanogenesis with a genome-scale metabolicreconstruction of Methanosarcina barkeri [J]. Mol Syst Biol,2006,2:2006.0004
[196] Rokem J.S., Vongsangnak W., Nielsen J. Comparative metabolic capabilities for Micrococcus luteusNCTC2665, the "Fleming" strain, and actinobacteria [J]. Biotechnol Bioeng,2011,108(11):2770-5
[197] Sigurdsson M.I., Jamshidi N., Steingrimsson E., et al. A detailed genome-wide reconstruction of mousemetabolism based on human Recon1[J]. BMC Syst Biol,2010,4:140
[198] Jamshidi N., Palsson B.O. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rvusing the in silico strain iNJ661and proposing alternative drug targets [J]. BMC Syst Biol,2007,1:26
[199] Suthers P.F., Dasika M.S., Kumar V.S., et al. A genome-scale metabolic reconstruction of Mycoplasmagenitalium, iPS189[J]. PLoS Comput Biol,2009,5(2): e1000285
[200] Gonzalez O., Oberwinkler T., Mansueto L., et al. Characterization of growth and metabolism of thehaloalkaliphile Natronomonas pharaonis [J]. PLoS Comput Biol,2010,6(6): e1000799
[201] Baart G.J., Zomer B., de Haan A., et al. Modeling Neisseria meningitidis metabolism: from genome tometabolic fluxes [J]. Genome Biol,2007,8(7): R136
[202] Sun J., Haveman S.A., Bui O., et al. Constraint-based modeling analysis of the metabolism of twoPelobacter species [J]. BMC Syst Biol,2010,4:174
[203] Sohn S.B., Graf A.B., Kim T.Y., et al. Genome-scale metabolic model of methylotrophic yeast Pichiapastoris and its use for in silico analysis of heterologous protein production [J]. Biotechnol J,2010,5(7):705-15
[204] Chung B.K., Selvarasu S., Andrea C., et al. Genome-scale metabolic reconstruction and in silico analysisof methylotrophic yeast Pichia pastoris for strain improvement [J]. Microb Cell Fact,2010,9:50
[205] Plata G., Hsiao T.L., Olszewski K.L., et al. Reconstruction and flux-balance analysis of the Plasmodiumfalciparum metabolic network [J]. Mol Syst Biol,2010,6:408
[206] Huthmacher C., Hoppe A., Bulik S., et al. Antimalarial drug targets in Plasmodium falciparum predictedby stage-specific metabolic network analysis [J]. BMC Syst Biol,2010,4:120
[207] Mazumdar V., Snitkin E.S., Amar S., et al. Metabolic network model of a human oral pathogen [J]. JBacteriol,2009,191(1):74-90
[208] Oberhardt M.A., Puchalka J., Fryer K.E., et al. Genome-scale metabolic network analysis of theopportunistic pathogen Pseudomonas aeruginosa PAO1[J]. J Bacteriol,2008,190(8):2790-803
[209] Sohn S.B., Kim T.Y., Park J.M., et al. In silico genome-scale metabolic analysis of Pseudomonas putidaKT2440for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival [J].Biotechnol J,2010,5(7):739-50
[210] Park J.M., Kim T.Y., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Ralstonia eutrophaH16for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and2-methyl citric acid production [J].BMC Syst Biol,2011,5:101
[211] Resendis-Antonio O., Hernandez M., Salazar E., et al. Systems biology of bacterial nitrogen fixation:high-throughput technology and its integrative description with constraint-based modeling [J]. BMC SystBiol,2011,5:120
[212] Imam S., Yilmaz S., Sohmen U., et al. iRsp1095: a genome-scale reconstruction of the Rhodobactersphaeroides metabolic network [J]. BMC Syst Biol,2011,5:116
[213] Aggarwal S., Karimi I.A., Lee D.Y. Reconstruction of a genome-scale metabolic network of Rhodococcuserythropolis for desulfurization studies [J]. Mol Biosyst,2011,7(11):3122-31
[214] Risso C., Sun J., Zhuang K., et al. Genome-scale comparison and constraint-based metabolicreconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens [J]. BMC Genomics,2009,10:447
[215] Nookaew I., Jewett M.C., Meechai A., et al. The genome-scale metabolic model iIN800of Saccharomycescerevisiae and its validation: a scaffold to query lipid metabolism [J]. BMC Syst Biol,2008,2:71
