RETRACTED ARTICLE: Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels

This article was retracted on 08 February 2020

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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.

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Change history

  • 08 February 2020

    The authors have retracted this article.

  • 08 February 2020

    The authors have retracted this article.

References

  1. 1.

    Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995

    CAS  Article  Google 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 8:561–568

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  3. 3.

    Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165–1188

    Article  Google 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 4:217–229

    PubMed  Article  CAS  Google Scholar 

  5. 5.

    Bott M, Niebisch A (2003) The respiratory chain of Corynebacterium glutamicum. J Biotechnol 104:129–153

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  6. 6.

    Brinkrolf K, Brune I, Tauch A (2007) The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. J Biotechnol 129:191–211

    CAS  PubMed  Article  Google 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 98:8563–8572

    CAS  PubMed  Article  PubMed Central  Google 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 21:3674–3676

    CAS  PubMed  Article  PubMed Central  Google 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 177:774–782

    CAS  PubMed  PubMed Central  Article  Google 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 95:14863–14868

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  11. 11.

    Garcia-Ochoa F, Gomez E (2009) Bioreactor scale-up and oxygen transfer rate in microbial processes: an overview. Biotechnol Adv 27:153–176

    CAS  PubMed  Article  PubMed Central  Google 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 36:911–925

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  13. 13.

    Garcia-Ochoa F, Gomez E, Santos VE, Merchuk JC (2010) Oxygen uptake rate in microbial processes: an overview. Biochem Eng J 49:289–307

    CAS  Article  Google 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 25:81–88

    CAS  PubMed  Article  PubMed Central  Google 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 93:95–106

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  16. 16.

    Hara KY, Kondo A (2015) ATP regulation in bioproduction. Microb Cell Fact 14:198

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  17. 17.

    Hermann T (2003) Industrial production of amino acids by coryneform bacteria. J Biotechnol 104:155–172

    CAS  PubMed  Article  PubMed Central  Google 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 167:20–28

    CAS  PubMed  Article  PubMed Central  Google 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 67:241–244

    Google 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 62:121–141

    CAS  Google 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 104:5–25

    CAS  PubMed  Article  PubMed Central  Google 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 51:877–880

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  23. 23.

    Kim SY, Kim JH, Oh DK (1997) Improvement of xylitol production by controlling oxygen supply in Candida parapsilosis. J Ferment Bioeng 83:267–270

    CAS  Article  Google 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 1827:699–708

    CAS  PubMed  Article  PubMed Central  Google 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 25:1966–1967

    CAS  PubMed  Article  PubMed Central  Google 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 562:70–79

    CAS  PubMed  PubMed Central  Article  Google 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 87:703–713

    CAS  PubMed  Article  PubMed Central  Google 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 25:1–13

    Article  CAS  Google 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 25:402–408

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  30. 30.

    Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426–428

    CAS  Article  Google Scholar 

  31. 31.

    Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    CAS  PubMed  PubMed Central  Article  Google 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 188:209–215

    CAS  PubMed  Article  Google 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–D614

    CAS  PubMed  Article  Google 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 14:888

    Article  CAS  Google 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 10:1707–1718

    CAS  PubMed  Article  Google Scholar 

  36. 36.

    Saier MH Jr, Reizer J (1994) The bacterial phosphotransferase system: new frontiers 30 years later. Mol Microbiol 13:755–764

    CAS  PubMed  Article  Google Scholar 

  37. 37.

    Saldanha AJ (2004) Java Treeview—extensible visualization of microarray data. Bioinformatics 20:3246–3248

    CAS  PubMed  PubMed Central  Article  Google 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 25:291–298

    CAS  PubMed  Article  Google Scholar 

  39. 39.

    Siezen RJ, Wilson G, Todt T (2010) Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. J Microbial Biotechnol 3:125–130

    CAS  Article  Google 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 32:478–484

    CAS  Article  Google 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 49:139–150

    CAS  PubMed  Article  PubMed Central  Google 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 10:57–63

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. 44.

    Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W (2006) Emerging Corynebacterium glutamicum systems biology. J Biotechnol 124:74–92

    CAS  PubMed  Article  PubMed Central  Google 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 111:24–32

    CAS  PubMed  PubMed Central  Article  Google 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 43:41–51

    CAS  Article  Google Scholar 

  47. 47.

    Xu Y, Zhong JJ (2011) Significance of oxygen supply in production of a novel antibiotic by Pseudomonas sp. Bioresour Technol 102:9167–9174

    CAS  PubMed  Article  PubMed Central  Google 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 90:1051–1061

    CAS  PubMed  Article  PubMed Central  Google 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 75–76:64–70

    PubMed  Article  CAS  PubMed Central  Google 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:W293–297

    CAS  Article  Google 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 7:246–250

    CAS  Article  Google 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:e20092

    CAS  PubMed  PubMed Central  Article  Google 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 291:3010–3018

    CAS  PubMed  Article  PubMed Central  Google Scholar 

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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).

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Correspondence to Yankun Yang or Zhonghu Bai.

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

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X. Liu and S. Yang are contributed equally to this work.

The authors have retracted this article [1] because a significant portion of the study has been previously published in Chinese [2]. This article is therefore redundant. All authors agree to this retraction.

[1] Liu, X., Yang, S., Wang, F. et al. J Ind Microbiol Biotechnol (2017) 44: 181. https://doi.org/10.1007/s10295-016-1854-3

[2] Yang YK, Wang F, Sun Y. Effect of different dissolved oxygen concentrations on metabolism in Corynebacterium glutamicum. Microbiology China. (2016) ;43:11. 10.13344/j.microbiol.china.150975.

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Liu, X., Yang, S., Wang, F. et al. RETRACTED ARTICLE: Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels. J Ind Microbiol Biotechnol 44, 181–195 (2017). https://doi.org/10.1007/s10295-016-1854-3

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Keywords

  • Corynebacterium glutamicum
  • Dissolved oxygen
  • Transcriptome
  • Metabolism
  • Bioprocess