Applied Microbiology and Biotechnology

, Volume 100, Issue 17, pp 7777–7785 | Cite as

Transcriptional analysis and adaptive evolution of Escherichia coli strains growing on acetate

  • Eashwar Rajaraman
  • Ankit Agarwal
  • Jacob Crigler
  • Rebecca Seipelt-Thiemann
  • Elliot Altman
  • Mark A. Eiteman
Bioenergy and biofuels

Abstract

Eighteen strains of Escherichia coli were compared for maximum specific growth rate (μMAX) on 85 mM acetate as the sole carbon source. The C strain ATCC8739 had the greatest growth rate (0.41 h−1) while SCS-1 had the slowest growth rate (0.15 h−1). Transcriptional analysis of three of the strains (ATCC8739, BL21, SMS-3-5) was conducted to elucidate why ATCC8739 had the greatest maximum growth rate. Seventy-one genes were upregulated 2-fold or greater in ATCC8739, while 128 genes were downregulated 2-fold or greater in ATCC8739 compared to BL21 and SMS-3-5. To generate a strain that could grow more quickly on acetate, ATCC8739 was cultured in a chemostat using a progressively increasing dilution rate. When the dilution rate reached 0.50 h−1, three isolated colonies each grew faster than ATCC8739 on 85 mM acetate, with MEC136 growing the fastest with a growth rate of 0.51 h−1, about 25 % greater than ATCC8739. Transcriptional analysis of MEC136 showed that eight genes were downregulated 2-fold or greater and one gene was upregulated 2-fold or greater compared to ATCC8739. Genomic sequencing revealed that MEC136 contained a single mutation, causing a serine to proline change in amino acid 266 of RpoA, the α subunit of the RNA polymerase core enzyme. The 260–270 amino acid region of RpoA has been shown to be a key region of the protein that affects the interaction of the α subunit of the RNA polymerase core enzyme with several global transcriptional activators, such as CRP and FNR.

Keywords

Acetic acid Growth rate Chemostat Adaptive evolution 

Supplementary material

253_2016_7724_MOESM1_ESM.pdf (95 kb)
ESM 1Table S1: Genes which are two-fold or more upregulated in ATCC8739 compared to SMS-3-5 and BL21. Table S2: Genes which are two-fold or more downregulated in ATCC8739 compared to SMS-3-5 and BL21. (PDF 95 kb)