[216] Mo M.L., Palsson B.O., Herrgard M.J. Connecting extracellular metabolomic measurements tointracellular flux states in yeast [J]. BMC Syst Biol,2009,3:37
[217] Dobson P.D., Smallbone K., Jameson D., et al. Further developments towards a genome-scale metabolicmodel of yeast [J]. BMC Syst Biol,2010,4:145
[218] Raghunathan A., Reed J., Shin S., et al. Constraint-based analysis of metabolic capacity of Salmonellatyphimurium during host-pathogen interaction [J]. BMC Syst Biol,2009,3:38
[219] AbuOun M., Suthers P.F., Jones G.I., et al. Genome scale reconstruction of a Salmonella metabolic model:comparison of similarity and differences with a commensal Escherichia coli strain [J]. J Biol Chem,2009,284(43):29480-8
[220] Thiele I., Hyduke D.R., Steeb B., et al. A community effort towards a knowledge-base and mathematicalmodel of the human pathogen Salmonella Typhimurium LT2[J]. BMC Syst Biol,2011,5:8
[221] Pinchuk G.E., Hill E.A., Geydebrekht O.V., et al. Constraint-based model of Shewanella oneidensis MR-1metabolism: a tool for data analysis and hypothesis generation [J]. PLoS Comput Biol,2010,6(6):e1000822
[222] Lee D.S., Burd H., Liu J., et al. Comparative genome-scale metabolic reconstruction and flux balanceanalysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets [J]. JBacteriol,2009,191(12):4015-24
[223] Pastink M.I., Teusink B., Hols P., et al. Genome-scale model of Streptococcus thermophilus LMG18311for metabolic comparison of lactic acid bacteria [J].Appl Environ Microbiol,2009,75(11):3627-33
[224] Alam M.T., Merlo M.E., Hodgson D.A., et al. Metabolic modeling and analysis of the metabolic switch inStreptomyces coelicolor [J]. BMC Genomics,2010,11:202
[225] Zhang Y., Thiele I., Weekes D., et al. Three-dimensional structural view of the central metabolic networkof Thermotoga maritima [J]. Science,2009,325(5947):1544-9
[226] Kim H.U., Kim S.Y., Jeong H., et al. Integrative genome-scale metabolic analysis of Vibrio vulnificus fordrug targeting and discovery [J]. Mol Syst Biol,2011,7:460
[227] Charusanti P., Chauhan S., McAteer K., et al. An experimentally-supported genome-scale metabolicnetwork reconstruction for Yersinia pestis CO92[J]. BMC Syst Biol,2011,5:163
[228] Widiastuti H., Kim J.Y., Selvarasu S., et al. Genome-scale modeling and in silico analysis of ethanologenicbacteria Zymomonas mobilis [J]. Biotechnol Bioeng,2011,108(3):655-65
[229] Hyduke D.R., Palsson B.O. Towards genome-scale signalling network reconstructions [J]. Nat Rev Genet,2010,11(4):297-307
[230] Jensen P.A., Lutz K.A., Papin J.A. TIGER: Toolbox for integrating genome-scale metabolic models,expression data, and transcriptional regulatory networks [J]. BMC Syst Biol,2011,5:147
[231] Thiele I., Jamshidi N., Fleming R.M., et al. Genome-scale reconstruction of Escherichia coli'stranscriptional and translational machinery: a knowledge base, its mathematical formulation, and itsfunctional characterization [J]. PLoS Comput Biol,2009,5(3): e1000312
[232] Thiele I., Palsson B.O. Aprotocol for generating a high-quality genome-scale metabolic reconstruction [J].Nat Protoc,2010,5(1):93-121
[233] Zelle R.M., de Hulster E., van Winden W.A., et al. Malic acid production by Saccharomyces cerevisiae:engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export [J]. Appl EnvironMicrobiol,2008,74(9):2766-77
[234] Lee S.Y., Kim J.M., Song H., et al. From genome sequence to integrated bioprocess for succinic acidproduction by Mannheimia succiniciproducens [J].Appl Microbiol Biotechnol,2008,79(1):11-22
[235] Alper H., Jin Y.S., Moxley J.F., et al. Identifying gene targets for the metabolic engineering of lycopenebiosynthesis in Escherichia coli [J]. Metab Eng,2005,7(3):155-64
[236] Choi H.S., Lee S.Y., Kim T.Y., et al. In silico identification of gene amplification targets for improvementof lycopene production [J]. Appl Environ Microbiol,2010,76(10):3097-105
