An Adaptation To Life In Acid Through A Novel Mevalonate Pathway

Vinokur, J.M.; Cummins, Matthew C.; Korman, Tyler P.; Bowie, James U.

doi:10.1038/srep39737

Cited by 36 publications

(53 citation statements)

References 41 publications

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“…MVA3P is then phosphorylated by a non-GHMP family kinase, MVA3P 5kinase, to form mevalonate 3,5-bisphosphate. The decarboxylation of the intermediate is catalyzed by another DMD homolog, bisphosphomevalonate decarboxylase (BMD), to yield IP (14). Interestingly, BMD does not require ATP to react, which suggests that the two functions of DMD (or PMD), phosphorylation and decarboxylation, were separately inherited by M3K and BMD, respectively.…”

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confidence: 99%

Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans -anhydromevalonate 5-phosphate

Hayakawa

Motoyama

Sobue

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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The modified mevalonate pathway is believed to be the upstream biosynthetic route for isoprenoids in general archaea. The partially identified pathway has been proposed to explain a mystery surrounding the lack of phosphomevalonate kinase and diphosphomevalonate decarboxylase by the discovery of a conserved enzyme, isopentenyl phosphate kinase. Phosphomevalonate decarboxylase was considered to be the missing link that would fill the vacancy in the pathway between mevalonate 5-phosphate and isopentenyl phosphate. This enzyme was recently discovered from haloarchaea and certain Chroloflexi bacteria, but their enzymes are close homologs of diphosphomevalonate decarboxylase, which are absent in most archaea. In this study, we used comparative genomic analysis to find two enzymes from a hyperthermophilic archaeon, , that can replace phosphomevalonate decarboxylase. One enzyme, which has been annotated as putative aconitase, catalyzes the dehydration of mevalonate 5-phosphate to form a previously unknown intermediate,-anhydromevalonate 5-phosphate. Then, another enzyme belonging to the UbiD-decarboxylase family, which likely requires a UbiX-like partner, converts the intermediate into isopentenyl phosphate. Their activities were confirmed by in vitro assay with recombinant enzymes and were also detected in cell-free extract from These data distinguish the modified mevalonate pathway of and likely, of the majority of archaea from all known mevalonate pathways, such as the eukaryote-type classical pathway, the haloarchaea-type modified pathway, and another modified pathway recently discovered from .

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confidence: 99%

Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans -anhydromevalonate 5-phosphate

Hayakawa

Motoyama

Sobue

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…[U- 13 C]MVA was prepared as described elsewhere (20). For the cloning of pto0478 encoding PtBMD, a pET28a(ϩ) plasmid containing the PtBMD gene (12), which was donated by J. M. Vinokur and J. R. Bowie, University of California, Los Angeles, was used as a template DNA. pJBEI-2999 plasmid was purchased from Addgene (Watertown, MA).…”

Section: Methodsmentioning

confidence: 99%

“…Although the M3K, M3P5K, and IPK genes are derived from T. acidophilum, various BMD genes have been utilized for plasmid construction. Based on the first report on BMD by Vinokur et al (12), P. torridus BMD, putative full-length T. acidophilum BMD, and truncated T. acidophilum BMD that starts from the Met30 residue were used to construct pBAD-TacM(PtBMD), pBAD-TacM(TaBMDfull), and pBAD-TacM(TaBMDtrunc), respectively. E. coli harboring pACYC-IBEidi was transformed with pBAD-ScMPD, pBAD-TacM(PtBMD), pBAD-TacM(TaBMDfull), and pBAD-TacM (TaBMDtrunc) to construct the strains ScMPD, TacM(PtBMD), TacM(TaBMDfull), and TacM(TaBMDtrunc), respectively ( Table 2).…”

