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RETRACTED ARTICLE: Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels

  • Xiuxia Liu
  • Sun Yang
  • Fen Wang
  • Xiaofeng Dai
  • Yankun YangEmail author
  • Zhonghu BaiEmail author
Fermentation, Cell Culture and Bioengineering - Original Paper

Abstract

The dissolved oxygen (DO) level of a culture of Corynebacterium glutamicum (C. glutamicum) in a bioreactor has a significant impact on the cellular redox potential and the distribution of energy and metabolites. In this study, to gain a deeper understanding of the effects of DO on the metabolism of C. glutamicum, we sought to systematically explore the influence of different DO concentrations on genetic regulation and metabolism through transcriptomic analysis. The results revealed that after 20 h of fermentation, oxygen limitation enhanced the glucose metabolism, pyruvate metabolism and carbon overflow, and restricted NAD+ availability. A high oxygen supply enhanced the TCA cycle and reduced glyoxylate metabolism. Several key genes involved in response of C. glutamicum to different oxygen concentrations were examined, which provided suggestions for target site modifications in developing optimized oxygen supply strategies. These data provided new insights into the relationship between oxygen supply and metabolism of C. glutamicum.

Keywords

Corynebacterium glutamicum Dissolved oxygen Transcriptome Metabolism Bioprocess 

Notes

Acknowledgements

This study was funded by the National Basic Research Program of China (973 Program) (Grant Number 2013CB733602), the Fundamental Research Funds for the Central Universities (Grant Number JUSRP51401A), the National Natural Science Foundation of China (Grant Number 31570034), and the Natural Science Foundation of Jiangsu Province (Grant Number BK20150148).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

10295_2016_1854_MOESM1_ESM.pdf (1.9 mb)
Supplementary material 1 (PDF 1951 kb)

