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A 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase Catalyzing The Proc. Natl. Acad. Sci. USA Vol. 95, pp. 9879–9884, August 1998 Biochemistry A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis SHUNJI TAKAHASHI*, TOMOHISA KUZUYAMA*, HIROYUKI WATANABE, AND HARUO SETO† Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan Communicated by Christopher T. Walsh, Harvard Medical School, Boston, MA, June 22, 1998 (received for review May 15, 1998) ABSTRACT Several eubacteria including Esherichia coli 3-phosphate (Fig. 1A). In the second step the intramolecular use an alternative nonmevalonate pathway for the biosynthe- rearrangement of DXP is assumed to give a hypothetical sis of isopentenyl diphosphate instead of the ubiquitous rearrangement intermediate 2-C-methylerythrose 4-phos- mevalonate pathway. In the alternative pathway, 2-C-methyl- phate, which is then converted to 2-C-methyl-D-erythritol D-erythritol or its 4-phosphate, which is proposed to be 4-phosphate (MEP) by an unspecified reduction process (7). formed from 1-deoxy-D-xylulose 5-phosphate via intramolec- Thus, precise details about the reductive mechanism for the ular rearrangement followed by reduction process, is one of formation of MEP remained to be unclear. the biosynthetic precursors of isopentenyl diphosphate. To A precedent for this biosynthetic rearrangement reaction is clone the gene(s) responsible for synthesis of 2-C-methyl-D- found in the biosynthesis of valine, isoleucine, and leucine. The erythritol 4-phosphate, we prepared and selected E. coli enzyme involved in this reaction ketol acid reductoisomerase mutants with an obligatory requirement for 2-C-methyleryth- (EC1.1.1.86) catalyzes rearrangement of 2-acetolactate to ritol for growth and survival. All the DNA fragments that yield 2,3-dihydroxyisovalerate with simultaneous reduction in complemented the defect in synthesizing 2-C-methyl-D- the presence of NADPH (Fig. 1B) (14–17). It should be noted erythritol 4-phosphate of these mutants contained the yaeM that a hypothetical compound with a keto function corre- gene, which is located at 4.2 min on the chromosomal map of sponding to 2-C-methylerythrose 4-phosphate had been ex- E. coli. The gene product showed significant homologies to cluded as a possible reaction product intermediate because of hypothetical proteins with unknown functions present in its inhibitory action on this reaction (15). By analogy with the Haemophilus influenzae, Synechocystis sp. PCC6803, Mycobac- reaction by ketol acid reductoisomerase, MEP could be syn- terium tuberculosis, Helicobacter pyroli, and Bacillus subtilis. The thesized by rearrangement and reduction of DXP in a single purified recombinant yaeM gene product was overexpressed in step. Therefore, we initially considered the possibility that E. coli and found to catalyze the formation of 2-C-methyl-D- MEP might be synthesized from DXP by the same reaction erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate mechanism used by ketol acid reductoisomerase. If the as- in the presence of NADPH. Replacement of NADPH with sumption were correct, an enzyme for synthesizing MEP from NADH decreased the reaction rate to about 1% of the original DXP might have sequence similarity to ketol acid reductoi- 1 1 1 rate. The enzyme required Mn2 ,Co2 ,orMg2 as well. These somerase. However, we were unable to find other proteins data clearly show that the yaeM gene encodes an enzyme, homologous to ketol acid reductoisomerase in the total ge- designated 1-deoxy-D-xylulose 5-phosphate reductoisomerase, nome sequence of Escherichia coli (18). This result suggested that synthesizes 2-C-methyl-D-erythritol 4-phosphate from that MEP may be synthesized in a different reaction mecha- 1-deoxy-D-xylulose 5-phosphate, in a single step by intramo- nism from that of ketol acid reductoisomerase. Therefore, no lecular rearrangement and reduction and that this gene is information about the enzyme(s) for MEP formation has been responsible for terpenoid biosynthesis in E. coli. obtained from our knowledge on ketol acid reductoisomerase. DXP is a biosynthetic intermediate not only of IPP but also Isoprenoids play important roles in all living organisms such as of thiamine and pyridoxol in E. coli (19–21). Therefore, the steroid hormones in mammals, carotenoids in plants, and synthesis of MEP from DXP seems to be the committed step ubiquinone or menaquinone in bacteria (1). Since the initial in IPP formation (Fig. 1A). This speculation has led us to the discovery of the mevalonate pathway in the 1950s, it was widely idea that auxotrophic mutants requiring MEP for growth and accepted that isopentenyl diphosphate (IPP), the fundamental survival should be promising hosts for the cloning of the gene unit in terpenoid biosynthesis, was only formed by condensa- responsible for synthesis of MEP, because such mutants would tion of acetyl CoA through the ubiquitous mevalonate path- possess a metabolic block(s) between DXP and MEP. To way. However, it