Section: Mutation Analysis Of Tacm3kmentioning

confidence: 99%

“…Intriguingly, M3K is also homologous to DMD. After the formation of MVA-3-P, another kinase, MVA-3-P 5-kinase (M3P5K), catalyzes its 5-phosphorylation (10), and a subsequent decarboxylation is catalyzed by another DMD homolog, 3,5-bisphosphomevalonate decarboxylase (BMD), to give isopentenyl phosphate (IP) (12). IP is then phosphorylated by IPK to yield IPP (13,14).…”

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confidence: 99%

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Conversion of Mevalonate 3-Kinase into 5-Phosphomevalonate 3-Kinase by Single Amino Acid Mutations

Motoyama

Sobue

Kawaide

et al. 2019

Appl Environ Microbiol

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Mevalonate 3-kinase plays a key role in a recently discovered modified mevalonate pathway specific to thermophilic archaea of the order Thermoplasmatales. The enzyme is homologous to diphosphomevalonate decarboxylase, which is involved in the widely distributed classical mevalonate pathway, and to phosphomevalonate decarboxylase, which is possessed by halophilic archaea and some Chloroflexi bacteria. Mevalonate 3-kinase catalyzes the ATP-dependent 3-phosphorylation of mevalonate but does not catalyze the subsequent decarboxylation as related decarboxylases do. In this study, a substrate-interacting glutamate residue of Thermoplasma acidophilum mevalonate 3-kinase was replaced by smaller amino acids, including its counterparts in diphosphomevalonate decarboxylase and phosphomevalonate decarboxylase, with the aim of altering substrate specificity. These single amino acid mutations resulted in the conversion of mevalonate 3-kinase into 5-phosphomevalonate 3-kinase, which can synthesize 3,5-bisphosphomevalonate from 5-phosphomevalonate. The mutants catalyzing the hitherto undiscovered reaction enabled the construction of an artificial mevalonate pathway in Escherichia coli cells, as was demonstrated by the accumulation of lycopene, a red carotenoid pigment. IMPORTANCE Isoprenoid is the largest family of natural compounds, including important bioactive molecules such as vitamins, hormones, and natural medicines. The mevalonate pathway is a target for metabolic engineering because it supplies precursors for isoprenoid biosynthesis. Mevalonate 3-kinase is an enzyme involved in the modified mevalonate pathway specific to limited species of thermophilic archaea. Replacement of a single amino acid residue in the active site of the enzyme changed its substrate preference and allowed the mutant enzymes to catalyze a previously undiscovered reaction. Using the genes encoding the mutant enzymes and other archaeal enzymes, we constructed an artificial mevalonate pathway, which can produce the precursor of isoprenoid through an unexplored route, in bacterial cells.

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“…Next, IP is phosphorylated by isopentenyl phosphate kinase (EC 2.7.4.46) to form IPP (Vannice et al, 2013;Dellas et al, 2013). A second modified MVA pathway was identified in Thermoplasma acidophilium (Vinokur et al, 2016(Vinokur et al, , 2014Azami et al, 2014) and is thought to exist in a select group of extreme acidophiles belonging to the order Thermoplasmatales, which also includes T. volcanium. In this pathway, mevalonate is phosphorylated by mevalonate 3-kinase (EC 2.7.1.185) to form mevalonate 3-phosphate, and two separate enzymes then catalyze the phosphorylation of the 5-OH group by ATP (mevalonate 3-phosphate 5-kinase; EC 2.7.1.186) and the decarboxylation (mevalonate 3,5-bisphosphate decarboxylase; EC 4.1.1.110) to form IP ( Fig.…”

Section: Introductionmentioning

confidence: 99%

Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota

Blank

Barnett

Ronnebaum

et al. 2020

Acta Crystallogr D Struct Biol

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Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix 5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.

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An Adaptation To Life In Acid Through A Novel Mevalonate Pathway

Cited by 36 publications

References 41 publications

Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans -anhydromevalonate 5-phosphate

Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans -anhydromevalonate 5-phosphate

Conversion of Mevalonate 3-Kinase into 5-Phosphomevalonate 3-Kinase by Single Amino Acid Mutations

Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota

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