Environmental control of pyruvate dehydrogenase complex expression in Escherichia coli

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1 FEMS Microbiology Letters 159 (1998) 325^329 Environmental control of pyruvate dehydrogenase complex expression in Escherichia coli Barrie Cassey, John R. Guest, Margaret M. Attwood * Department of Molecular Biology and Biotechnology, University of She eld, Western Bank, She eld S10 2TN, UK Received 17 September 1997; revised 14 December 1997; accepted 18 December 1997 Abstract The effects of changing environmental conditions on expression of the pdh operon were studied in strains containing pyruvate dehydrogenase (PDH) complexes having either one or three lipoyl domains per lipoate acetyltransferase chain. The expression of the pdh operon was lowered during growth on reduced carbon sources and when the mode of energy generation was changed from aerobic respiration to anaerobic respiration and fermentation. In contrast, growth at non-optimal ph increased expression. Operon expression was generally higher in the 1 lip strain compared to the 3 lip strain. Expression of the pdh operon was shown to be tightly controlled in response to environmental stimuli, consistent with its importance in defining metabolic flux. z 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. Keywords: Pyruvate metabolism; Pyruvate dehydrogenase complex; Gene expression; Environmental control; Redox; Escherichia coli 1. Introduction In Escherichia coli, pyruvate is metabolised primarily by the pyruvate dehydrogenase (PDH) complex during aerobic growth, pyruvate formate-lyase (PFL) being increasingly used under anaerobic conditions [1^3]. The PDH complex catalyses the NAD -linked oxidative decarboxylation of pyruvate to acetyl-coa and CO 2. The E. coli complex contains multiple copies of three enzymatic subunits: pyruvate dehydrogenase (E1p); lipoate acetyltransferase (E2p); and lipoamide dehydrogenase (E3); expressed from the pdh operon, pdhr-aceef-lpda [1]. * Corresponding author. Tel.: +44 (114) ; Fax: +44 (114) Synthesis of the complex is controlled at the transcriptional level by the pyruvate-responsive autoregulator, PdhR, which binds immediately downstream of the pdh promoter to repress transcription in the absence of pyruvate [4]. The PDH complex is also controlled at the enzyme level due to its inhibition by acetyl-coa [5] and the NADH-sensitivity of the E3 subunit [6]. In E. coli, the E2p subunits have three lipoyl domains joined by exible linkers which allow them to ful l their role in active-site coupling within the assembled complex [2]. Genetically engineered strains with fewer than three lipoyl domains per E2p chain have been shown to be metabolically disadvantaged relative to the wild-type strain [2,7]. Here, two strains with VpdhR-aceEP-lacZ reporter prophages, were used to investigate the e ects of various environmental stimuli on pdh operon expres / 98 / $19.00 ß 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. PII S (97)

