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Journal of Bacteriology, March 2002, p. 1571-1577, Vol. 184, No. 6
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.6.1571-1577.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Renata Dziak,2 Guo-Qin Cai,1,
and Trevor C. Charles1,2*
Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9 ,1 Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada2
Received 11 September 2001/ Accepted 4 December 2001
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Degradation of PHB is initiated by the depolymerization of the PHB granules, catalyzed by PHB depolymerase. A central enzyme in the PHB cycle is D-(-)-3-hydroxybutyrate dehydrogenase (BDH; EC 1.1.1.30; encoded by bdhA), which catalyzes the oxidation of the immediate PHB depolymerization product D-(-)-3-hydroxybutyrate (DHB) to acetoacetate (AA). The AA product of this reaction is activated to acetoacetyl-CoA by the enzyme acetoacetyl-CoA synthetase (AACS; EC 6.2.1.16), encoded by acsA2 in Sinorhizobium meliloti (5, 7, 15). The final step in the degradation portion of the PHB cycle yields two molecules of acetyl-CoA from one molecule of acetoacetyl-CoA via ketothiolase (EC 2.3.1.9). S. meliloti acsA2 mutants are able to grow with acetate as a carbon source but not with AA; acsA1 (7, 15) mutants, which do not produce acetyl-CoA synthetase (EC 6.2.1.1), are unable to grow on acetate but are able to grow on AA (20). While wild-type S. meliloti is able to grow using either DHB or AA, it is unable to use L-(+)-3-hydroxybutyrate (LHB) as a sole source of carbon.
Although there is a considerable body of research on the biochemistry and genetics of bacterial PHB synthesis, apart from our recent studies on the PHB degradation pathway of S. meliloti (1, 5, 8), not much is known about the genetics of the bacterial PHB degradation pathway(s) or assimilation of 3-hydroxybutyrate (3-HB). Our studies of the PHB cycle have included the isolation and characterization of transposon Tn5 insertion mutants that show altered growth on minimal media containing DL-3-hydroxybutyrate (DLHB) and/or AA as a sole carbon source (8). To ensure that these mutants had lesions specific to the PHB degradation pathway, we screened for mutants that were unaffected in the ability to utilize acetate and glucose (8). This screening protocol resulted in the initial isolation and characterization of bdhA and acsA2 mutants.
In addition to the mutants that were unable to grow on 3-HB and AA, we also isolated a mutant that exhibited an enhanced growth rate on these carbon sources (8). The Tn5 insertion in this mutant was found to be closely linked in
M12 transduction to the acsA2 gene. The Age (for AA growth-enhanced) phenotype was postulated to be due to a regulatory mutation that specifically alters growth on the PHB degradation pathway intermediates 3-HB and AA, since growth on glucose or acetate remained unaffected. In this report, we show that spontaneous mutations that restore growth of the bdhA mutant on DLHB minimal medium, without restoration of BDH activity, are tightly linked to the age mutation previously reported. We also offer evidence that the apparent suppression phenotype is a consequence of elevated AcsA2 levels, is specific for utilization of LHB but not DHB, and is in fact due to appearance of an L-(+)-3-hydroxybutyryl-CoA synthetase (LHBCS)-dependent pathway for utilization of LHB.
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TABLE 1. Strains, plasmids, and transposons used in this study
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Genetics and molecular biology.
Bacterial conjugation,
M12 transductions, construction of a Tn5-233 random insertion bank in Rm1021, homogenotizations, and transposon replacements were carried out as described previously (10, 12, 13). Standard methods were used for DNA manipulations (2).
Enzyme assays. Preparation of cell extracts, protein determination, and assays for BDH activity (NADH formation) and for AACS and acetyl-CoA synthetase activities (acetyl-CoA formation coupled to reduction of NAD+ via malate dehydrogenase and citrate synthase) were carried out as described previously (5, 8). NADH formation was measured using an Ultrospec 2000 spectrophotometer (Amersham Pharmacia Biotech, Baie d'Urfé, Canada). For an assay of AACS activity of purified protein samples, a sonicated cell extract (20 µl of an 11-mg/ml sample) from a culture of TY-grown strain Rm11364 (an acsA1 acsA2 double mutant) was added as a source of thiolase to convert acetoacetyl-CoA to acetyl-CoA; the amount of acetyl-CoA production was then determined in the assay. LHBCS activity was assayed by coupling the reaction to L-3-hydroxyacyl-CoA dehydrogenase. The reaction mixture (1 ml) contained LHB (varying amounts for kinetic studies with purified protein; 22 µmol for assay of crude extracts), Tris-Cl (200 µmol; pH 8.4), MgCl2 (10 µmol), NAD (10 µmol), CoA (0.2 µmol), L-3-hydroxyacyl-CoA dehydrogenase (8 U, from bovine liver [Sigma-Aldrich]), KCl (100 µmol), ATP (20 µmol), and cell extract or purified protein. The reaction was initiated by addition of ATP. The rate of NADH formation was monitored at 340 nm.
