Table of Contents
ISRN Microbiology
Volume 2011, Article ID 469053, 6 pages
http://dx.doi.org/10.5402/2011/469053
Research Article

Glucan Biosynthesis Protein G Is a Suitable Reference Gene in Escherichia coli K-12

1Raffles Institution, One Raffles Institution Lane, Singapore 575954
2Department of Zoology, The University of Melbourne, Genetics Lane, Parkville, Victoria 3010, Australia

Received 29 August 2011; Accepted 13 October 2011

Academic Editors: H. I. Atabay and H.-P. Horz

Copyright © 2011 Sean S. J. Heng et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. O. Fedrigo, L. R. Warner, A. D. Pfefferle, C. C. Babbitt, P. Cruz-Gordillo, and G. A. Wray, “A pipeline to determine RT-QPCR control genes for evolutionary studies: application to primate gene expression across multiple tissues,” PLoS ONE, vol. 5, no. 9, Article ID e12545, pp. 1–7, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. N. Agabian, L. Thomashow, M. Milhausen, and K. Stuart, “Structural analysis of variant and invariant genes in trypanosomes,” American Journal of Tropical Medicine and Hygiene, vol. 29, supplement, no. 5, pp. 1043–1049, 1980. View at Google Scholar · View at Scopus
  3. T. Czechowski, M. Stitt, T. Altmann, M. K. Udvardi, and W. R. Scheible, “Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis,” Plant Physiology, vol. 139, no. 1, pp. 5–17, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Jain, A. Nijhawan, A. K. Tyagi, and J. P. Khurana, “Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR,” Biochemical and Biophysical Research Communications, vol. 345, no. 2, pp. 646–651, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. N. Nicot, J. F. Hausman, L. Hoffmann, and D. Evers, “Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress,” Journal of Experimental Botany, vol. 56, no. 421, pp. 2907–2914, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. U. E. M. Gibson, C. A. Heid, and P. M. Williams, “A novel method for real time quantitative RT-PCR,” Genome Research, vol. 6, no. 10, pp. 995–1001, 1996. View at Google Scholar · View at Scopus
  7. S. R. Stürzenbaum and P. Kille, “Control genes in quantitative molecular biological techniques: the variability of invariance,” Comparative Biochemistry and Physiology. B, vol. 130, no. 3, pp. 281–289, 2001. View at Publisher · View at Google Scholar
  8. G. W. Takle, I. K. Toth, and M. B. Brurberg, “Evaluation of reference genes for real-time RT-PCR expression studies in the plant pathogen Pectobacterium atrosepticum,” BMC Plant Biology, vol. 7, article 50, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. N. C. Noriega, S. G. Kohama, and H. F. Urbanski, “κMicroarray analysis of relative gene expression stability for selection of internal reference genes in the rhesus macaque brain,” BMC Molecular Biology, vol. 11, article 47, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. T. Remans, K. Smeets, K. Opdenakker, D. Mathijsen, J. Vangronsveld, and A. Cuypers, “Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations,” Planta, vol. 227, no. 6, pp. 1343–1349, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. E. M. Glare, M. Divjak, M. J. Bailey, and E. H. Walters, “β-actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels,” Thorax, vol. 57, no. 9, pp. 765–770, 2002. View at Publisher · View at Google Scholar · View at Scopus
  12. L. Gutierrez, M. Mauriat, S. Guénin et al., “The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants,” Plant Biotechnology Journal, vol. 6, no. 6, pp. 609–618, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. P. A. Nieto, P. C. Covarrubias, E. Jedlicki, D. S. Holmes, and R. Quatrini, “Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans,” BMC Molecular Biology, vol. 10, article 63, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. J. E. Barrick, D. S. Yu, S. H. Yoon et al., “Genome evolution and adaptation in a long-term experiment with Escherichia coli,” Nature, vol. 461, no. 7268, pp. 1243–1247, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. T. F. Cooper, D. E. Rozen, and R. E. Lenski, “Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 3, pp. 1072–1077, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. B. Janke, U. Dobrindt, J. Hacker, and G. Blum-Oehler, “A subtractive hybridisation analysis of genomic differences between the uropathogenic E. coli strain 536 and the E. coli K-12 strain MG1655,” FEMS Microbiology Letters, vol. 199, no. 1, pp. 61–66, 2001. View at Publisher · View at Google Scholar · View at Scopus
  17. N. A. Khan and G. J. Goldsworthy, “Novel model to study virulence determinants of Escherichia coli K1,” Infection and Immunity, vol. 75, no. 12, pp. 5735–5739, 2007. View at Publisher · View at Google Scholar · View at Scopus
  18. P. Kuhnert, J. Hacker, I. Mühldorfer, A. P. Burnens, J. Nicolet, and J. Frey, “Detection system for Escherichia coli-specific virulence genes: absence of virulence determinants in B and C strains,” Applied and Environmental Microbiology, vol. 63, no. 2, pp. 703–709, 1997. View at Google Scholar · View at Scopus
