The Thiamine Biosynthetic Enzyme ThiC Catalyzes Multiple Turnovers and Is Inhibited by S-Adenosylmethionine (AdoMet) Metabolites

Palmer, Lauren D.; Downs, Diana M.

doi:10.1074/jbc.m113.500280

Cited by 45 publications

(46 citation statements)

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“…The ThiC reaction has been reconstituted in vitro and is not affected by AICAR, indicating the effect in vivo was indirect (26). The present study was initiated to determine the mechanism by which AICAR accumulation inhibits the conversion of AIR to HMP.…”

Section: Discussionmentioning

confidence: 99%

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Amino-4-Imidazolecarboxamide Ribotide Directly Inhibits Coenzyme A Biosynthesis in Salmonella enterica

Bazurto

Downs

2014

J Bacteriol

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Historically, cellular metabolism has been described in the context of discrete metabolic units (e.g., biosynthetic or degradative pathways), a perspective that facilitated efforts to understand metabolic components such as enzymes and metabolites. In reality, these units are integrated to form a complex metabolic network whose connectivity is mediated extensively by metabolites. Under appropriate circumstances (i.e., growth conditions or strain background), dynamic changes of intracellular metabolite levels can have significant impacts on cellular fitness, by providing unexpected mechanisms for survival (1, 2) or compromising growth. Dissecting metabolic integration in bacteria and understanding the diverse roles of metabolites can reveal paradigms that are conserved across phylogenetic kingdoms. Defining these paradigms provides insights into the consequences of perturbing the metabolic network that can be exploited for desired outcomes.

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Section: Discussionmentioning

confidence: 99%

“…AIR is converted to HMP by the S-adenosylmethionine radical protein ThiC (23,24). In vivo, decreased coenzyme A (CoA) levels result in lowered ThiC activity (14,25) and yet, in vitro, ThiC activity does not require-and is not improved by-the addition of CoA to the reaction (26).…”

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confidence: 99%

Amino-4-Imidazolecarboxamide Ribotide Directly Inhibits Coenzyme A Biosynthesis in Salmonella enterica

Bazurto

Downs

2014

J Bacteriol

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“…The plates were incubated at 37°C for 18 h and assessed for growth. ThiC assay components (ThiC, authentic AIR, and purified SAM) were a gift from L. D. Palmer and were prepared as previously described (19,31). Previous experiments determined that a bioassay with DM7185 reliably detected 1 pmol of HMP (L. D. Palmer, unpublished data).…”

Section: Methodsmentioning

confidence: 99%

“…The accumulation of AICAR is known to affect diverse areas of bacterial metabolism, including adenosine homeostasis (12), gluconeogenesis (13), and symbiosis (14). In S. enterica, AICAR has been shown to indirectly inhibit thiamine synthesis at the ThiC step (15)(16)(17)(18)(19) and directly inhibit pantothenate synthesis at the PanC-catalyzed step (18).…”

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Aminoimidazole Carboxamide Ribotide Exerts Opposing Effects on Thiamine Synthesis in Salmonella enterica

2015

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In Salmonella enterica, the thiamine biosynthetic intermediate 5-aminoimidazole ribotide (AIR) can be synthesized de novo independently of the early purine biosynthetic reactions. This secondary route to AIR synthesis is dependent on (i) 5-amino-4-imidazolecarboxamide ribotide (AICAR) accumulation, (ii) a functional phosphoribosylaminoimidazole-succinocarboxamide (SAICAR) synthetase (PurC; EC 6.3.2.6), and (iii) methionine and lysine in the growth medium. Studies presented here show that AICAR is a direct precursor to AIR in vivo. PurC-dependent conversion of AICAR to AIR was recreated in vitro. Physiological studies showed that exogenous nutrients (e.g., methionine and lysine) antagonize the inhibitory effects of AICAR on the ThiC reaction and decreased the cellular thiamine requirement. Finally, genetic results identified multiple loci that impacted the effect of AICAR on thiamine synthesis and implicated cellular aspartate levels in AICAR-dependent AIR synthesis. Together, the data here clarify the mechanism that allows conditional growth of a strain lacking the first five biosynthetic enzymes, and they provide additional insights into the complexity of the metabolic network and its plasticity. IMPORTANCEIn bacteria, the pyrimidine moiety of thiamine is derived from aminoimidazole ribotide (AIR), an intermediate in purine biosynthesis. A previous study described conditions under which AIR synthesis is independent of purine biosynthesis. This work is an extension of that previous study and describes a new synthetic pathway to thiamine that depends on a novel thiamine precursor and a secondary activity of the biosynthetic enzyme PurC. These findings provide mechanistic details of redundancy in the synthesis of a metabolite that is essential for nucleotide and coenzyme biosynthesis. Metabolic modifications that allow the new pathway to function or enhance it are also described.

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“…The thiamine biosynthesis pathway (TBP) utilizes a set of committed enzymes catalyzing the independent synthesis of 4-amino-5-hydroxy-2-methylpyrimidine (HMP) and 4-methyl-5-␤-hydroxyethylthiazole (HET) moieties and their subsequent phosphorylation and coupling into a single molecule of thiamine phosphate, which is finally phosphorylated to TPP by the ThiL kinase (2). The pyrimidine moiety of thiamine, HMP pyrophosphate (HMP-PP), is synthesized from aminoimidazole ribotide (AIR), an intermediate of the purine biosynthesis pathway, by using HMP phosphate (HMP-P) synthase (ThiC) and HMP-P kinase (ThiD) (3). The HMP-PP synthesis pathway is conserved between Bacteria and Archaea; however, the synthesis of the thiazole moiety of thiamine, HET phosphate (HET-P), is catalyzed by two different biochemical routes (4).…”

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A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea

Rodionov

Leyn

et al. 2017

J Bacteriol

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Thiamine (vitamin B 1 ) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPPresponsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the Crenarchaeota phylum as well as in the Halobacteria and Thermococci classes of the Euryarchaeota. ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by in vitro DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon Metallosphaera yellowstonensis MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition.IMPORTANCE Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B 1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.KEYWORDS Archaea, comparative genomics, regulon reconstruction, thiamine metabolism, transcriptional regulation

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The Thiamine Biosynthetic Enzyme ThiC Catalyzes Multiple Turnovers and Is Inhibited by S-Adenosylmethionine (AdoMet) Metabolites

Cited by 45 publications

References 47 publications

Amino-4-Imidazolecarboxamide Ribotide Directly Inhibits Coenzyme A Biosynthesis in Salmonella enterica

Amino-4-Imidazolecarboxamide Ribotide Directly Inhibits Coenzyme A Biosynthesis in Salmonella enterica

Aminoimidazole Carboxamide Ribotide Exerts Opposing Effects on Thiamine Synthesis in Salmonella enterica

A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea

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