Overexpression of acsA2 and purification of AcsA2. The Novagen (Madison, Wis.) pET30 Xa/LIC (ligation-independent cloning) kit was used. Primers contained vector-compatible overhangs (underlined) and were designed according to the coding sequence of acsA2 (acsA2licfor, 5'-GGTATTGAGGGTCGCCAAGCAGAACGACCTTTGT-3'; acsA2licrev, 5'-AGAGGAGAGTTAGAGCCAGCCGGCACTACGACA-3') and synthesized by Sigma-Aldrich. The PCR mixture contained 3 µl of 25 mM MgCl2, 5 µl of 10x Tli DNA polymerase reaction buffer (Promega, Madison, Wis.), 1 µl of 10 mM deoxynucleoside triphosphate mix, 2.5 µl of each primer (10 pmol/µl), 2.5 U of Tli proofreading polymerase (Promega), 0.2 µg of RCR2011 genomic DNA as the template, and deionized H2O to make up the final volume to 50 µl. Reactions were carried out in an Eppendorf Mastercycler Gradient thermocycler (Brinkmann Instruments, Mississauga, Canada) using a hot-start amplification protocol (94°C for 2 min; 30 cycles of denaturation at 94°C for 30 s, annealing at 55°C for 30 s, and extension at 72°C for 150 s, followed by a final extension at 72°C for 10 min). The single PCR product obtained was purified using the QIAquick PCR purification kit (Qiagen, Mississauga, Canada), followed by extraction with 1 volume of chloroform-isoamyl alcohol (24:1). The purified PCR product was cloned into pET-30 Xa/LIC using T4 DNA polymerase according to the manufacturer's instructions. Escherichia coli NovaBlue competent cells were transformed with the reaction mixture, and kanamycin-resistant cells containing the desired recombinant plasmid, pRD112, were thus obtained.
Plasmid pRD112 was transferred into expression strain E. coli BL21(DE3)pLysS, and a 5-ml volume of a saturated LB-chloramphenicol-kanamycin culture was used to inoculate a 2.8-liter Fernbach flask containing 500 ml of LB-chloramphenicol-kanamycin. Growth under noninducing conditions was carried out at 37°C with shaking at 200 rpm for 2 h, after which isopropyl-ß-D-thiogalactopyranoside (IPTG) was added to a final concentration of 1 mM, and cells were incubated for another 3 h. Cells were lysed using Bugbuster plus Benzonase (Novagen). Insoluble cell debris was removed by centrifugation, the resulting extract (ca. 8 ml) was applied to a His·Bind resin column (Novagen) with a 1-ml column bed, and 1-ml eluted fractions were collected. Purified protein was visualized as a single band of ca. 72 kDa, and the remaining protein preparation was stored at -70°C in elution buffer containing 50% glycerol.
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FIG. 1. Growth kinetics of the wild-type strain and representative mutants on different carbon sources. Strains used were Rm1021 (wild type) ( ), Rm11172 (age-1::Tn5-Tp) ( ), Rm11107 (bdhA1::Tn5) (), and Rm11281 (bdhA1::Tn5 age-1::Tn5-Tp) ( ). Carbon sources used were 10 mM glucose(A), 30 mM acetate (B), 15 mM AA (C), and 15 mM DLHB (D).
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TABLE 2. Enzyme activities of cell extracts of DLHB-grown culturesa
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To facilitate further characterization of the spontaneous mutations, a selectable genetic marker was linked to them. A
M12 transducing lysate was prepared on a pool of Tn5-233 (Gmr-Spr) insertion mutants. The Tn5-233 insertions were transduced into the second-site mutants Rm11192, Rm11196, and Rm11198, and the resulting Gmr-Spr transductants were screened by replica plating for inability to grow on DLHB, indicating cotransduction of the Tn5-233 insertion with the wild-type allele counterpart of the second-site mutation. Tn5-233 insertions linked to the second-site alleles were thus isolated. Strains Rm11218, Rm11219, and Rm11223 each carry a Tn5-233 insertion linked to the second-site allele in Rm11192 (shb-1), Rm11196 (shb-3), and Rm11198 (shb-4), respectively.
The cotransduction linkage of the Tn5-233 insertions and the second-site alleles was determined by two-factor transduction analysis. In separate backcrosses, each of the linked Tn5-233 insertions was transduced into the corresponding original suppressor strain. The resulting Gmr-Spr transductants were tested for inability to utilize DLHB. This provided a measurement of the cotransduction frequency of the wild-type counterpart of the suppressor alleles and each linked Tn5-233 insertion (Fig. 2). One of the linked Tn5-233 insertions,
218::Tn5-233, was transduced into each of the independently isolated suppressor strains, and similar linkages to each suppressor allele were found, suggesting that all of the suppressor alleles map to the same locus. The
218::Tn5-233 insertion was also found to have a similar linkage to the age-1::Tn5 insertion, suggesting that the spontaneous suppressor alleles are located near the age-1 locus on the S. meliloti chromosome and that the mechanisms of DLHB suppression in the spontaneous suppressor strains and the age-1 strain are likely similar. Furthermore, the cell extracts of the suppressor strain Rm11192 did not possess BDH activity (Table 2).