[237] Driouch H., Melzer G., Wittmann C. Integration of in vivo and in silico metabolic fluxes for improvementof recombinant protein production [J]. Metab Eng,2012,14(1):47-58
[238] Wilson K. Preparation of genomic DNA from bacteria [J]. Curr Protoc Mol Biol,2001, Chapter2: Unit24
[239] Delcher A.L., Harmon D., Kasif S., et al. Improved microbial gene identification with GLIMMER [J].NucleicAcids Res,1999,27(23):4636-41
[240] Salzberg S.L., Delcher A.L., Kasif S., et al. Microbial gene identification using interpolated Markovmodels [J]. NucleicAcids Res,1998,26(2):544-8
[241] Tatusov R.L., Galperin M.Y., Natale D.A., et al. The COG database: a tool for genome-scale analysis ofprotein functions and evolution [J]. Nucleic Acids Res,2000,28(1):33-6
[242] Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNAgenes in genomicsequence [J]. NucleicAcids Res,1997,25(5):955-64
[243] Lagesen K., Hallin P., Rodland E.A., et al. RNAmmer: consistent and rapid annotation of ribosomal RNAgenes [J]. Nucleic Acids Res,2007,35(9):3100-8
[244] Kurtz S., Phillippy A., Delcher A.L., et al. Versatile and open software for comparing large genomes [J].Genome Biol,2004,5(2): R12
[245] Carver T., Thomson N., Bleasby A., et al. DNAPlotter: circular and linear interactive genome visualization[J]. Bioinformatics,2009,25(1):119-20
[246] Meng H., Wang Y., Hua Q., et al. In silico Analysis and Experimental Improvement of TaxadieneHeterologous Biosynthesis in Escherichia coli [J]. Biotechnol Bioproc E,2011,16(2):205-15
[247] Meng H., Lu Z., Wang Y., et al. In silico improvement of heterologous biosynthesis of erythromycinprecursor6-deoxyerythronolide B in Escherichia coli [J]. Biotechnol Bioproc E,2011,16(3):445-56
[248] Dauner M., Sauer U. Stoichiometric growth model for riboflavin-producing Bacillus subtilis [J].Biotechnol Bioeng,2001,76(2):132-43
[249]王健,周昌平,张蓓,等.鸟苷产生菌的代谢途径分析[J].生物加工过程,2004,2(2):74-48
[250] Wei X.X., Chen G.Q. Applications of the VHb gene vgb for improved microbial fermentation processes [J].Methods Enzymol,2008,436:273-87
[251] Zhu H., Sun S., Zhang S. Enhanced production of total flavones and exopolysaccharides viaVitreoscillahemoglobin biosynthesis in Phellinus igniarius [J]. Bioresour Technol,2011,102(2):1747-51
[252] Wu J.M., Fu W.C. Intracellular co-expression of Vitreoscilla hemoglobin enhances cell performance andbeta-galactosidase production in Pichia pastoris [J]. J Biosci Bioeng,2012,113(3):332-7
[253] Luo W.H., Guo Y., Han S.Y. High-level expression of douchi fibrinolytic enzyme (DFE) in Bacillussubtilis WB800[J]. Chin J Appl Environ Biol,2007,13(4):565-9
[254] McInerney J.O. GCUA: general codon usage analysis [J]. Bioinformatics,1998,14(4):372-3
[255] Puigbo P., Guzman E., Romeu A., et al. OPTIMIZER: a web server for optimizing the codon usage ofDNAsequences [J]. NucleicAcids Res,2007,35(Web Server issue): W126-31
[256] Puigbo P., Romeu A., Garcia-Vallve S. HEG-DB: a database of predicted highly expressed genes inprokaryotic complete genomes under translational selection [J]. Nucleic Acids Res,2008,36(Databaseissue): D524-7
[257] Dikshit K.L., Webster D.A. Cloning, characterization and expression of the bacterial globin gene fromVitreoscilla in Escherichia coli [J]. Gene,1988,70(2):377-86
[258]刘清术.透明颤菌血红蛋白基因在解淀粉芽孢杆菌FZB42中的重组表达及其功能研究[D].湖南师范大学硕士学位论文,2009
[259]鲍朋,陈宁,温廷益.修饰的谷氨酰胺磷酸核糖焦磷酸转酰胺酶对鸟苷产量的影响[J].安徽农业科学,2011,39(17):10097-8
[260]周军智,邹永康,戴红梅,等.大肠杆菌ptsHIcrr操纵子的快速敲除及敲除菌生长性能测定[J].微生物学通报,2010,37(8):1146-52
[261]韩聪,张惟材,游松,等.大肠杆菌ptsG基因敲除及其缺陷株生长特性研究[J].生物工程学报,2004,20(1):16-20
[262] Kilstrup M., Martinussen J. Atranscriptional activator, homologous to the Bacillus subtilis PurR repressor,is required for expression of purine biosynthetic genes in Lactococcus lactis [J]. J Bacteriol,1998,180(15):3907-16