The Physiological Role of the Ribulose Monophosphate Pathway in Bacteria and Archaea

Kato, Nobuo; Yurimoto, Hiroya; Thauer, Rudolf K.

doi:10.1271/bbb.70.10

Cited by 122 publications

(109 citation statements)

References 33 publications

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“…Abbreviations: HPS, 3-hexulose-6-phosphate synthase; PHI, 6-phospho-3-hexuloisomerase; RPI, ribose-5-phosphate isomerase; TK, transketolase. dromethanopterin, enabling subsequent oxidation to CO 2 (374,381). FAE is found in many methanogenic Archaea as well as in Archaeoglobus spp.…”

Section: Fig 19mentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

266

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Fig 19mentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

266

294

View full text Add to dashboard Cite

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“…Methanol utilization and 13 C-methanol-derived labeling of intracellular metabolites were first demonstrated in Corynebacterium glutamicum by expressing the mdh gene from B. methanolicus and the hps and phi genes from Bacillus subtilis (16,17). A similar approach was also demonstrated in E. coli, where Mdh2 from B. methanolicus PB1 was coexpressed with Hps and Phi from B. methanolicus MGA3 to increase the production of 13 C-labeled intracellular metabolites compared with the control strain expressing Mdh3 alone (15). Although these reports provide evidence that the RuMP pathway can be transferred to nonnative methylotrophs, the rate of methanol consumption is significantly lower than those reported for native methyltrophs.…”

mentioning

confidence: 99%

“…1A) (7,13), D-arabino-3-hexulose 6-phosphate (6HP) is first produced by a condensation reaction between formaldehyde and ribulose 5-phosphate (Ru5P) by 3-hexulose-6-phosphate synthase (Hps) (6,13,14). This is followed by the isomerization of heluxose 6-phosphate (H6P) by 6-phospho-3-hexuloseisomerase (Phi) (6,13,14) into fructose 6-phosphate (F6P), which can either enter central metabolism Significance Methane, the major natural-gas component, can be converted industrially to syngas (a mixture of CO 2 , CO, and H 2 ), which is used to produce methanol, an important industrial precursor for producing commodity and specialty chemicals. Unlike methanol's chemical conversion, which requires high temperature and pressure, its biological conversion, proceeding through its oxidation to formaldehyde, takes place at ambient conditions but suffers from relative low rates.…”

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confidence: 99%

Scaffoldless engineered enzyme assembly for enhanced methanol utilization

Price

Chen

Whitaker

et al. 2016

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

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Methanol is an important feedstock derived from natural gas and can be chemically converted into commodity and specialty chemicals at high pressure and temperature. Although biological conversion of methanol can proceed at ambient conditions, there is a dearth of engineered microorganisms that use methanol to produce metabolites. In nature, methanol dehydrogenase (Mdh), which converts methanol to formaldehyde, highly favors the reverse reaction. Thus, efficient coupling with the irreversible sequestration of formaldehyde by 3-hexulose-6-phosphate synthase (Hps) and 6-phospho-3-hexuloseisomerase (Phi) serves as the key driving force to pull the pathway equilibrium toward central metabolism. An emerging strategy to promote efficient substrate channeling is to spatially organize pathway enzymes in an engineered assembly to provide kinetic driving forces that promote carbon flux in a desirable direction. Here, we report a scaffoldless, self-assembly strategy to organize Mdh, Hps, and Phi into an engineered supramolecular enzyme complex using an SH3-ligand interaction pair, which enhances methanol conversion to fructose-6-phosphate (F6P). To increase methanol consumption, an "NADH Sink" was created using Escherichia coli lactate dehydrogenase as an NADH scavenger, thereby preventing reversible formaldehyde reduction. Combination of the two strategies improved in vitro F6P production by 97-fold compared with unassembled enzymes. The beneficial effect of supramolecular enzyme assembly was also realized in vivo as the engineered enzyme assembly improved whole-cell methanol consumption rate by ninefold. This approach will ultimately allow direct coupling of enhanced F6P synthesis with other metabolic engineering strategies for the production of many desired metabolites from methanol. methane | methylotophs | supramolcular | scaffold | substrate channeling

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“…Two of the clusters, spanning ro00487 to ro00489 and ro11327 to ro11332 (i.e., 9 genes in total), are predicted to encode partially overlapping ribulose monophosphate pathways (35). In this pathway, formaldehyde is captured by ribulose 5-phosphate in a reaction catalyzed by 3-hexulose-6-phosphate synthase (HPS; Ro00489 and Ro11329).…”

Section: Growth Of Rha1 On P-hydroxycinnamatesmentioning

confidence: 99%

Characterization of p -Hydroxycinnamate Catabolism in a Soil Actinobacterium

et al. 2014

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p-Hydroxycinnamates, such as ferulate and p-coumarate, are components of plant cell walls and have a number of commercial applications. Rhodococcus jostii RHA1 (RHA1) catabolizes ferulate via vanillate and the ␤-ketoadipate pathway. Here, we used transcriptomics to identify genes in RHA1 that are upregulated during growth on ferulate versus benzoate. The upregulated genes included three transcriptional units predicted to encode the uptake and ␤-oxidative deacetylation of p-hydroxycinnamates: couHTL, couNOM, and couR. Neither ⌬couL mutants nor ⌬couO mutants grew on p-hydroxycinnamates, but they did grow on vanillate. Among several p-hydroxycinnamates, CouL catalyzed the thioesterification of p-coumarate and caffeate most efficiently (k cat /K m ‫؍‬ ϳ400 mM ؊1 s ؊1 ). p-Coumarate was also RHA1's preferred growth substrate, suggesting that CouL is a determinant of the pathway's specificity. CouL did not catalyze the activation of sinapate, in similarity to two p-coumaric acid:coenzyme A (CoA) ligases from plants, and contains the same bulged loop that helps determine substrate specificity in the plant homologues. The couO mutant accumulated 4-hydroxy-3-methoxyphenyl-␤-ketopropionate in the culture supernatant when incubated with ferulate, supporting ␤-oxidative deacetylation. This phenotype was not complemented with a D257N variant of CouO, consistent with the predicted role of Asp257 as a metal ligand in this amidohydrolase superfamily member. These data suggest that CouO functionally replaces the ␤-ketothiolase and acyl-CoA thioesterase that occur in canonical ␤-oxidative pathways. Finally, the transcriptomics data suggest the involvement of two distinct formaldehyde detoxification pathways in vanillate catabolism and identify a eugenol catabolic pathway. The results of this study augment our understanding of the bacterial catabolism of aromatics from renewable feedstocks.

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The Physiological Role of the Ribulose Monophosphate Pathway in Bacteria and Archaea

Cited by 122 publications

References 33 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Scaffoldless engineered enzyme assembly for enhanced methanol utilization

Characterization of p -Hydroxycinnamate Catabolism in a Soil Actinobacterium

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