Ontology highlight
ABSTRACT:
PROVIDER: PRJNA962542 | ENA |
REPOSITORIES: ENA
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Project description:uncultured bacterium cbbL-ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit Raw sequence reads
| PRJNA765939 | ENA
Project description:uncultured bacterium cbbL-ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit Raw sequence reads
| PRJNA766221 | ENA
Project description:Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the core rate-limiting enzyme of photosynthetic carbon metabolism, is regulated by acetylation, yet its upstream acetyltransferases remain largely uncharacterized. Here, we identified a novel soybean acetyltransferase GmGNAT10, which interacts with Rubisco and other photosynthetic enzymes via IP-MS/MS interactomics. Quantitative acetylomics under fluctuating light revealed dramatic genotypic differences in acetylation levels of key RbcL lysine residues (K23, K175, K236) between wild-type and GmGNAT10 mutants. Our findings expand the mechanistic understanding of chloroplast non-histone acetylation in fine-tuning photosynthetic carbon metabolism.
2026-04-28 | PXD077705 |
Project description:The small chloroplastic protein CP12 has multiple functions, including the regulation of enzymes in the Calvin-Benson-Bassham cycle. Here, we investigated its role in the acclimation of Chlamydomonas reinhardtii to varying CO2 availability. This alga has a CO2 concentrating mechanism that increases the supply of CO2 to ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and involves hallmarks such as HCO3- transporters and carbonic anhydrases as well as the condensation of RuBisCO within the pyrenoid via its interaction with a scaffold protein namedEssential Pyrenoid Component 1 (EPYC1). We showed that compared to the wild type, at high CO2, C. reinhardtii CP12 deletion mutants, or partially complemented mutants, have less phosphoribulokinase and ribulose-1,5-bisphosphate (RuBP) indicating that the regeneration of RuBP is regulated by CP12. In the absence of CP12, the expected relocation of RuBisCO towards the pyrenoid was not observed upon transition from high to very low CO2, contrary to WT cells. The CP12 deletion mutants are a unique example where the induction of CO2 concentrating mechanism hallmarks at very low CO2 was not accompanied by RuBisCO relocation. Altogether, these results suggest that CP12 contributes to the coordination between RuBP regeneration, RuBisCO location and CO2 acquisition.
2026-02-16 | PXD065761 | Pride
Project description:The impact of engineered nanomaterials intentionally or incidentally released in the environment on photosynthetic proteins remains largely unknown. Herein, we report positively charged iron oxide (Fe3O4) nanoparticles experience transformations in Arabidopsis thaliana plants in vivo that alter the formation and function of Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) protein corona, a key enzyme in the global carbon cycle. Elucidating rules of how nanoparticle properties and their transformations affect photosynthetic coronas will lead to more sustainable nanotechnology approaches for agriculture and the environment.
2025-03-04 | PXD055951 | JPOST Repository
Project description:Carbon dioxide is vital to the chemistry of life processes including including metabolism, cellular homeostasis, and pathogenesis. CO2 forms carbamates on the neutral N-terminal a-amino- and lysine e-amino-groups that regulate the activities of ribulose 1,5-bisphosphate carboxylase/oxygenase and haemoglobin, however, very few protein other carbamates are known. Tools for the systematic identification of protein carbamylation sites have not been developed owing to the reversibility of carbamate formation, and in consequence carbamylation is typically overlooked. Here we demonstrate methods to identify protein carbamates using triethyloxonium ions to covalently trap CO2 on proteins for proteomic analysis. Our method delivers evidence to support the hypothesis that carbamylation is widespread in biology, and understanding its role should significantly advance our understanding of cellular CO2 interactions.
2018-10-23 | PXD007753 | Pride
Project description:Cyanidioschyzon merolae (C. merolae) is an acidophilic red alga growing in a naturally low carbon dioxide (CO2) environment. Although it uses a ribulose 1,5-bisphosphate carboxylase/oxygenase with high affinity for CO2, the survival of C. merolae relies on functional photorespiratory metabolism. In this study, we quantified the transcriptomic response of C. merolae to changes in CO2 conditions. We found distinct changes upon shifts between CO2 conditions, such as a concerted up-regulation of photorespiratory genes and responses to carbon starvation. We used the transcriptome data set to explore a hypothetical CO2 concentrating mechanism in C. merolae, based on the assumption that photorespiratory genes and possible candidate genes involved in a CO2 concentrating mechanism are co-expressed. A putative bicarbonate transport protein and two α-carbonic anhydrases were identified, which showed enhanced transcript levels under reduced CO2 conditions. Genes encoding enzymes of a PEP-CK-type C4 pathway were co-regulated with the photorespiratory gene cluster. We propose a model of a hypothetical low CO2 compensation mechanism in C. merolae integrating these low CO2-inducible components.
