RuBisCO activity assays: a simplified biochemical redox approach for in vitro quantification and an RNA sensor approach for in vivo monitoring

Journal Article · 13 March 2024 · Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-024-02357-6 · OSTI ID:2323943

Faisal, Muhammad; Sarnaik, Aditya P.; Kannoju, Nandini; Hajinajaf, Nima; Asad, Muhammad Javaid; Davis, Ryan W.; Varman, Arul M.

Abstract Background Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant soluble protein in nature. Extensive studies have been conducted for improving its activity in photosynthesis through approaches like protein engineering. Concurrently, multiple biochemical and radiolabeling assays have been developed for determining its activity. Although these existing assays yield reliable results, they require addition of multiple external components, rendering them less convenient and expensive. Therefore, in this study, we have developed two relatively cheaper, convenient, and easily reproducible assays for quantitative and qualitative estimation of RuBisCO activity. Results We simplified a contemporary NADH based spectrophotometric RuBisCO assay by using cyanobacterial cell lysate as the source for Calvin cycle enzymes. We analyzed the influence of inorganic carbon substrates, CO ₂ and NaHCO ₃ , and varying protein concentrations on RuBisCO activity. Ribulose-1,5-bisphosphate (RuBP) consumption rates for the cultures grown under 5% CO ₂ were 5–7 times higher than the ones grown with 20 mM NaHCO ₃ , at different protein concentrations. The difference could be due to the impaired activity of carbonic anhydrase in the cell lysate, which is required for the conversion of HCO ₃ ⁻ to CO ₂ . The highest RuBisCO activity of 2.13 nmol of NAD ⁺ / µg of Chl-a/ min was observed with 50 µg of protein and 5% CO ₂ . Additionally, we developed a novel RNA-sensor based fluorescence assay that is based on the principle of tracking the kinetics of ATP hydrolysis to ADP during the conversion of 3-phosphoglycerate (3-PG) to 1,3-bisphosphoglycerate (1,3-BPG) in the Calvin cycle. Under in vitro conditions, the fluorometric assay exhibited  ~ 3.4-fold slower reaction rate (0.37 min ⁻¹ ) than the biochemical assay when using 5% CO ₂ . We also confirmed the in vivo application of this assay, where increase in the fluorescence was observed with the recombinant strain of Synechocystis sp. PCC 6803 (SSL142) expressing the ADP-specific RNA sensor, compared to the WT. In addition, SSL142 exhibited three-fold higher fluorescence when supplemented with 20 mM NaHCO ₃ as compared to the cells that were grown without NaHCO ₃ supplementation. Conclusions Overall, we have developed a simplified biochemical assay for monitoring RuBisCO activity and demonstrated that it can provide reliable results as compared to the prior literature. Furthermore, the biochemical assay using 5% CO ₂ (100% relative activity) provided faster RuBP consumption rate compared to the biochemical assay utilizing 20 mM NaHCO ₃ (30.70% relative activity) and the in vitro fluorometric assay using 5% CO ₂ (29.64% relative activity). Therefore, the absorbance-based biochemical assay using 5% CO ₂ or higher would be suitable for in vitro quantification of the RuBisCO activity. On the other hand, the RNA-sensor based in vivo fluorometric assay can be applied for qualitative analysis and be used for high-throughput screening of RuBisCO variants. As RuBisCO is an enzyme shared amongst all the photoautotrophs, the assays developed in this study can easily be extended for analyzing the RuBisCO activities even in microalgae and higher plants.

• Research Organization: Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
• Sponsoring Organization: USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)
• Grant/Contract Number: NA0003525
• OSTI ID: 2323943
• Journal Information: Microbial Cell Factories, Journal Name: Microbial Cell Factories Journal Issue: 1 Vol. 23; ISSN 1475-2859
• Publisher: Springer Science + Business MediaCopyright Statement
• Country of Publication: United Kingdom
• Language: English