References

  1. 1.
    Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995CrossRefGoogle Scholar
  2. 2.
    Bai Y, Zhou PP, Fan P, Zhu YM, Tong Y, Wang HB, Yu LJ (2015) Four-stage dissolved oxygen strategy based on multi-scale analysis for improving spinosad yield by Saccharopolyspora spinosa ATCC49460. Microb Biotechnol 8:561–568PubMedPubMedCentralCrossRefGoogle Scholar
  3. 3.
    Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165–1188CrossRefGoogle Scholar
  4. 4.
    Berríos-Rivera Bennett GN, San KY (2002) Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase. Metab Eng 4:217–229PubMedCrossRefGoogle Scholar
  5. 5.
    Bott M, Niebisch A (2003) The respiratory chain of Corynebacterium glutamicum. J Biotechnol 104:129–153PubMedCrossRefPubMedCentralGoogle Scholar
  6. 6.
    Brinkrolf K, Brune I, Tauch A (2007) The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. J Biotechnol 129:191–211PubMedCrossRefGoogle Scholar
  7. 7.
    Buchholz J, Graf M, Freund A, Busche T, Kalinowski J, Blombach B, Takors R (2014) CO2/HCO3 perturbations of simulated large scale gradients in a scale-down device cause fast transcriptional responses in Corynebacterium glutamicum. Appl Microbiol Biotechnol 98:8563–8572PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Eikmanns BJ, Rittmann D, Sahm H (1995) Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme. J Bacteriol 177:774–782PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–14868PubMedCrossRefPubMedCentralGoogle Scholar
  11. 11.
    Garcia-Ochoa F, Gomez E (2009) Bioreactor scale-up and oxygen transfer rate in microbial processes: an overview. Biotechnol Adv 27:153–176PubMedCrossRefPubMedCentralGoogle Scholar
  12. 12.
    Garcia-Ochoa F, Gomez E, Alcon A, Santos VE (2013) The effect of hydrodynamic stress on the growth of Xanthomonas campestris cultures in a stirred and sparged tank bioreactor. Bioprocess Biosyst Eng 36:911–925PubMedCrossRefPubMedCentralGoogle Scholar
  13. 13.
    Garcia-Ochoa F, Gomez E, Santos VE, Merchuk JC (2010) Oxygen uptake rate in microbial processes: an overview. Biochem Eng J 49:289–307CrossRefGoogle Scholar
  14. 14.
    Ge XY, Xu Y, Chen X, Zhang LY (2015) Regulation of metabolic flux in Lactobacillus casei for lactic acid production by overexpressed ldhL gene with two-stage oxygen supply strategy. J Microbiol Biotechnol 25:81–88PubMedCrossRefPubMedCentralGoogle Scholar
  15. 15.
    Gopinath V, Murali A, Dhar KS, Nampoothiri KM (2012) Corynebacterium glutamicum as a potent biocatalyst for the bioconversion of pentose sugars to value-added products. Appl Microbiol Biotechnol 93:95–106PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Hara KY, Kondo A (2015) ATP regulation in bioproduction. Microb Cell Fact 14:198PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Hermann T (2003) Industrial production of amino acids by coryneform bacteria. J Biotechnol 104:155–172PubMedCrossRefPubMedCentralGoogle Scholar
  18. 18.
    Hong EJ, Kim Kim ES, Kim Y, Lee HS (2016) Involvement of the osrR gene in the hydrogen peroxide-mediated stress response of Corynebacterium glutamicum. Res Microbiol 167:20–28PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    II’chenko AP, Shishkanova NV, Chernyavskaya OG, Finogenova TV (1998) Oxygen concentration as a factor controlling central metabolism and citric acid biosynthesis in the yeast Yarrowia lipolytica grown on ethanol. Microbiology 67:241–244Google Scholar
  20. 20.
    Joshi J, Elias C, Patole M (1996) Role of hydrodynamic shear in the cultivation of animal, plant and microbial cells. Biochem Eng J 62:121–141Google Scholar
  21. 21.
    Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Krämer R, Linke B, McHardy AC, Meyer F, Möckel B, Pfefferle W, Pühler A, Rey DA, Rückert C, Rupp O, Sahm H, Wendisch VF, Wiegräbe I, Tauch A (2003) The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins. J Biotechnol 104:5–25PubMedCrossRefPubMedCentralGoogle Scholar
  22. 22.
    Kim HI, Nam JY, Cho JY, Lee CS, Park YJ (2013) Next-generation sequencing-based transcriptome analysis of l-lysine-producing Corynebacterium glutamicum ATCC 21300 strain. J Microbiol 51:877–880PubMedCrossRefPubMedCentralGoogle Scholar
  23. 23.
    Kim SY, Kim JH, Oh DK (1997) Improvement of xylitol production by controlling oxygen supply in Candida parapsilosis. J Ferment Bioeng 83:267–270CrossRefGoogle Scholar
  24. 24.
    Koch-Koerfges A, Pfelzer N, Platzen L, Oldiges M, Bott M (2013) Conversion of Corynebacterium glutamicum from an aerobic respiring to an aerobic fermenting bacterium by inactivation of the respiratory chain. Biochim Biophys Acta 1827:699–708PubMedCrossRefPubMedCentralGoogle Scholar
  25. 25.
    Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    Lietzan AD, Lin Y, St Maurice M (2014) The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase. Arch Biochem Biophys 562:70–79PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Lindner SN, Knebel S, Pallerla SR, Schoberth SM, Wendisch VF (2010) Cg2091 encodes a polyphosphate/ATP-dependent glucokinase of Corynebacterium glutamicum. Appl Microbiol Biotechnol 87:703–713PubMedCrossRefPubMedCentralGoogle Scholar
  28. 28.
    Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z (2015) Expression of recombinant protein using Corynebacterium Glutamicum: progress, challenges and applications. Crit Rev Biotechnol 25:1–13CrossRefGoogle Scholar
  29. 29.
    Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−∆∆CT method. Methods 25:402–408PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426–428CrossRefGoogle Scholar
  31. 31.
    Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Park SY, Kim HK, Yoo SK, Oh TK, Lee JK (2000) Characterization of glk, a gene coding for glucose kinase of Corynebacterium glutamicum. FEMS Microbiol Lett 188:209–215PubMedCrossRefGoogle Scholar
  33. 33.
    Pauling J, Röttger R, Tauch A, Azevedo V, Baumbach J (2012) CoryneRegNet 6.0—updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res 40:D610–D614PubMedCrossRefGoogle Scholar
  34. 34.
    Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J (2013) Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. BMC Genom 14:888CrossRefGoogle Scholar
  35. 35.
    Pinto AC, Melo-Barbosa HP, Miyoshi A, Silva A, Azevedo V (2011) Application of RNA-seq to reveal the transcript profile in bacteria. Genet Mol Res 10:1707–1718PubMedCrossRefGoogle Scholar
  36. 36.
    Saier MH Jr, Reizer J (1994) The bacterial phosphotransferase system: new frontiers 30 years later. Mol Microbiol 13:755–764PubMedCrossRefGoogle Scholar
  37. 37.
    Saldanha AJ (2004) Java Treeview—extensible visualization of microarray data. Bioinformatics 20:3246–3248PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Shimizu H, Tanaka H, Nakato A, Nagahisa K, Kimura E, Shioya S (2003) Effects of the changes in enzyme activities on metabolic flux redistribution around the 2-oxoglutarate branch in glutamate production by Corynebacterium glutamicum. Bioprocess Biosyst Eng 25:291–298PubMedCrossRefGoogle Scholar
  39. 39.
    Siezen RJ, Wilson G, Todt T (2010) Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. J Microbial Biotechnol 3:125–130CrossRefGoogle Scholar
  40. 40.
    Tang Y, Zhong J (2003) Role of oxygen supply in submerged fermentation of Ganoderma lucidum for production of Ganoderma polysaccharide and ganoderic acid. Enzyme Microb Tech 32:478–484CrossRefGoogle Scholar
  41. 41.
    Tsai PS, Hatzimanikatis V, Bailey JE (1996) Effect of Vitreoscilla hemoglobin dosage on microaerobic Escherichia coli carbon and energy metabolism. Biotechnol Bioeng 49:139–150PubMedCrossRefPubMedCentralGoogle Scholar
  42. 42.
    Wang JY (2002) Biochemistry. Higher Education Press, Beijing (in Chinese) Google Scholar
  43. 43.
    Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedPubMedCentralCrossRefGoogle Scholar
  44. 44.
    Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W (2006) Emerging Corynebacterium glutamicum systems biology. J Biotechnol 124:74–92PubMedCrossRefPubMedCentralGoogle Scholar
  45. 45.
    Wimpenny JWT, Firth A (1972) Levels of nicotinamide adenine dinucleotide and reduced nicotinamide adenine dinucleotide in facultative bacteria and the effect of oxygen. J Bacteriol 111:24–32PubMedPubMedCentralCrossRefGoogle Scholar
  46. 46.
    Xu H, Dou W, Xu H, Zhang X, Rao Z, Shi Z (2009) A two-stage oxygen supply strategy for enhanced l-arginine production by Corynebacterium crenatum based on metabolic fluxes analysis. J Biochem Eng J 43:41–51CrossRefGoogle Scholar
  47. 47.
    Xu Y, Zhong JJ (2011) Significance of oxygen supply in production of a novel antibiotic by Pseudomonas sp. Bioresour Technol 102:9167–9174PubMedCrossRefPubMedCentralGoogle Scholar
  48. 48.
    Yamamoto S, Sakai M, Inui M, Yukawa H (2011) Diversity of metabolic shift in response to oxygen deprivation in Corynebacterium glutamicum and its close relatives. Appl Microbiol Biotechnol 90:1051–1061PubMedCrossRefPubMedCentralGoogle Scholar
  49. 49.
    Yang JK, Xiong W, Xu L, Li J, Zhao XJ (2015) Constitutive expression of Campylobacter jejuni truncated hemoglobin CtrHb improves the growth of Escherichia coli cell under aerobic and anaerobic conditions. Enzyme Microb Technol 75–76:64–70PubMedCrossRefPubMedCentralGoogle Scholar
  50. 50.
    Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (Web Server issue) 34:W293–297CrossRefGoogle Scholar
  51. 51.
    Yegneswaran PK, Gray MR, Thompson BG (1991) Effect of dissolved oxygen control on growth and antibiotic production in Streptomyces clavuligerus fermentations. Biotechnol Progr 7:246–250CrossRefGoogle Scholar
  52. 52.
    Yu WB, Gao SH, Yin CY, Zhou Y, Ye BC (2011) Comparative transcriptome analysis of Bacillus subtilis responding to dissolved oxygen in adenosine fermentation. PLoS One 6:e20092PubMedPubMedCentralCrossRefGoogle Scholar
  53. 53.
    Zhang Y, French SL, Beyer AL, Schneider DA (2016) The transcription factor THO promotes transcription initiation and elongation by RNA polymerase I. J Biol Chem 291:3010–3018PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2016

Authors and Affiliations

  1. 1.National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityWuxiChina
  2. 2.The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of BiotechnologyJiangnan UniversityWuxiChina
  3. 3.The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of BiotechnologyJiangnan UniversityWuxiChina

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