A Second Pathway to Degrade Pyrimidine Nucleic Acid Precursors in Eukaryotes

Andersen, Gorm; Björnberg, Olof; Poláková, Silvia; Pynyaha, Yuriy V.; Rasmussen, Anna Andersson; Møller, Kasper; Hofer, Anders; Moritz, Thomas; Sandrini, Michael; Merico, Annamaria; Compagno, Concetta; Åkerlund, Hans‐Erik; Gojković, Zoran; Piškur, Jure

doi:10.1016/j.jmb.2008.05.029

Cited by 46 publications

(70 citation statements)

References 31 publications

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“…Although the enzyme that initiates the oxidative pathway was originally called uracil oxidase, it is a classical monooxygenase (28). An additional pathway (not shown) has recently been proposed in Saccharomyces kluyveri (1). DMSO.…”

Section: Methodsmentioning

confidence: 99%

“…DMSO. One-dimensional (1D) 13 C spectra were recorded on a Bruker Avance 600-MHz spectrometer equipped with a CPTXI cryoprobe in 4 to 16 h and a Bruker Avance 800-MHz spectrometer equipped with a TXI probe in 24 to 48 h. In all cases, 1 H decoupling was applied during acquisition, and data were zerofilled once before analysis. Spectra recorded in H 2 O were referenced to 4,4-dimethyl-4-silapentane-1 sulfonic acid (DSS; 0 ppm), and samples dissolved in DMSO were referenced to tetramethylsilane (TMS; which replaces the DMSO resonance at 39.5 ppm).…”

Section: Methodsmentioning

confidence: 99%

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The Rut Pathway for Pyrimidine Degradation: Novel Chemistry and Toxicity Problems

Kim

Pelton

Inwood³

et al. 2010

J Bacteriol

103

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The Rut pathway is composed of seven proteins, all of which are required by Escherichia coli K-12 to grow on uracil as the sole nitrogen source. The RutA and RutB proteins are central: no spontaneous suppressors arise in strains lacking them. RutA works in conjunction with a flavin reductase (RutF or a substitute) to catalyze a novel reaction. It directly cleaves the uracil ring between N-3 and C-4 to yield ureidoacrylate, as established by both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. Although ureidoacrylate appears to arise by hydrolysis, the requirements for the reaction and the incorporation of 18 O at C-4 from molecular oxygen indicate otherwise. Mass spectrometry revealed the presence of a small amount of product with the mass of ureidoacrylate peracid in reaction mixtures, and we infer that this is the direct product of RutA. In vitro RutB cleaves ureidoacrylate hydrolytically to release 2 mol of ammonium, malonic semialdehyde, and carbon dioxide. Presumably the direct products are aminoacrylate and carbamate, both of which hydrolyze spontaneously. Together with bioinformatic predictions and published crystal structures, genetic and physiological studies allow us to predict functions for RutC, -D, and -E. In vivo we postulate that RutB hydrolyzes the peracid of ureidoacrylate to yield the peracid of aminoacrylate. We speculate that RutC reduces aminoacrylate peracid to aminoacrylate and RutD increases the rate of spontaneous hydrolysis of aminoacrylate. The function of RutE appears to be the same as that of YdfG, which reduces malonic semialdehyde to 3-hydroxypropionic acid. RutG appears to be a uracil transporter.The rut (pyrimidine utilization) operon of Escherichia coli K-12 contains seven genes (rutA to -G) (31,38). A divergently transcribed gene (rutR) codes for a regulator. The RutR regulator is now known to control not only pyrimidine degradation but also pyrimidine biosynthesis and perhaps a number of other things (44,45). In the presence of uracil, RutR repression of the rut operon is relieved.Superimposed on specific regulation of the rut operon by RutR is general control by nitrogen regulatory protein C (NtrC), indicating that the function of the Rut pathway is to release nitrogen (31, 59). The rut operon was discovered in E. coli K-12 as one of the most highly expressed operons under NtrC control. In vivo it yields 2 mol of utilizable nitrogen per mol of uracil or thymine and 1 mol of 3-hydroxypropionic acid or 2-methyl 3-hydroxypropionic acid, respectively, as a waste product (Fig. 1). Waste products are excreted into the medium. (Lactic acid is 2-hydroxypropionic acid.) Wild-type E. coli K-12 can use uridine as the sole nitrogen source at temperatures up to 22°C but not higher. It is chemotactic to pyrimidine bases by means of the methyl-accepting chemoreceptor TAP (taxis toward dipeptides), but this response is not temperature dependent (30).In the known reductive and oxidative pathways for degradation of the pyrimidine ring (22, 48, 52), the C-5-C-6 double bond ...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Rut Pathway for Pyrimidine Degradation: Novel Chemistry and Toxicity Problems

Kim

Pelton

Inwood³

et al. 2010

J Bacteriol

103

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“…The primarily marine substrate DMSP is by far not the only source of 3-hydroxypropionate in nature, but instead, 3-hydroxypropionate is the product or intermediate of the breakdown of many substrates in a variety of environments (4,18,29,30,31,33,41). It will therefore not be surprising to also find many nonmarine organisms that will be able to derive carbon from 3-hydroxypropionate.…”

Section: Discussionmentioning

confidence: 99%

“…Another metabolic processes involving 3-hydroxypropionate is uracil degradation. 3-Hydroxypropionate has also been identified as the end product of two different pathways for uracil degradation in bacteria like Escherichia coli as well as in the yeast Saccharomyces kluyveri (4,29,32). Yet another metabolic process involving 3-hydroxypropionate is the anaerobic metabolism of glycerol.…”