  19. J. Vandesompele, K. de Preter, F. Pattyn et al., “Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes,” Genome biology, vol. 3, no. 7, pp. 0034.1–0034.11, 2002. View at Google Scholar · View at Scopus
  20. C. L. Andersen, J. L. Jensen, and T. F. Ørntoft, “Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets,” Cancer Research, vol. 64, no. 15, pp. 5245–5250, 2004. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Kubista, R. Sindelka, A. Tichopad, A. Bergkvist, D. Lindh, and A. Forooran, “The prime technique. Real-time PCR data analysis,” GIT Laboratory Journal, vol. 9, no. 10, pp. 33–35, 2007. View at Google Scholar
  22. E. Wurmbach, T. Yuen, and S. C. Sealfon, “Focused microarray analysis,” Methods, vol. 31, no. 4, pp. 306–316, 2003. View at Publisher · View at Google Scholar · View at Scopus
  23. C. Y. Chia, C. W. X. Lim, W. T. Leong, and M. H. T. Ling, “High expression stability of microtubule affinity regulating kinase 3 (MARK3) makes it a reliable reference gene,” IUBMB Life, vol. 62, no. 3, pp. 200–203, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. L. P. Boava, M. L. Laia, T. R. Jacob et al., “Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using RT-qPCR,” BMC Research Notes, vol. 3, article no. 43, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. S. Holm, “A simple sequentially rejective multiple test procedure,” Scandinavian Journal of Statistics, vol. 6, no. 2, pp. 65–70, 1979. View at Google Scholar
  26. P. Khatri and S. Drǎghici, “Ontological analysis of gene expression data: current tools, limitations, and open problems,” Bioinformatics, vol. 21, no. 18, pp. 3587–3595, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. A. M. Lewin and I. C. Grieve, “Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data,” BMC Bioinformatics, vol. 7, article 426, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. S. Zhang, J. Cao, Y. M. Kong, and R. H. Scheuermann, “GO-Bayes: gene ontology-based overrepresentation analysis using a Bayesian approach,” Bioinformatics, vol. 26, no. 7, Article ID btq059, pp. 905–911, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. T. Durfee, A. M. Hansen, H. Zhi, F. R. Blattner, and J. J. Ding, “Transcription profiling of the stringent response in Escherichia coli,” Journal of Bacteriology, vol. 190, no. 3, pp. 1084–1096, 2008. View at Publisher · View at Google Scholar · View at Scopus
  30. R. S. Dhindsa, “Glutathione Status and Protein Synthesis during Drought and Subsequent Rehydration in Tortula ruralis,” Plant Physiology, vol. 83, no. 4, pp. 816–819, 1987. View at Google Scholar
  31. S. Yoshida, A. Kaibara, K. Yamasaki, N. Ishibashi, T. Noake, and T. Kakegawa, “Effect of glutamine supplementation on protein metabolism and glutathione in tumor-bearing rats,” Journal of Parenteral and Enteral Nutrition, vol. 19, no. 6, pp. 492–497, 1995. View at Google Scholar · View at Scopus
  32. R. Tanaka and A. Tanaka, “Tetrapyrrole biosynthesis in higher plants,” Annual Review of Plant Biology, vol. 58, pp. 321–346, 2007. View at Publisher · View at Google Scholar · View at Scopus
  33. A. Wehrmann, B. Phillipp, H. Sahm, and L. Eggeling, “Different modes of diaminopimelate synthesis and their role in cell wall integrity: a study with Corynebacterium glutamicum,” Journal of Bacteriology, vol. 180, no. 12, pp. 3159–3165, 1998. View at Google Scholar · View at Scopus
  34. O. Huisman, R. D'Ari, and S. Gottesman, “Cell-division control in Escherichia coli: specific induction of the SOS function SfiA protein is sufficient to block septation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 81, no. 14 I, pp. 4490–4494, 1984. View at Google Scholar · View at Scopus
  35. R. J. Wang, H. G. Morse, and M. L. Morse, “Carbohydrate accumulation and metabolism in Escherichia coli: characteristics of the reversions of ctr mutations,” The Journal of Bacteriology, vol. 104, no. 3, pp. 1318–1324, 1970. View at Google Scholar
  36. J. van Heijenoort, “Formation of the glycan chains in the synthesis of bacterial peptidoglycan,” Glycobiology, vol. 11, no. 3, pp. 25–36, 2001. View at Google Scholar · View at Scopus
  37. I. Loubens, L. Debarbieux, A. Bohin, J. M. Lacroix, and J. P. Bohin, “Homology between a genetic locus (mdoA) involved in the osmoregulated biosynthesis of periplasmic glucans in Escherichia coli and a genetic locus (hrpM) controlling pathogenicity of Pseudomonas syringae,” Molecular Microbiology, vol. 10, no. 2, pp. 329–340, 1993. View at Publisher · View at Google Scholar · View at Scopus
  38. J. P. Bohin, “Osmoregulated periplasmic glucans in Proteobacteria,” FEMS Microbiology Letters, vol. 186, no. 1, pp. 11–19, 2000. View at Publisher · View at Google Scholar · View at Scopus
  39. F. Page, S. Altabe, N. Hugouvieux-Cotte-Pattat, J. M. Lacroix, J. Robert-Baudouy, and J. P. Bohin, “Osmoregulated periplasmic glucan synthesis is required for Erwinia chrysanthemi pathogenicity,” Journal of Bacteriology, vol. 183, no. 10, pp. 3134–3141, 2001. View at Publisher · View at Google Scholar · View at Scopus