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Volume 6, Issue 10

Expanded roles of pyruvate-sensing PdhR in transcription regulation of the K-12 genome: fatty acid catabolism and cell motility Open Access

Abstract

The transcription factor PdhR has been recognized as the master regulator of the pyruvate catabolism pathway in , including both NAD-linked oxidative decarboxylation of pyruvate to acetyl-CoA by PDHc (pyruvate dehydrogenase complex) and respiratory electron transport of NADH to oxygen by Ndh-CyoABCD enzymes. To identify the whole set of regulatory targets under the control of pyruvate-sensing PdhR, we performed genomic SELEX (gSELEX) screening . A total of 35 PdhR-binding sites were identified along the K-12 genome, including previously identified targets. Possible involvement of PdhR in regulation of the newly identified target genes was analysed in detail by gel shift assay, RT-qPCR and Northern blot analysis. The results indicated the participation of PdhR in positive regulation of fatty acid degradation genes and negative regulation of cell mobility genes. In fact, GC analysis indicated an increase in free fatty acids in the mutant lacking PdhR. We propose that PdhR is a bifunctional global regulator for control of a total of 16–23 targets, including not only the genes involved in central carbon metabolism but also some genes for the surrounding pyruvate-sensing cellular pathways such as fatty acid degradation and flagella formation. The activity of PdhR is controlled by pyruvate, the key node between a wide variety of metabolic pathways, including generation of metabolic energy and cell building blocks.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cell motility , Escherichia coli , fatty acid β-oxidation , gSELEX , PdhR , pyruvate and transcription regulation
Funding
This study was supported by the:
  • Ministry of Education, Culture, Sports, Science and Technology (Award 25430173)
    • Principle Award Recipient: Akira Ishihama
  • Ministry of Education, Culture, Sports, Science and Technology (Award 18310133)
    • Principle Award Recipient: Akira Ishihama
  • Ministry of Education, Culture, Sports, Science and Technology (Award 19K06618)
    • Principle Award Recipient: Tomohiro Shimada
  • Nagase Science Technology Foundation
    • Principle Award Recipient: Tomohiro Shimada
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2020-09-25
2024-04-24
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References

  1. Haydon DJ, Quail MA, Guest JR. A mutation causing constitutive synthesis of the pyruvate dehydrogenase complex in Escherichia coli is located within the pdhR gene. FEBS Lett 1993; 336:43–47 [View Article][PubMed]
     [Google Scholar]
  2. Quail MA, Guest JR. Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli . Mol Microbiol 1995; 15:519–529 [View Article][PubMed]
     [Google Scholar]
  3. Ogasawara H, Ishida Y, Yamada K, Yamamoto K, Ishihama A. PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli . J Bacteriol 2007; 189:5534–5541 [View Article][PubMed]
     [Google Scholar]
  4. Göhler AK, Kökpinar O, Schmidt-Heck W, Geffers R, Guthke R et al. More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli . BMC Syst Biol 2011; 5:197 [View Article][PubMed]
     [Google Scholar]
  5. Salgado H, Gama-Castro S, Martínez-Antonio A, Díaz-Peredo E, Sánchez-Solano F et al. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 2004; 32:303D–306 [View Article][PubMed]
     [Google Scholar]
  6. Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L et al. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res 2013; 41:D203–D213 [View Article][PubMed]
     [Google Scholar]
  7. Sauer U, Eikmanns BJ. The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 2005; 29:765–794 [View Article][PubMed]
     [Google Scholar]
  8. Holms H. Flux analysis and control of the central metabolic pathways in Escherichia coli . FEMS Microbiol Rev 1996; 19:85–116 [View Article][PubMed]
     [Google Scholar]
  9. Shimada T, Fujita N, Maeda M, Ishihama A. Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells 2005; 10:907–918 [View Article][PubMed]
     [Google Scholar]
  10. Shimada T, Ogasawara H, Ishihama A. Genomic SELEX screening of regulatory targets of Escherichia coli transcription factors. Methods Mol Biol 2018; 1837:49–69 [View Article][PubMed]
     [Google Scholar]
  11. Shimada T, Ishihama A, Busby SJW, Grainger DC. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res 2008; 36:3950–3955 [View Article][PubMed]
     [Google Scholar]
  12. Ishihama A, Shimada T, Yamazaki Y. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res 2016; 44:2058–2074 [View Article][PubMed]
     [Google Scholar]
  13. Shimada T, Yokoyama Y, Anzai T, Yamamoto K, Ishihama A. Regulatory role of PlaR (YiaJ) for plant utilization in Escherichia coli K-12. Sci Rep 2019; 9:20415 [View Article][PubMed]