2 326 B. Cassey et al. / FEMS Microbiology Letters 159 (1998) 325^329 sion in strains that synthesise PDH complexes having only one or three lipoyl domains per E2p chain. 2. Materials and methods 2.1. Bacteria, phages and culture methods Two isogenic derivatives of E. coli W3110 (prototroph) encoding PDH complexes having one lipoyl domain (JRG2931, 1 lip) or three (JRG2933, 3 lip) per E2p subunit [7] were used. The corresponding monolysogens, JRG3059 (1 lip, VG239) and JRG3060 (3 lip, VG239), each contain a VpdhRaceEP-lacZ translational fusion prophage, used to monitor pdh expression [1]. The lysogens could not be grown in continuous culture due to prophage instability. The minimal medium [7] for batch and chemostat cultures (500 and 700 ml, respectively) was supplemented with di erent carbon sources (mm): pyruvate, 40; gluconate, 20; glucose, 20; or mannitol, 20. Temperature (37³C), ph (value þ 0.1), and dissolved oxygen ( s 50% air saturation for aerobic cultures) were controlled [7]. Anaerobic cultures were established aerobically and allowed to become anaerobic by removing the air supply and later sparging with nitrogen gas (500 ml min 31 ) at a constant agitator speed (400 rpm). Inocula (50 ml) were grown aerobically for 16 h in the medium required for each experiment L-Galactosidase assay and measurement of NADH/NAD ratios Samples (30^35 ml) from exponential-phase batch cultures were harvested (4000 rpm, 15 min), washed in bu er (K 2 HPO 4, 40 mm; MgCl 2, 4 mm), and the bacterial pellets stored at 320³C for subsequent and ultrasonic disruption at 4³C in 0.5 ml of the same bu er [7]. L-Galactosidase activity (va 420 h 31 mg protein 31 in cell-free extract) was measured [8] using a Labsystems iems plate-reader with a at-bottomed microtitre plate and protein was assayed by the Bio-Rad procedure with Q-globulin as standard. Speci c activities were averaged from triplicate samples from two or more independent cultures. Nucleotides were extracted and assayed [9] using ash-frozen samples (5 ml, in liquid N 2 ) taken from high density steady-state carbon-limited cultures. The quoted ratios are averages from two independent samples. 3. Results and discussion 3.1. E ects of carbon source on pdh expression Growth of E. coli in media containing di erent carbon sources leads to changes in cellular redox state [10], cell metabolism and yield [11]. The e ects of carbon source on pdh expression in E. coli were studied with aerobic batch cultures of two pdhraceep-lacz reporter strains, JRG3059 (1 lip) and JRG3060 (3 lip), grown at a constant ph 7.0 with pyruvate, gluconate, glucose or mannitol as sole carbon and energy sources. The substrates were chosen to represent di erent oxido-reduction states (gluconate, glucose, mannitol) or the capacity to relieve transcription repression by PdhR at the pdh promoter (pyruvate) [4]. The L-galactosidase activities re ect combined changes in pdh transcription and translation (Fig. 1a) and as expected, they were highest during growth on pyruvate. With the other substrates, a direct relationship was observed between the level of pdh expression and the oxido-reduction state of the substrate, even though the di erences in theoretical energy yields are relatively small for aerobic catabolism. Expression of the pdh operon was consistently higher in the 1 lip strain. The NADH/ NAD ratios in JRG2933 (3 lip non-lysogenic parent of JRG3060) con rmed that there is a relationship between PDH complex synthesis and increasing intracellular NADH/NAD ratio, gluconate 6 glucose 6 mannitol (Fig. 1d). The high ratios in pyruvate-grown cultures may be due to an increase in carbon ux through the PDH complex stemming from the induction of pdh expression by pyruvate. It would also appear that the high NADH/NAD ratios associated with some substrates repress pdh expression, directly or indirectly E ects of terminal electron acceptor on pdh expression E. coli can use di erent modes of energy transduc-

3 B. Cassey et al. / FEMS Microbiology Letters 159 (1998) 325^ Fig. 1. The e ects of environmental changes on pdh expression and NADH/NAD ratio. Expression of the pdh operon is indicated by the L-galactosidase activities (va 420 h 31 mg protein 31 ) of mid-exponential-phase batch cultures of strains containing a pdh-lacz reporter fusion, E JRG3059 (1 lip), and F JRG3060 (3 lip), during growth: a: with di erent carbon sources; b: with di erent terminal electron acceptors, oxygen (do 2 s 50%), nitrate (100 mm), ferricyanide (50 mm), fumarate (50 mm), and none added (fermentation); and c: with glucose at di erent external ph values. The NADH/NAD ratios are shown for carbon-limited chemostat cultures of JRG2933 (3 lip) grown: d: with di erent substrates at ph 7; and e: with limiting glucose at di erent ph values. tion to support growth, so in the absence of oxygen, aerobic respiration is replaced by anaerobic respiration with alternative terminal electron acceptors, or by fermentation. The reporter strains were accordingly grown in controlled batch cultures with glucose and electron acceptors having signi cantly di erent electrochemical mid-point potentials (E m, mv): oxygen (+815); nitrate (+420); ferricyanide (+360); fumarate (+30); and none (3412, endogenous acetyl). With some exceptions, pdh expression was highest under aerobic conditions, falling with decreasing electron acceptor potential to low levels during fumarate respiration and fermentation, where the complex is probably inactive (Fig. 1b). This suggests that the e ciency of energy generation (and hence nucleotide recycling) in uences pdh expression. Expres-