References

  1. Andrews S (2014) FastQC. A quality control tool for high throughput sequence data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Accessed June–December 2014
  2. Arnold CN, Mcelhanon J, Lee A, Leonhart R, Siegele DA (2001) Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response. J Bacteriol 183:2178–2186CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bartley LE, Ronald PC (2009) Plant and microbial research seeks biofuel production from lignocellulose. Calif Agric 63:178–184CrossRefGoogle Scholar
  4. Beatty CM, Browning DF, Busby SJW, Wolfe AJ (2003) Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism. J Bacteriol 185:5148–5157CrossRefPubMedPubMedCentralGoogle Scholar
  5. Blaby IK, Lyons BJ, Wroclawska-Hughes E, Phillips GCF, Pyle TP, Chamberlin SG, Benner SA, Lyons TJ, de Crécy-Lagard V, de Crécy E (2012) Experimental evolution of a facultative thermophile from a mesophilic ancestor. Appl Environ Microbiol 78:144–155CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  7. Carvalho GBM, Mussatto SI, Candido EJ, Silva J (2006) Comparison of different procedures for the detoxification of eucalyptus hemicellulosic hydrolysate for use in fermentative processes. J Chem Technol Biotechnol 81:152–157CrossRefGoogle Scholar
  8. de Crécy E, Metzgar D, Allen C, Penicaud M, Lyons B, Hansen CJ, de Crécy-Lagard V (2007) Development of a novel continuous culture device for experimental evolution of bacterial populations. Appl Microbiol Biotechnol 77:489–496CrossRefPubMedGoogle Scholar
  9. Dykhuizen DE, Hartl DL (1983) Selection in chemostats. Microbiol Rev 47:150–168PubMedPubMedCentralGoogle Scholar
  10. Eiteman MA, Chastain MJ (1997) Optimization of the ion-exchange analysis of organic acids from fermentation. Anal Chim Acta 338:69–75CrossRefGoogle Scholar
  11. Foster JW (2004) Escherichia coli acid tolerance: tales of an amateur acidophile. Nat Rev Microbiol 2:898–907CrossRefPubMedGoogle Scholar
  12. Grainger DC, Busby SJW (2008) Global regulators of transcription in Escherichia coli: mechanisms of action and methods for study. Adv Appl Microbiol 65:93–113CrossRefPubMedGoogle Scholar
  13. Gutierrez A, Elez M, Clermont O, Denamur E, Matic I (2011) Escherichia coli YafP protein modulates DNA damaging property of the nitroaromatic compounds. Nucleic Acids Res 39:4192–4201CrossRefPubMedPubMedCentralGoogle Scholar
  14. Harvey RJ (1973) Growth and initiation of protein-synthesis in Escherichia coli in presence of trimethoprim. J Bacteriol 114:309–322PubMedPubMedCentralGoogle Scholar
  15. Hjortmo S, Patring J, Andlid T (2008) Growth rate and medium composition strongly affect folate content in Saccharomyces cerevisiae. Int J Food Microbiol 123:93–100CrossRefPubMedGoogle Scholar
  16. Klinke HB, Thomsen AB, Ahring BK (2004) Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl Microbiol Biotechnol 66:10–26CrossRefPubMedGoogle Scholar
  17. Lahtvee PJ, Valgepea K, Nahku R, Abner K, Adamberg K, Vilu R (2009) Steady state growth space study of Lactococcus lactis in A-stat cultures. Ant Van Leeuw 96:487–496CrossRefGoogle Scholar
  18. Lakshmanaswamy A, Rajaraman E, Eiteman MA, Altman E (2011) Microbial removal of acetate selectively from sugar mixtures. J Ind Microbiol Biotechnol 38:1477–1484CrossRefPubMedGoogle Scholar
  19. Lan S, Veiseh M, Zhang M (2005) Surface modification of silicon and gold-patterned silicon surfaces for improved biocompatibility and cell patterning selectivity. Biosens Bioelect 20:1697–1708CrossRefGoogle Scholar
  20. Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefPubMedPubMedCentralGoogle Scholar
  21. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  22. Liu TG, Khosla C (2010) Genetic engineering of Escherichia coli for biofuel production. Annu Rev Genet 44:53–69CrossRefPubMedGoogle Scholar
  23. Luli GW, Strohl WR (1990) Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations. Appl Environ Microbiol 56:1004–1011PubMedPubMedCentralGoogle Scholar
  24. Maesen TJM, Lako E (1952) The influence of acetate on the fermentation of Baker’s yeast. Biochim Biophys Acta 9:106–107CrossRefPubMedGoogle Scholar
  25. Murakami K, Fujita N, Ishihama A (1996) Transcription factor recognition surface on the RNA polymerase α subunit is involved in contact with the DNA enhancer element. EMBO J 15:4358–4367PubMedPubMedCentralGoogle Scholar
  26. Nègre D, Bonod-Bidaud C, Oudot C, Prost J-F, Kolbl A, Ishihama A, Cozzone AJ, Cortay J-C (1997) DNA flexibility of the UP element is a major determinant for transcriptional activation at the Escherichia coli acetate promoter. Nucleic Acids Res 25:713–718CrossRefPubMedPubMedCentralGoogle Scholar
  27. Papra A, Gadegaard N, Larsen NB (2001) Characterization of ultrathin poly(ethylene glycol) monolayers on silicon substrates. Langmuir 17:1457–1460CrossRefGoogle Scholar
  28. Parawira W, Tekere M (2011) Biotechnological strategies to overcome inhibitors in lignocellulose hydrolysates for ethanol production: review. Crit Rev Biotechnol 31:20–31CrossRefPubMedGoogle Scholar
  29. Pearse AJ, Wolf RE Jr (1994) Determination of the growth rate-regulated steps in expression of the Escherichia coli K-12 gnd gene. J Bacteriol 176:115–122CrossRefGoogle Scholar
  30. Pease AJ, Roa BR, Luo W, Winkler ME (2002) Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12. J Bacteriol 184:1359–1369CrossRefPubMedPubMedCentralGoogle Scholar