     [Google Scholar]
  14. Berg JM, Tymoczko JL, Stryer L. Biochemistry, 7th ed. New York, NY: W.H.Freeman; 2010
     [Google Scholar]
  15. Macnab RM. Genetics and biogenesis of bacterial flagella. Annu Rev Genet 1992; 26:131–158 [View Article][PubMed]
     [Google Scholar]
  16. Ishihama A. Building a complete image of genome regulation in the model organism Escherichia coli . J Gen Appl Microbiol 2018; 63:311–324 [View Article][PubMed]
     [Google Scholar]
  17. Kundu TK, Kusano S, Ishihama A. Promoter selectivity of Escherichia coli RNA polymerase σF holoenzyme involved in transcription of flagellar and chemotaxis genes. J Bacteriol 1997; 179:4264–4269 [View Article][PubMed]
     [Google Scholar]
  18. Pesavento C, Hengge R. The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity. Nucleic Acids Res 2012; 40:4783–4793 [View Article][PubMed]
     [Google Scholar]
  19. Campbell JW, Morgan-Kiss RM, Cronan JE. A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic beta-oxidation pathway. Mol Microbiol 2003; 47:793–805 [View Article][PubMed]
     [Google Scholar]
  20. Cronan JE, Subrahmanyam S. FadR, transcriptional co-ordination of metabolic expediency. Mol Microbiol 1998; 29:937–943 [View Article][PubMed]
     [Google Scholar]
  21. Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ et al. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng 2012; 14:653–660 [View Article][PubMed]
     [Google Scholar]
  22. Vilhena C, Kaganovitch E, Shin JY, Grünberger A, Behr S et al. A single-cell view of the BtsSR/YpdAB pyruvate sensing network in Escherichia coli and its biological relevance. J Bacteriol 2018; 200:e00536–17 [View Article][PubMed]
     [Google Scholar]
  23. Miyake Y, Inaba T, Watanabe H, Teramoto J, Yamamoto K et al. Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) in Escherichia coli K-12. FEMS Microbiol Lett 2019; 366:fnz009 [View Article]
     [Google Scholar]
  24. Ishihama A. Prokaryotic genome regulation: a revolutionary paradigm. Proc Jpn Acad Ser B Phys Biol Sci 2012; 88:485–508 [View Article][PubMed]
     [Google Scholar]
  25. Shimada T, Ogasawara H, Ishihama A. Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. Nucleic Acids Res 2018; 46:3921–3936 [View Article][PubMed]
     [Google Scholar]
  26. Shimada T, Fujita N, Yamamoto K, Ishihama A. Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS One 2011; 6:e20081 [View Article][PubMed]
     [Google Scholar]
  27. Shimada T, Yamamoto K, Ishihama A. Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli . J Bacteriol 2011; 193:649–659 [View Article][PubMed]
     [Google Scholar]
  28. Kolb A, Busby S, Buc H, Garges S, Adhya S. Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 1993; 62:749–797 [View Article][PubMed]
     [Google Scholar]
  29. Nanchen A, Schicker A, Revelles O, Sauer U. Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli . J Bacteriol 2008; 190:2323–2330 [View Article][PubMed]
     [Google Scholar]
  30. Fic E, Bonarek P, Gorecki A, Kedracka-Krok S, Mikolajczak J et al. cAMP receptor protein from Escherichia coli as a model of signal transduction in proteins-a review. J Mol Microbiol Biotechnol 2009; 17:1–11 [View Article][PubMed]
     [Google Scholar]
  31. Won HS, Lee YS, Lee SH, Lee BJ. Structural overview on the allosteric activation of cyclic AMP receptor protein. Biochim Biophys Acta 2009; 1794:1299–1308 [View Article][PubMed]
     [Google Scholar]
  32. Ramseier TM. Cra and the control of carbon flux via metabolic pathways. Res Microbiol 1996; 147:489–493 [View Article][PubMed]
     [Google Scholar]
  33. Ramseier TM, Nègre D, Cortay JC, Scarabel M, Cozzone AJ et al. In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium . J Mol Biol 1993; 234:28–44 [View Article][PubMed]
     [Google Scholar]
  34. Nègre D, Bonod-Bidaud C, Geourjon C, Deléage G, Cozzone AJ et al. Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR. Mol Microbiol 1996; 21:257–266 [View Article][PubMed]
     [Google Scholar]
  35. Fujita Y, Matsuoka H, Hirooka K. Regulation of fatty acid metabolism in bacteria. Mol Microbiol 2007; 66:829–839 [View Article][PubMed]
     [Google Scholar]
  36. Schulz H. Beta oxidation of fatty acids. Biochim Biophys Acta 1991; 1081:109–120 [View Article][PubMed]
     [Google Scholar]
  37. Overath P, Pauli G, Schairer HU. Fatty acid degradation in Escherichia coli. An inducible acyl-CoA synthetase, the mapping of old-mutations, and the isolation of regulatory mutants. Eur J Biochem 1969; 7:559–574[PubMed]
     [Google Scholar]
  38. Simons RW, Egan PA, Chute HT, Nunn WD. Regulation of fatty acid degradation in Escherichia coli: isolation and characterization of strains bearing insertion and temperature-sensitive mutations in gene fadR . J Bacteriol 1980; 142:621–632 [View Article][PubMed]