4 328 B. Cassey et al. / FEMS Microbiology Letters 159 (1998) 325^329 sion of the pdh operon was generally higher in the 1 lip strain, particularly during nitrate respiration, where expression in this strain greatly exceeded that observed under any other condition. During nitrate respiration the PDH complex and pyruvate formate-lyase are both active, but at sub-maximal levels [3]. Presumably, the 1 lip-pdh complex has to be expressed at greatly elevated levels in order to meet the required carbon ux to acetyl-coa. During fermentation, the pdh operon was still expressed (Fig. 1b). This is consistent with the lower but continued synthesis of PDH complex subunits during fermentative growth [12] E ects of ph on pdh expression The e ects of ph were examined using controlled batch cultures growing with glucose at ph 6, 7, and 8 (Fig. 1c). Expression of the pdh operon increased as the ph diverged from the optimum value, and the e ects were again more apparent in the 1 lip strain. The intracellular NADH/NAD ratios of glucoselimited cultures of JRG2933 (3 lip non-lysogenic parental strain) increased as the environmental ph increased from 6.0 to 8.0 (Fig. 1e). A similar trend has been observed with anaerobic cultures of Enterococcus faecalis [9]. The current studies with pdh-lacz reporters show that pdh expression is modulated (in vivo) in response to the environment. The results, which re ect changes in transcription and translation rather than enzymatic activity, indicate that pdh expression is higher in the 1 lip strain than in the 3 lip strain under all conditions except fumarate respiration and fermentation (where the PDH complex is not essential). Presumably, pdh expression could be increased in the 1 lip strain, via pyruvate induction, in an attempt to compensate for the lower e ciency of carbon ux through the modi ed PDH complex [7]. Also, in the wild-type strain, it would appear that pdh expression is repressed under conditions of NADH (and acetyl-coa/acetyl phosphate) accumulation. This could be mediated by ArcA, which represses in response to such stimuli, or via a potentiation of PdhR-mediated repression by the same stimuli. The role of ArcA in regulating PDH complex synthesis is uncertain because although anaerobic PDH complex activity is increased 1.7-fold (back to the aerobic level) in an arca mutant [13], the pdh promoter appears not to be repressed by ArcA in studies with lacz fusions [1]. Acknowledgments This work was supported by a project grant and studentship from the Biotechnology Directorate of the Biotechnology and Biological Sciences Research Council. References [1] Quail, M.A., Haydon, D.J. and Guest, J.R. (1994) The pdhraceef-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol. Microbiol. 12, 95^104. [2] Guest, J.R., Quail, M.A., Daveè, E., Cassey, B. and Attwood, M.M. (1996) Regulatory and other aspects of pyruvate dehydrogenase complex synthesis in Escherichia coli. In: Biochemistry and Physiology of Thiamin Diphosphate Enzymes (Bisswanger, H. and Schellenberger, A., Eds.), pp. 326^333. Intemann, Prien. [3] Kaiser, M. and Sawers, G. (1994) Pyruvate formate-lyase is not essential for nitrate respiration by Escherichia coli. FEMS Microbiol. Lett. 117, 163^168. [4] Quail, M.A. and Guest, J.R. (1995) Puri cation, characterisation and mode of action of PdhR, the transcriptional repressor of the pdhr-aceef-lpd operon of Escherichia coli. Mol. Microbiol. 15, 519^529. [5] Schwartz, E.R. and Reed, L.J. (1970) Regulation and the activity of the pyruvate dehydrogenase complex of Escherichia coli. Biochemistry 9, 1434^1439. [6] Snoep, J.L., de Graef, M.R., Westphal, A.H., de Kok, A., Teixeria de Mattos, M.J. and Neijssel, O.M. (1993) Di erences in sensitivity to NADH of puri ed pyruvate dehydrogenase complexes of Enterococcus faecalis, Lactococcus lactis, Azotobacter vinelandii and Escherichia coli: implications for their activity in vivo. FEMS Microbiol. Lett. 81, 63^66. [7] Daveè, E., Guest, J.R. and Attwood, M.A. (1995) Metabolic engineering in Escherichia coli: lowering the lipoyl domain content of the pyruvate dehydrogenase complex adversely a ects the growth rate and yield. Microbiology 141, 1838^ [8] Phillips-Jones, M.K., Watson, F.J. and Martin, R. (1993) The 3P codon e ect on UAG suppressor trna is di erent in Escherichia coli and human cells. J. Mol. Biol. 233, 1^6. [9] Snoep, J.L., Teixeira de Mattos, M.J., Postma, P.W. and Neijssel, O.M. (1990) Involvement of pyruvate dehydrogenase in product formation in pyruvate-limited anaerobic chemostat cultures of Enterococcus faecalis NCTC 775. Arch. Microbiol. 154, 50^55. [10] Leonardo, M.R., Dailly, Y. and Clark, D.P. (1996) Role of

5 B. Cassey et al. / FEMS Microbiology Letters 159 (1998) 325^ NAD in regulating the adhe gene of Escherichia coli. J. Bacteriol. 178, 6013^6018. [11] Hemp ing, W.P. and Mainzer, S.E. (1975) E ects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture. J. Bacteriol. 123, 1076^1087. [12] Smith, M.W. and Neidhardt, F.C. (1983) 2-oxoacid dehydrogenase complexes of Escherichia coli: cellular amounts and patterns of synthesis. J. Bacteriol. 156, 81^88. [13] Iuchi, S. and Lin, E.C.C. (1988) arca(dye): a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. USA 85, 1888^ 1892.