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confidence: 99%

Rhodobacter sphaeroides Uses a Reductive Route via Propionyl Coenzyme A To Assimilate 3-Hydroxypropionate

et al. 2012

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3-Hydroxypropionate is a product or intermediate of the carbon metabolism of organisms from all three domains of life. However, little is known about how carbon derived from 3-hydroxypropionate is assimilated by organisms that can utilize this C 3 compound as a carbon source. This work uses the model bacterium Rhodobacter sphaeroides to begin to elucidate how 3-hydroxypropionate can be incorporated into cell constituents. To this end, a quantitative assay for 3-hydroxypropionate was developed by using recombinant propionyl coenzyme A (propionyl-CoA) synthase from Chloroflexus aurantiacus. Using this assay, we demonstrate that R. sphaeroides can utilize 3-hydroxypropionate as the sole carbon source and energy source. We establish that acetyl-CoA is not the exclusive entry point for 3-hydroxypropionate into the central carbon metabolism and that the reductive conversion of 3-hydroxypropionate to propionyl-CoA is a necessary route for the assimilation of this molecule by R. sphaeroides. Our conclusion is based on the following findings: (i) crotonyl-CoA carboxylase/reductase, a key enzyme of the ethylmalonylCoA pathway for acetyl-CoA assimilation, was not essential for growth with 3-hydroxypropionate, as demonstrated by mutant analyses and enzyme activity measurements; (ii) the reductive conversion of 3-hydroxypropionate or acrylate to propionyl-CoA was detected in cell extracts of R. sphaeroides grown with 3-hydroxypropionate, and both activities were upregulated compared to the activities of succinate-grown cells; and (iii) the inactivation of acuI, encoding a candidate acrylyl-CoA reductase, resulted in a 3-hydroxypropionate-negative growth phenotype. The C 3 compound 3-hydroxypropionate (CH 2 OH-CH 2 -COO Ϫ ) is increasingly being recognized as an important intermediate or end product of carbon metabolism in a variety of organisms. So far, there are at least five known metabolic processes involving 3-hydroxypropionate. One process is propionyl coenzyme A (propionyl-CoA) metabolism in plants. Propionyl-CoA is derived from the breakdown of chlorophyll, odd-chain fatty acids, or amino acids like isoleucine and is oxidized to 3-hydroxypropionate and probably further oxidized to acetyl-CoA (18,30,36). Some animals and algae may also metabolize propionate via a similar route (11,20,28). Another process involves autotrophic CO 2 fixation pathways. In bacteria and archaea, the reductive conversion of acetyl-CoA and CO 2 to propionyl-CoA via 3-hydroxypropionate is part of two CO 2 fixation pathways; however, different enzymes are used in either pathway to catalyze the common steps in the conversion of acetylCoA and CO 2 to propionyl-CoA (8, 9, 21, 39). For example, the reductive conversion of 3-hydroxypropionate to propionyl-CoA is catalyzed by a fusion protein, named propionyl-CoA synthase, in Chloroflexus aurantiacus (3-hydroxypropionate bi-cycle), whereas Metallosphaera sedula (hydroxypropionate/4-hydroxybutyrate cycle) requires three separate enzymes to catalyze the same reaction sequence (1,42). A third process is ...

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“…Polyhydroxyalkanoate utilization also results in acetyl-CoA (and sometimes propionyl-CoA) formation. Finally, beta-alanine and the abundant osmoprotectant dimethylsulfoniopropionate can be metabolized via 3-hydroxypropionate (2,3,28,39,43). Interestingly, various widespread bacteria appear to have acquired genes of the first part of the 3-hydroxypropionate bi-cycle, possibly for the same purpose of coassimilation.…”

mentioning

confidence: 99%

Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus

Zarzycki

Fuchs

2011

Appl Environ Microbiol

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Chloroflexus aurantiacus is a facultative autotrophic green nonsulfur bacterium that grows phototrophically in thermal springs and forms microbial mats with cyanobacteria. Cyanobacteria produce glycolate during the day (photorespiration) and excrete fermentation products at night. C. aurantiacus uses the 3-hydroxypropionate bi-cycle for autotrophic carbon fixation. This pathway was thought to be also suited for the coassimilation of various organic substrates such as glycolate, acetate, propionate, 3-hydroxypropionate, lactate, butyrate, or succinate. To test this possibility, we added these compounds at a 5 mM concentration to autotrophically pregrown cells. Although the provided amounts of H 2 and CO 2 allowed continuing photoautotrophic growth, cells immediately consumed most substrates at rates equaling the rate of autotrophic carbon fixation. Using [ 14 C]acetate, half of the labeled organic carbon was incorporated into cell mass. Our data suggest that C. aurantiacus uses the 3-hydroxypropionate bi-cycle, together with the glyoxylate cycle, to channel organic substrates into the central carbon metabolism. Enzyme activities of the 3-hydroxypropionate bi-cycle were marginally affected when cells were grown heterotrophically with such organic substrates. The 3-hydroxypropionate bi-cycle in Chloroflexi is unique and was likely fostered in an environment in which traces of organic compounds can be coassimilated. Other bacteria living under oligotrophic conditions acquired genes of a rudimentary 3-hydroxypropionate bi-cycle, possibly for the same purpose. Examples are Chloroherpeton thalassium, Erythrobacter sp. strain NAP-1, Nitrococcus mobilis, and marine gammaproteobacteria of the OM60/ NOR5 clade such as Congregibacter litoralis.

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A Second Pathway to Degrade Pyrimidine Nucleic Acid Precursors in Eukaryotes

Cited by 46 publications

References 31 publications

The Rut Pathway for Pyrimidine Degradation: Novel Chemistry and Toxicity Problems

The Rut Pathway for Pyrimidine Degradation: Novel Chemistry and Toxicity Problems

Rhodobacter sphaeroides Uses a Reductive Route via Propionyl Coenzyme A To Assimilate 3-Hydroxypropionate

Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus

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