     [Google Scholar]
  39. Bekker M, Alexeeva S, Laan W, Sawers G, Teixeira de Mattos J et al. The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool. J Bacteriol 2010; 192:746–754 [View Article][PubMed]
     [Google Scholar]
  40. Alvarez AF, Georgellis D. In vitro and in vivo analysis of the ArcB/A redox signaling pathway. Methods Enzymol 2010; 471:205–228 [View Article][PubMed]
     [Google Scholar]
  41. Higashitani A, Nishimura Y, Hara H, Aiba H, Mizuno T et al. Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli . Mol Gen Genet 1993; 240:339–347 [View Article][PubMed]
     [Google Scholar]
  42. Feng Y, Cronan JE. Crosstalk of Escherichia coli FadR with global regulators in expression of fatty acid transport genes. PLoS One 2012; 7:e46275 [View Article][PubMed]
     [Google Scholar]
  43. Feng Y, Cronan JE. Overlapping repressor binding sites result in additive regulation of Escherichia coli FadH by FadR and ArcA. J Bacteriol 2010; 192:4289–4299 [View Article][PubMed]
     [Google Scholar]
  44. Lin CY, Awano N, Masuda H, Park JH, Inouye M. Transcriptional repressor HipB regulates the multiple promoters in Escherichia coli . J Mol Microbiol Biotechnol 2013; 23:440–447 [View Article][PubMed]
     [Google Scholar]
  45. Shimada T, Tanaka K, Ishihama A. The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PLoS One 2017; 12:e0179181 [View Article][PubMed]
     [Google Scholar]
  46. Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP et al. Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment. PLoS One 2011; 6:e25501 [View Article][PubMed]
     [Google Scholar]
  47. Miller SP, Chen R, Karschnia EJ, Romfo C, Dean A et al. Locations of the regulatory sites for isocitrate dehydrogenase kinase/phosphatase. J Biol Chem 2000; 275:833–839 [View Article][PubMed]
     [Google Scholar]
  48. Asención Diez MD, Aleanzi MC, Iglesias AA, Ballicora MA. A novel dual allosteric activation mechanism of Escherichia coli ADP-glucose pyrophosphorylase: the role of pyruvate. PLoS One 2014; 9:e103888 [View Article][PubMed]
     [Google Scholar]
  49. Link H, Kochanowski K, Sauer U. Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo . Nat Biotechnol 2013; 31:357–361 [View Article][PubMed]
     [Google Scholar]
  50. Lorca GL, Ezersky A, Lunin VV, Walker JR, Altamentova S et al. Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator. J Biol Chem 2007; 282:16476–16491 [View Article][PubMed]
     [Google Scholar]
  51. Jishage M, Ishihama A. Variation in RNA polymerase sigma subunit composition within different stocks of Escherichia coli W3110. J Bacteriol 1997; 179:959–963 [View Article][PubMed]
     [Google Scholar]
  52. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 2000; 97:6640–6645 [View Article][PubMed]
     [Google Scholar]
  53. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006; 2:2006.0008 [View Article][PubMed]
     [Google Scholar]
  54. Cherepanov PP, Wackernagel W. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 1995; 158:9–14 [View Article][PubMed]
     [Google Scholar]
  55. Shimada T, Bridier A, Briandet R, Ishihama A. Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS. Mol Microbiol 2011; 82:378–397 [View Article][PubMed]
     [Google Scholar]
  56. Yang J, Chen X, McDermaid A, Ma Q. DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. Bioinformatics 2017; 33:2586–2588 [View Article][PubMed]
     [Google Scholar]
  57. Shimada T, Takada H, Yamamoto K, Ishihama A. Expanded roles of two-component response regulator OmpR in Escherichia coli: genomic SELEX search for novel regulation targets. Genes Cells 2015; 20:915–931 [View Article][PubMed]
     [Google Scholar]
  58. Liu T, Vora H, Khosla C. Quantitative analysis and engineering of fatty acid biosynthesis in E. coli . Metab Eng 2010; 12:378–386 [View Article][PubMed]
     [Google Scholar]
  59. Lu X, Vora H, Khosla C. Overproduction of free fatty acids in E. coli: implications for biodiesel production. Metab Eng 2008; 10:333–339 [View Article][PubMed]
     [Google Scholar]
  60. Imamura S, Kawase Y, Kobayashi I, Sone T, Era A et al. Target of rapamycin (TOR) plays a critical role in triacylglycerol accumulation in microalgae. Plant Mol Biol 2015; 89:309–318 [View Article][PubMed]
     [Google Scholar]
  61. Shimada T, Saito N, Maeda M, Tanaka K, Ishihama A. Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets. Microb Genom 2015; 1:e000001 [View Article][PubMed]
     [Google Scholar]
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Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility
M Gen 6, e000442 (2020); https://doi.org/10.1099/mgen.0.000442
/content/journal/mgen/10.1099/mgen.0.000442
/content/journal/mgen/10.1099/mgen.0.000442
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