Phosphoribulokinase: Current Perspectives on the Structure/Function Basis for Regulation and Catalysis

Miziorko, Henry M.

doi:10.1002/9780470123201.ch3

Cited by 20 publications

(21 citation statements)

References 105 publications

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“…BLAST search with PRK of cyanobacterium Synechococcus PCC7942 against archaeal protein database identified PRK homologues in Archaea. Photosynthetic PRKs are classified into two groups from photosynthetic bacteria and plant-type oxygenic phototrophs such as plants, algae and cyanobacteria41011. Archaeal PRK homologues show approximately 30% amino acid sequence identity with PRKs in photosynthetic organisms and form a clade clearly distinct from those of bacterial and plant-type PRKs in a phylogenetic tree (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In this cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) fixes CO 2 with RuBP to yield 3-phosphoglycerate (3-PGA), from which RuBP is regenerated3. Phosphoribulokinase (PRK) synthesizes RuBP from ribulose-5-phosphate (Ru5P) in the final step in RuBP regeneration34. RuBisCO and PRK are representative and unique enzymes of the photosynthetic Calvin–Benson cycle5.…”

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confidence: 99%

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A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

et al. 2017

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Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown.

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Section: Resultsmentioning

confidence: 99%

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A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

et al. 2017

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“…2003). In photosynthetic bacteria, however, PRK was shown to be allosterically activated but was insensitive to redox regulation (Miziorko 2000). This lack of activation was linked to the absence of two regulatory cysteine residues that are present in all redox‐sensitive PRK sequences.…”

Section: Discussionmentioning

confidence: 99%

“…In many photosynthetic organisms, such as higher plants, algae, and cyanobacteria, PRK is regulated by thioredoxins (Wolosiuk and Buchanan 1978, Rault et al 1991, Avilan et al 2000, Geck and Hartman 2000, Kobayashi et al 2003. In photosynthetic bacteria, however, PRK was shown to be allosterically activated but was insensitive to redox regulation (Miziorko 2000). This lack of activation was linked to the absence of two regulatory cysteine residues that are present in all redox-sensitive PRK sequences.…”

Section: Discussionmentioning

confidence: 99%

Regulation of phosphoribulokinase and glyceraldehyde 3‐phosphate dehydrogenase in a freshwater diatom, Asterionella formosa¹

Boggetto

Gontero

Maberly

2007

Journal of Phycology

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The regulation of phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was investigated in a freshwater pennate diatom, Asterionella formosa Hassall, and compared to the well-studied chlorophyte Chlamydomonas reinhardtii P. A. Dang. As has been reported for a marine centric diatom, in A. formosa, PRK was not regulated by reduction with dithiothreitol (DTT) apart from a weak induction in the presence of NADPH and DTT. However, NADPH-GAPDH was strongly activated when reduced, in contrast to a previous report on a diatom. Surprisingly, it was inhibited by NADPH, unlike in C. reinhardtii, while NADH-GAPDH was not affected. NADH-GAPDH was also strongly activated by DTT in contrast to most other photosynthetic cells. In A. formosa, unlike C. reinhardtii, 1,3-bisphosphoglycerate, the substrate of GAPDH, activated this enzyme, even in the absence of DTT, when using both NADH and NADPH as cofactors. Some of these kinetic behaviors are consistent with regulation by proteinprotein interactions involving CP12, a small protein that links PRK and GAPDH in cyanobacteria, green algae, and higher plants. This conclusion was supported by immunodetection of CP12 in crude extracts of A. formosa, using antibodies raised against CP12 from C. reinhardtii. This is the first report of the existence of CP12 in a diatom, but CP12 may be a common feature of diatoms since a bioinformatic search suggested that it was also present in the Thalassiosira pseudonana Hasle et Heimdal genome v3.0. Despite the presence of CP12, this work provides further support for the differential regulation of Calvin cycle enzymes in diatoms compared to green algae.

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“…3c). While PRKs from prokaryotes and eukaryotes share key features of the active site for RuBP synthesis, there are major differences in primary sequence, quaternary structure and regulation of the enzymes (Miziorko, 1998). Over the region of sequence comparison between spinach and R. sphaeroides, one relative insertion (of 15 residues) in the plant sequence and three (of 10, 11 and 3 residues) in the proteobacterial sequence were all absent in cyanobacteria and S. acidophilus.…”

Section: Discussionmentioning

confidence: 99%

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

2007

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The Calvin-Benson-Bassham (CBB) cycle has been extensively studied in proteobacteria, cyanobacteria, algae and plants, but hardly at all in Gram-positive bacteria. Some characteristics of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) and a cluster of potential CBB cycle genes in a Gram-positive bacterium are described in this study with two species of Sulfobacillus (Gram-positive, facultatively autotrophic, mineral sulfide-oxidizing acidophiles). In contrast to the Gram-negative, iron-oxidizing acidophile Acidithiobacillus ferrooxidans, Sulfobacillus thermosulfidooxidans grew poorly autotrophically unless the CO 2 concentration was enhanced over that in air. However, the RuBisCO of each organism showed similar affinities for CO 2 and for ribulose 1,5-bisphosphate, and similar apparent derepression of activity under CO 2 limitation. The red-type, form I RuBisCO of Sulfobacillus acidophilus was confirmed as closely related to that of the anoxygenic phototroph Oscillochloris trichoides. Eight genes potentially involved in the CBB cycle in S. acidophilus were clustered in the order cbbA, cbbP, cbbE, cbbL, cbbS, cbbX, cbbG and cbbT.

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Phosphoribulokinase: Current Perspectives on the Structure/Function Basis for Regulation and Catalysis

Cited by 20 publications

References 105 publications

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

Regulation of phosphoribulokinase and glyceraldehyde 3‐phosphate dehydrogenase in a freshwater diatom, Asterionella formosa¹

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

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Phosphoribulokinase: Current Perspectives on the Structure/Function Basis for Regulation and Catalysis

Cited by 20 publications

References 105 publications

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

Regulation of phosphoribulokinase and glyceraldehyde 3‐phosphate dehydrogenase in a freshwater diatom, Asterionella formosa1

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

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Regulation of phosphoribulokinase and glyceraldehyde 3‐phosphate dehydrogenase in a freshwater diatom, Asterionella formosa¹