  31. Pedersen S, Bloch PL, Reeh S, Neidhardt FC (1978) Patterns of protein-synthesis in Escherichia coli—catalog of amount of 140 individual proteins at different growth-rates. Cell 14:179–190CrossRefPubMedGoogle Scholar
  32. Pettersen RC (1984) The chemical composition of wood. In: Roswell R (ed) The chemistry of solid wood. American Chemical Society, Washington, DC, pp 57–126CrossRefGoogle Scholar
  33. Poolman B, Knolm J, van der Does C, Henderson PJF, Liang WJ, Leblanc G, Pourcher T, Musveteau I (1996) Cation and sugar selectivity determinants in a novel family of transport proteins. Mol Microbiol 19:911–922CrossRefPubMedGoogle Scholar
  34. Ren CP, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WA, Pallen MJ (2004) The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J Bacteriol 186:3547–3560CrossRefPubMedPubMedCentralGoogle Scholar
  35. Roe AJ, Mclaggan D, Davidson I, O’Byrne C, Booth IR (1998) Perturbation of anion balance during inhibition of growth of Escherichia coli by weak acids. J Bacteriol 180:767–772PubMedPubMedCentralGoogle Scholar
  36. Roe AJ, O’Byrne C, Mclaggan D, Booth IR (2002) Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiol 148:2215–2222CrossRefGoogle Scholar
  37. Sakai S, Tsuchida Y, Nakamoto H, Okino S, Ichihashi O, Kawaguchi H, Watanabe T, Inui M, Yukawa H (2007) Effect of lignocellulose-derived inhibitors on growth of and ethanol production by growth-arrested Corynebacterium glutamicum R. Appl Environ Microbiol 73:6349–6353Google Scholar
  38. Sauer U (2001) Evolutionary engineering of industrially important microbial phenotypes. Adv Biochem Eng Biotechnol 73:129–169PubMedGoogle Scholar
  39. Savery NJ, Lloyd GS, Kainz M, Gaal T, Ross W, Ebright RH, Gourse RL, Busby SJW (1998) Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase α subunit. EMBO J 17:3439–3447CrossRefPubMedPubMedCentralGoogle Scholar
  40. Savery NJ, Lloyd GS, Busby SJW, Thomas MS, Ebright RH, Gourse RL (2002) Determinants of the C-terminal domain of the Escherichia coli RNA polymerase α subunit important for transcription at Class I Cyclic AMP Receptor Protein-dependent promoters. J Bacteriol 184:2273–2280CrossRefPubMedPubMedCentralGoogle Scholar
  41. Stephanopoulos G (2007) Challenges in engineering microbes for biofuels production. Science 315:801–804CrossRefPubMedGoogle Scholar
  42. Sun Y, Cheng JY (2002) Hydrolysis of lignocellulosic materials for ethanol production: a review. Biores Technol 83:1–11CrossRefGoogle Scholar
  43. Takahashi CM, Takahashi DF, Carvalhal MLC, Alterthum F (1999) Effects of acetate on the growth and fermentation performance of Escherichia coli KO11. Appl Biochem Biotechnol 81:193–203CrossRefPubMedGoogle Scholar
  44. Tao K, Zou C, Fujita N, Ishihama A (1995) Mapping of the OxyR protein contact site in the C-terminal region of RNA polymerase α subunit. J Bacteriol 177:6740–6744CrossRefPubMedPubMedCentralGoogle Scholar
  45. Tao H, Bausch C, Richmond C, Blattner FR, Conway T (1999) Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181:6425–6440PubMedPubMedCentralGoogle Scholar
  46. Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192CrossRefPubMedGoogle Scholar
  47. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, El Karoui M, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Saint Ruf C, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EPC, Denamu E (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344CrossRefPubMedPubMedCentralGoogle Scholar
  48. Trĉek J, Mira NP, Jarboe LR (2015) Adaptation and tolerance to bacteria against acetic acid. Appl Microbiol Biotechnol 99:6215–6229CrossRefPubMedGoogle Scholar
  49. Um BH, Friedman B, van Walsum GP (2011) Conditioning hardwood-derived pre-pulping extracts for use in fermentation through removal and recovery of acetic acid using trioctylphosphine oxide (TOPO). Holzforschung 65:51–58CrossRefGoogle Scholar
  50. Wong M, Wright M, Woodley JM, Lye GJ (2009) Enhanced recombinant protein synthesis in batch and fed-batch Escherichia coli fermentation based on removal of inhibitory acetate by electrodialysis. J Chem Technol Biotechnol 84:1284–1291CrossRefGoogle Scholar
  51. Wong M, Woodley JM, Lye GJ (2010) Application of bipolar electrodialysis to E. coli fermentation for simultaneous acetate removal and pH control. Biotechnol Lett 32:1053–1057CrossRefPubMedGoogle Scholar
  52. Xia T, Eiteman MA, Altman E (2012) Simultaneous utilization of glucose, xylose and arabinonse in the presence of acetate by a consortium of Escherichia coli strains. Microb. Cell Fact.  11:77 doi:10.1186/1475-2859-11-77
  53. Yang J, Murakami K, Camakaris H, Fujita N, Ishihama A, Pittard AJ (1997) Amino acid residues in the α-subunit C-terminal domain of Escherichia coli RNA polymerase involved in activation of transcription from the mtr promoter. J Bacteriol 179:6187–6191CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Eashwar Rajaraman
    • 1
  • Ankit Agarwal
    • 2
    • 4
  • Jacob Crigler
    • 3
  • Rebecca Seipelt-Thiemann
    • 3
  • Elliot Altman
    • 3
  • Mark A. Eiteman
    • 1
    • 2
  1. 1.BioChemical Engineering, College of EngineeringUniversity of GeorgiaAthensUSA
  2. 2.Department of MicrobiologyUniversity of GeorgiaAthensUSA
  3. 3.Department of BiologyMiddle Tennessee State UniversityMurfreesboroUSA
  4. 4.Present address: Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUSA

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