High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii—An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle

Abstract

The Calvin–Benson cycle is the key metabolic pathway of photosynthesis responsible for carbon fixation and relies on eleven conserved enzymes. Ribose-5-phosphate isomerase (RPI) isomerizes ribose-5-phosphate into ribulose-5-phosphate and contributes to the regeneration of the Rubisco substrate. Plant RPI is the target of diverse post-translational modifications including phosphorylation and thiol-based modifications to presumably adjust its activity to the photosynthetic electron flow. Here, we describe the first experimental structure of a photosynthetic RPI at 1.4 Å resolution. Our structure confirms the composition of the catalytic pocket of the enzyme. We describe the homo-dimeric state of the protein that we observed in the crystal and in solution. We also map the positions of previously reported post-translational modifications and propose mechanisms by which they may impact the catalytic parameters. The structural data will inform the biochemical modeling of photosynthesis.

Physiological Biochemistry-Combined Transcriptomic Analysis Reveals Mechanism of Bacillus cereus G2 Improved Salt-Stress Tolerance of Glycyrrhiza uralensis Fisch. Seedlings by Balancing Carbohydrate Metabolism

“…However, whether the upregulation of the GPD gene under salt stress can help G. uralensis reduce the production of ROS and promote the synthesis of starch and sucrose remains to be confirmed by further studies. In the regeneration stage, RPI not only isomerizes ribose-5-phosphate into ribulose-5-phosphate but also helps in the regeneration of the Rubisco substrate ( Moigne et al, 2020 ); therefore, the upregulation of the gene-encoding RPI could contribute to providing sufficient Rubisco substrates for G. uralensis seedling under salt stress. However, our results found that G2 had little effect on the gene related to carbon fixation in photosynthetic organisms in G. uralensis under salt stress.…”

Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate

“…For instance, crystal structures have been determined for RPI from a variety of different organisms such as the bacterium Escherichia coli (PDB ID: 1LKZ) ( Rangarajan et al., 2002 ), the unicellular eukaryote Saccharomyces cerevisiae (PDB ID: 1XTZ) ( Graille et al., 2005 ), the archaeon Pyrococcus horikoshii (PDB ID: 1LK5) ( Ishikawa et al., 2002 ), and numerous human parasites including the protozoan Plasmodium falciparum (PDB ID: 2F8M) ( Holmes et al., 2006 ) and the euglenoid Trypanosoma cruzi (PDB ID: 3M1P) ( Stern et al., 2011 ). In contrast, structural data of plant RPI isoforms is limited, and only the crystallographic structure of RPI from the model green alga Chlamydomonas reinhardtii (CrRPI, PDB ID: 6ZXT) has been experimentally determined ( Le Moigne et al., 2020 ).…”

“…The domain is composed of a six-strand β-sheet flanked by four α-helices and is connected to the carboxy-terminal lid domain through a short β-sheet ( Figure 2B ). The lid domain is composed of a four-strand antiparallel β-sheet and two α-helices and contributes to the formation of the homo-dimeric structure, which has been validated in vitro with recombinant CrRPI ( Le Moigne et al., 2020 ).…”

“…At the same time, the sulphur atom of Cys175 is the most exposed to the solvent ( Figure 5A ), which could facilitate the reaction with oxidative molecules ( e.g. , hydrogen peroxide and nitrosoglutathione), thus making it the most likely target of redox modifications ( Le Moigne et al., 2020 ). However, biochemical evidence of this regulation remains insufficient.…”

“…The aim of this review is to summarize the current understanding of the structural features of the photosynthetic enzymes RPI, RPE, and PRK, as well as their catalytic and regulatory properties with regard to their physiological role in the CBB cycle. We focused our work on these last three enzymatic steps of the CBB cycle because crystal structures of photosynthetic RPI, RPE, and PRK have recently been determined, thus allowing a better understanding of their structure/function relationship and their putative post-translational regulatory mechanisms ( Gurrieri et al., 2019 ; Le Moigne et al., 2020 ; Meloni et al., 2022 ). Unless otherwise stated, we will describe the proteins from the model green microalga Chlamydomonas reinhardtii , from which the most extensive molecular data about the CBB cycle has been produced.…”