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FIG. 2. Genetic map of the S. meliloti chromosome, showing the locations of the acsA2 gene, required for utilization of AA, and age-1, an insertion in which results in an increased growth rate on AA and HB. Arrows indicate positions and orientations of Tn5-mob insertions. The positions of the auxotrophic markers are from the genetic map of the chromosome (17). The positions of the mapped loci are approximate and are based on conjugation and transduction linkage data (8). The relative order of the Tn5-233 insertions and the suppressor alleles depicted is arbitrary. Cotransduction frequencies are given as percentages below the arrows. The tail of each arrow indicates the donor marker and the head represents the recipient in transduction.
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FIG. 3. Growth kinetics of Rm1021 (wild type) and Rm11107 (bdhA1::Tn5) containing multiple copies of acsA2 (pGQ105) or parent vector plasmid (pSP329) on different carbon sources. Strains used were Rm1021(pSP329) ( ), Rm1021(pGQ105) ( ), Rm11107(pSP329) (), and Rm11107(pGQ105) ( ). Carbon sources were 10 mM glucose (A), 30 mM acetate (B), 15 mM AA (C), 15 mM DLHB (D), 15 mM DHB (E), and 15 mM LHB (F).
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Ability to grow on LHB upon provision of multiple acsA2 copies suggested that the AcsA2 enzyme either is directly involved in assimilation of LHB by utilizing LHB as an alternative substrate or may act indirectly by influencing the expression of a latent LHBCS-encoding gene or enzyme activity. To test this, we developed an assay for LHBCS activity based on the coupling of LHB activation to the enzyme L-3-hydroxyacyl-CoA dehydrogenase (see Materials and Methods) and used the assay to measure the levels of LHBCS-specific activity in the mutant and acsA2-overexpressing strains (Table 2). While LHBCS was not detectable in the wild-type strain, it was clearly present in extracts from strains that were able to utilize LHB and exhibited enhanced AACS activity. The LHB utilization property is therefore directly related to the introduction of LHBCS enzyme activity resulting from increased expression of acsA2.
Substrate specificity of purified AcsA2 protein. To test whether the LHBCS enzyme activity detected above was directly due to AcsA2, we carried out enzyme assays with a purified AcsA2 protein preparation. The purified His-tagged AcsA2 protein was active with either AA (i.e., AACS activity) or LHB (i.e., LHBCS activity) as the substrate, but no activity was detected with acetate as the substrate. No AACS activity was detected when the assay was carried out in the absence of the thiolase activity provided by addition of the Rm11364 cell extract. The apparent Km and Vmax for AA were 0.30 ± 0.05 mM and 479 ± 12 nmol/min/mg, respectively, compared to 20 ± 3 mM and 259 ± 12 nmol/min/mg for LHB. This further confirms that the LHBCS activity in S. meliloti cells that overexpress acsA2 is directly due to the increased levels of AcsA2.
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There are several possible metabolic fates for LHB following activation to LHB-CoA. It could be further metabolized by 3-hydroxyacyl-CoA dehydrogenase, yielding acetoacetyl-CoA, or by 3-hydroxybutyryl-CoA epimerase, yielding DHB-CoA. Both of these enzyme activities are predicted to be encoded by the fadB gene (23) that is present in the S. meliloti genome (7, 15). The genome sequence also predicts at least three additional genes encoding 3-hydroxybutyryl-CoA dehydrogenase. Whether either or both of these possible pathways are used during growth on LHB could be tested by mutational analysis of these genes in S. meliloti.
Is LHB a naturally utilized carbon source for wild-type S. meliloti? We have clearly demonstrated that the organism has the genetic capacity to utilize LHB as a carbon source. Simple up-regulation of the gene expression, without alteration of the coding sequence, was sufficient to confer LHB activation ability on the organism. We have also shown that presence of LHB inhibits the ability to utilize DHB as a carbon source (Fig. 3D and E). The inability of the wild-type cell to utilize LHB is perhaps due to the lack of acsA2 gene expression induction, or even its inhibition, by exogenous LHB. When the cell is utilizing AA generated from the oxidation of DHB under carbon-limiting conditions, the ability to utilize exogenous LHB could perhaps be deleterious to the maintenance of the PHB degradation process. This might explain why wild-type S. meliloti preferentially utilizes DHB over LHB. It is conceivable, however, that under certain environmental and/or physiological conditions, expression of the acsA2 gene is sufficiently induced by intracellular metabolites and/or by other extracellular environmental signals to result in significant levels of LHB activation.
Tli polymerase was a generous gift of VWR Canlab.
Present address: Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada. ![]()
Present address: BASF Corporation Consumer Products & Life Science Division, Agricultural Products Center, Research Triangle Park, NC 27709. ![]()
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3-cis-
2-trans-enoyl-CoA isomerase, and enoyl-CoA hydratase in addition to 3-hydroxyacyl-CoA dehydrogenase. J. Bacteriol. 170:2543-2548.
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