A short history of RubisCO: the rise and fall (?) of Nature's predominant CO2 fixing enzyme

Erb, Tobias J.; Zarzycki, Jan

doi:10.1016/j.copbio.2017.07.017

Cited by 254 publications

(203 citation statements)

References 60 publications

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“…Rather, form III Rubiscos have a catabolic role in the removal of intermediates formed by ribonucleoside 5=-monophosphate catabolism and directing the ribose moiety carbons to central metabolism. The biochemical, structural, and phylogenetic relations of the Rubiscos have been reviewed in detail previously (104)(105)(106)(107)(108)(109).…”

Section: Rubiscomentioning

confidence: 99%

“…Form IV Rubisco catalyzing enolization without subsequent carboxylation may represent an ancestral Rubisco to which the carboxylation process was added later in evolution and where forms III, II/III, and I appeared. Additionally, the Calvin-Benson-Bassham cycle may have evolved from ancient nucleotide metabolism (108). In line with this suggestion, Schönheit and colleagues proposed that "a simple interpretation is that the type III Rubisco pathway [i.e., the pentose bisphosphate pathway] is an ancient relic of the first heterotrophic metabolisms in archaea, Rubisco later being transferred to bacteria, where it is less common among obligate heterotrophs, and, where it-in timeultimately became assimilated into dedicated carbon dioxide fixation in the Calvin[-Benson-Bassham] cycle" and that "ribose was probably the first abundant sugar" (157), and as mentioned above, PRibP may be regarded as an ancient phosphoribosyl donor that became replaced by PRPP in "modern" organisms.…”

Section: Evolution and Phylogenymentioning

confidence: 99%

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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism

Hove‐Jensen

Brodersen

Manav

2019

Microbiol Mol Biol Rev

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SUMMARYRibosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its “big brother” phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups,Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.

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Section: Rubiscomentioning

confidence: 99%

Section: Evolution and Phylogenymentioning

confidence: 99%

The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism

Hove‐Jensen

Brodersen

Manav

2019

Microbiol Mol Biol Rev

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“…Besides the reductive acetyl-CoA pathway and the reductive TCA cycleboth of which are believed to have originated early in the evolution of metabolism 10 the other carbon fixation routes are thought to have evolved by recruiting enzymes from other metabolic pathways. For example, Rubiscothe carboxylating enzyme of the RuBP cycleprobably evolved from a non-CO2-fixing ancestral enzyme, thus emerging in a non-autotrophic context 11 . Similarly, acetyl-CoA carboxylase likely originated as a key component of fatty acid biosynthesis before being recruited into carbon fixation pathways in several prokaryotic lineages 2,3 .…”

Section: Introductionmentioning

confidence: 99%

Awakening a latent carbon fixation cycle inEscherichia coli

Satanowski

Dronsella

Noor

et al. 2020

Preprint

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Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth. Our study exemplifies a trajectory for the emergence of carbon fixation in a heterotrophic organism and demonstrates a synthetic pathway of biotechnological interest.

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“…The Calvin-Benson-Bassham (CBB) cycle 1 is the predominant of the six naturally occurring CO 2 fixation pathways 2,3 . Its key enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme found in the biosphere and fixates around 90% of the inorganic carbon converted into biomass 4 .…”

Section: Introductionmentioning

confidence: 99%

A synthetic Calvin cycle enables autotrophic growth in yeast

Gassler

Sauer

Gasser

et al. 2019

Preprint

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33The methylotrophic yeast Pichia pastoris is frequently used for heterologous protein 34 production and it assimilates methanol efficiently via the xylulose-5-phosphate pathway. This 35 pathway is entirely localized in the peroxisomes and has striking similarities to the Calvin-36Benson-Bassham (CBB) cycle, which is used by a plethora of organisms like plants to 37 assimilate CO2 and is likewise compartmentalized in chloroplasts. By metabolic engineering 38 the methanol assimilation pathway of P. pastoris was re-wired to a CO2 fixation pathway 39 resembling the CBB cycle. This new yeast strain efficiently assimilates CO2 into biomass and 40 utilizes it as its sole carbon source, which changes the lifestyle from heterotrophic to 41 autotrophic. 42In total eight genes, including genes encoding for RuBisCO and phosphoribulokinase, were 43 integrated into the genome of P. pastoris, while three endogenous genes were deleted to 44 block methanol assimilation. The enzymes necessary for the synthetic CBB cycle were 45 targeted to the peroxisome. Methanol oxidation, which yields NADH, is employed for energy 46 generation defining the lifestyle as chemoorganoautotrophic. This work demonstrates that the 47 lifestyle of an organism can be changed from chemoorganoheterotrophic to 48 3 chemoorganoautotrophic by metabolic engineering. The resulting strain can grow 49 exponentially and perform multiple cell doublings on CO2 as sole carbon source with a µmax 50 of 0.008 h -1 . 51

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A short history of RubisCO: the rise and fall (?) of Nature's predominant CO2 fixing enzyme

Cited by 254 publications

References 60 publications

The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism

The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism

Awakening a latent carbon fixation cycle inEscherichia coli

A synthetic Calvin cycle enables autotrophic growth in yeast

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