2017-07-31 | GSE100372 | GEO
Project description:The fixation of dissolved inorganic carbon (DIC) such as CO2 and bicarbonate is fundamental to the global primary production. Many autotrophs depend on a diversity of CO2-concentrating mechanisms (CCMs) to overcome the inefficiency of ribulose-1,5-bisphosphate carboxylase/oxygenase and the limited supply of DIC. While cyanobacterial CCMs are well characterized, analogous systems in chemolithoautotrophs, specifically active DIC uptake systems have long been overlooked. Here, we present the first cryo-EM analysis of DAB2, an essential membrane-associated complex for CO₂ uptake in Halothiobacillus neapolitanus. The cytoplasmic subunit DabA2 displays a β-carbonic anhydrase-like fold, while the transmembrane subunit DabB2 resembles the proton-conducting subunits of respiratory Complex I. Purified DAB2 binds CO₂ independent of proton motive force (PMF) however, did not spontaneously hydrate CO2. Structural analysis reveals a deeply buried active site only accessible via gated substrate tunnels, suggesting substrate access and catalysis are tightly regulated. The transmembrane helix of DabA2 forms the proton pathway and potentially couples proton translocation to the catalysis. These features define a vectorial CO2 hydration mechanism that prohibits reverse bicarbonate dehydration. Our findings establish DAB2 as a prototype of a previously unrecognized family of PMF-driven carbonic anhydrases, elucidating a novel strategy for CO₂ capture in non-photosynthetic autotrophs.
2026-04-17 | PXD076189 | Pride
Project description:The introduction of alternative CO2-fixing pathways such as formate synthesis and assimilation may improve the efficiency of biological carbon fixation that appears to be limited by the enzymatic properties of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we aimed to establish a formate assimilation pathway in the model cyanobacterium Synechocystis sp. PCC 6803. The formate-tetrahydrofolate ligase (FTL) from Methylobacterium extorquens AM1 was expressed in Synechocystis to enable formate assimilation and reduce the loss of fixed carbon in the photorespiratory pathway. Transgenic strains accumulated serine and 3-phosphoglycerate, and consumed more 2-phosphoglycolate and glycine, which seemed to reflect the efficient utilization of formate. However, labelling experiments showed that the serine accumulation was not due to the expected incorporation of formate. DNA-microarray experiments were performed to analyze possible transcriptome changes due to ftl expression. Marked changes in expression of genes encoding proteins associated with serine biosynthesis and enzymes involved in nitrogen and C1 metabolism revealed that ftl expression had a regulatory impact on these metabolic routes. Our results indicate that the expression of new pathways could have a severe impact on the cellular regulatory network, which hampers the establishment of newly designed pathways.
2020-01-17 | GSE143785 | GEO
Project description:Random mutagenesis was applied to produce a new wheat mutant (RYNO3926) with superior characteristics regarding tolerance to water deficit treatment and rapid recovery from water stress conditions. Under water stress conditions mutant plants reached maturity faster and produced more seeds than its wild type wheat progenitor Further, whereas wild-type Tugela DN plants died within 7 days after induction of water stress, mutant plants survived by maintaining a higher relative moisture content (RMC), increased total chlorophyll, a higher photosynthesis rate and stomatal conductance suggesting that the mutant may possess a “stay green”’ phenotype. Analysis of the proteome of mutant plants revealed that they better regulate post-translational modification (SUMOylation) and have increased expression of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) proteins. Mutant plants also expressed unique proteins associated with dehydration tolerance including abscisic stress-ripening protein, cold induced protein, cold-responsive protein, dehydrin, Group 3 late embryogenesis and also a lipoprotein (LAlv9) belonging to the family of lipocalins. Overall, our results suggest that our new mutant RYNO3936 has a potential for inclusion in future breeding programs to improve drought tolerance under dryland conditions.
2021-09-09 | PXD019464 | Pride