has been disclosed recently that many organ- obtain such mutants, we used 2-C-methylerythritol (ME), the isms including several bacteria, green algae, and chloroplasts free alcohol of MEP, in place of MEP to overcome the of higher plants use an alternative mevalonate-independent problem associated with uptake of phosphorylated compounds pathway (nonmevalonate pathway) for the formation of IPP into cells. Fortunately, ME is used by E. coli in the place of (2–9). Several recent experimental findings lend additional MEP (7). As an additional advantage, this strategy enabled us supports to the operation of this pathway in terpenoid biosyn- to avoid somewhat tedious procedures for preparation of the thesis (10–13). phosphate ester MEP. With chemically synthesized ME (7) in According to Rohmer and coworkers (4, 9), the initial step hand, we tried to isolate the mutants that could grow on a of this pathway is the formation of 1-deoxy-D-xylulose 4-phos- phate (DXP) by condensation of pyruvate and glyceraldehyde Abbreviations: IPP, isopentenyl diphosphate; DX, 1-deoxyxylulose; DXP, 1-deoxy-D-xylulose 5-phosphate; ME, 2-C-methylerythritol; The publication costs of this article were defrayed in part by page charge MEP, 2-C-methyl-D-erythritol 4-phosphate. Data deposition: The sequence reported in this paper has been payment. This article must therefore be hereby marked ‘‘advertisement’’ in deposited in the GenBank database (accession no. AB013300). accordance with 18 U.S.C. §1734 solely to indicate this fact. *S.T. and T.K. contributed equally to this work. © 1998 by The National Academy of Sciences 0027-8424y98y959879-6$2.00y0 †To whom reprint requests should be addressed. e-mail: c00402@ PNAS is available online at www.pnas.org. simail.ne.jp. 9879 Downloaded by guest on September 25, 2021 9880 Biochemistry: Takahashi et al. Proc. Natl. Acad. Sci. USA 95 (1998) FIG. 1. Hypothetical alternative nonmevalonate pathway for IPP biosynthesis (A) and ketol acid reductoisomerase reaction (B). minimal medium containing ME but not in the absence of ME. genomic library of E. coli W3110 for cloning a gene(s) respon- Such mutants should not be able to synthesize MEP and, sible for synthesizing MEP. The mutants described above were hence, should be unable to grow on the minimal medium that transformed with the genomic library, and then ampicillin- lacks ME. resistant transformants were selected on Luria–Bertani (LB) We show in this study that the yaeM gene (GenBank (24) plates without ME. Plasmids, designated pMEW41, 73, accession no. AE000126.) at 4.2 min on the E. coli chromosome 106, and 112 (see Fig. 3), were extracted from these transfor- complemented the IPP biosynthesis coding region of all the mants and sequenced as described bellow. isolated mutants. We also demonstrate that the yaeM gene DNA Sequence Analysis. DNA sequence was determined by product, designated DXP reductoisomerase, catalyzes in- the dideoxynucleotide chain-termination method (27) with an tramolecular rearrangement and reduction of DXP to form automated sequencer (Li-cor, model 4000L) and the protocol MEP in a single step. Preliminary results of this work have of the supplier. A homology search with protein databases was been reported (22). performed by the FASTA program (28, 29). Construction of the Plasmid for Overexpression of the yaeM MATERIALS AND METHODS Gene. On the basis of the entire nucleotide sequence of the yaeM gene from E. coli W3110, two oligonucleotide primers, Bacterial Strains. The E. coli K-12 strains W3110 (wild- 59-GGGGGATCCAAGCAACTCACCATTCTGGGC-39 (59 type) and JM109 (recA1, endA1, gyrA96, thi, hsdR17, supE44, 9 D y 9 1 q D of the yaeM gene) and 5 -GGGGGATCCGCTTGC- relA1, (lac-proAB) F [traD36, proAB , LacI , lacZ M15]) GAGACGCATCACCTC-39 (39 of the yaeM gene), including (23) were used in this study. W3110 was provided by Hajime BamHI restriction sites (italic) were synthesized (Amersham Tokuda (Institute of Molecular and Cellular Biosciences, Pharmacia). These primers were then used with total DNA University of Tokyo). JM109 was purchased from Takara from W3110 to amplify the yaeM gene. By using Taq DNA Shuzo (Kyoto). polymerase (Boehringer) and the protocol of the supplier, a Mutagenesis of E. coli. W3110 by N-Methyl-N9-nitro-N- 1,209-bp fragment for the yaeM gene was amplified. The PCR nitrosoguanidine. N-Methyl-N9-nitro-N-nitrosoguanidine fragment was cleaved with BamHI and cloned into pUC118 (Nacalai Tesque, Kyoto) was used as a mutagen to obtain mutants defective in biosynthesis of MEP. N-Methyl-N9-nitro- (Takara). Strain JM109 was used as a recipient in this trans- N-nitrosoguanidine-treated W3110 cells were grown on M9 formation. Clones were analyzed for the correct insert by DNA plates (24) containing 0.1% ME, which was chemically syn- sequencing as described above. The correct fragment was thesized as reported (7). Agarose (ultra PURE, GIBCOy cloned into the multicloning site (BamHI) of the expression BRL) was used for preparation of M9 plates.
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