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11 results for “Rubisco”
Rubisco limited photosynthesis rates of Red mangrove leaves at Key Largo, Watson River Chickee, Taylor Slough, and Little Rabbit Key, South Florida (FCE) from July 2001 to August 2001
Determine the Rubisco limited carboxylation rates of red mangrove ( species Rhizophora mangle) leaves. This information will be used to model carbon sequestration by Red mangroves.
Maximum carboxylation rate estimation with chlorophyll content as a proxy of rubisco content
<p>The maximum carboxylation rate (Vcmax) is a key parameter in determining the plant photosynthesis rate per unit leaf area. However, most terrestrial biosphere models currently treat Vcmax as constants changing only with plant functional types, leading to large uncertainties in modelled carbon fluxes. Vcmax is tightly linked with <span>Ribulose-1,5-bisphosphate carboxylase/oxygenase (</span>Rubisco). Here we investigated the relationship between leaf chlorophyll content and Rubisco (Chl-Rub) within a winter wheat paddock. With chlorophyll as a proxy of Rubisco, a semi-mechanistic model was developed to model Vcmax<sub>25.</sub> The Chl-Rub relationship was validated using measurements in a temperate forest in Canada. The results showed that Rubisco was strongly correlated with chlorophyll (R<sup>2</sup> = 0.96, p < 0.001) for winter wheat, due to the absorption of light energy by chlorophyll and the amount of CO<sub>2</sub> catalysed by Rubisco are tightly coupled<span>.</span> Incorporating the Chl-Rub relationship into the semi-mechanistic model, the root mean square error of modelled Vcmax<sub>25</sub> was the lowest among all estimation models. The slopes of Chl-Rub relations were almost identical for the winter wheat and temperate forest, demonstrating the potential for using leaf chlorophyll content as a proxy of leaf Rubisco in modelled Vcmax<sub>25</sub> at large spatial scales. We anticipate that improving Vcmax<sub>25</sub> estimates over time and space will reduce uncertainties in terrestrial biosphere models and improve the estimates of global carbon budgets.</p>
Molecular dynamics simulations for "Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time"
<p>This repository contains the molecular dynamics simulation files for the extant and ancestral RuBisCOs, presented in Amritkar2024 et. al.</p> <p>There are two separate folders, one for the regular MD simulations and the other for MD simulations with gas trajectories.</p> <p>Both folders have the simulation trajectory `.dcd` files and the `.pdb` for their corresponding protein structures.</p> <p>The trajectory files are dried, i.e. water molecules have been removed from them.</p> <p>The data encompasses over 7 extant (pdb ids: 1BWV, 3ZXW, 6FTL, 6URA, 7SNV, 8RUC, 9RUB) and 8 ancestral (Anc-I/I', Anc-I', Anc-I, Anc-IAB, Anc-ICD, Anc-IA, Anc-IB, Anc-I-without-RbcS) RuBisCO complexes.</p> <p>This study performed three types of simulations: with water molecules (labeled as exp01), with water + CO2 molecules (labeled as exp02), and with water + O2 molecules (labeled as exp04).</p> <p>There are two replicates for the exp01 simulations and the simulation length for each is 250 ns.</p> <p>The <em>exp02</em> and <em>exp04</em> files are not present for the RbcS-less (Anc-I/I', Anc-I', Anc-I-without_RbcS, 6URA, and 9RUB) RuBisCOs. The simulation length for the gas simulations is 75 ns and one replicate.</p> <p>Each file is named "<em>RuBisCO-system"</em>."<em>simulation-type</em>".md"replicate-number".dry."<em>pdb or dcd</em>".</p> <p>The files are named with respect to each RuBisCO-id in small (No caps). Anc-I/I' is represented as "anciip" and Anc-I' is represented as "ancip".</p>
Input files and structures for article "Carbon dioxide fixation in RuBisCO is protonation state dependent and irreversible"
<p>Pdb file and amber topology of the initial RuBisCO model together with parameter files for the MD simulations with AMBER to equilibrate the system.</p> <p>Structures of reactant, transition state and products in the enzyme RuBisCo used to correct the activation and reaction free energies. Molpro input files used in the projector-based embedding calculations are provided. The same holds for the calculations involving the Zn cation. </p> <p>Optimized structures used to calculate descriptors with conceptual DFT. </p>
Data for "Predicting Rubisco:Linker Condensation from Titration in the Dilute Phase"
<p>Data for the Figures of "Predicting Rubisco:Linker Condensation from Titration in the Dilute Phase" are stored on this repository.</p> <p>Microscopy images are stored on BioStudies: <a href="https://doi.org/10.6019/S-BIAD1097" target="_blank" rel="noopener">https://doi.org/10.6019/S-BIAD1097</a>. </p> <p>Code used to analyse the microscopy images: <a href="https://github.com/ejh516/pystachio-smt">https://github.com/ejh516/pystachio-smt</a></p> <p>Code used for single-molecule calculations: <a href="https://github.com/CharleySchaefer/RubiscoMonomers">https://github.com/CharleySchaefer/RubiscoMonomers</a></p>
Raw data for "Ancestral structure prediction reveals the conformational impact of the RuBisCO small subunit across time".
<p>The repository contains raw data for the article "Ancestral structure prediction reveals the conformational impact of the RuBisCO small subunit across time".</p> <p>The repository contains:</p> <ol> <li>Dataset for the RbcL and RbcS sequences along with the inferred sequences for the ancestors of interest</li> <li>Phylogenetic tree for the concatenated and separate RbcL-RbcS sequences.</li> <li>Structures for the extant and ancestral RuBisCO complexes used in the study.</li> <li>Solvated pdb files for creating the topology files required for MD-simulations.</li> </ol>
Maximum carboxylation rate estimation with chlorophyll content as a proxy of rubisco content
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Data from: Identification and characterization of Rubisco activase genes in Oryza punctata
Rubisco activase (Rca), a specific chaperone, catalyzes the in vivo activation of Rubisco, and thus plays a major role in plant photosynthesis. Although the genes encoding Rubisco activase have been studied in many model or economic plants, few studies have analyzed their homologs in the plants that closely related to crop species. In this study, an Rca gene was identified and characterized in a wild relative of rice, O. punctata Kotschy ex Steud. The gene was 2747 bp long and possessed six exons and five introns with 47% GC content. Further, cDNA sequencing produced two transcripts RcaL and RcaS that differed in the sequence by an inclusion of 99 bp at the carboxy terminus of RcaL. Sequence comparison between the two transcripts and the genomic DNA showed that there was a 20-bp alternative splicing event that occurred at the fifth intron of the gene leading to the synthesis of a short polypeptide. The leaf transcriptome analysis showed that RcaS had a higher expression level than that of RcaL in a normal growth environment. In addition, the yeast two-hybrid assays displayed the small isoform of Rubisco activase in close contact with the large subunit of the Rubisco in this species, supporting the side-on binding model of interaction between two proteins. This study broadens our understanding of the molecular characteristics of some essential genes in photosynthesis.
Data from: Identification and characterization of Rubisco activase genes in Oryza punctata
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Modifying plant photosynthesis and growth via simultaneous chloroplast transformation of Rubisco large and small subunits
<p>Engineering improved Rubisco poses a crucial strategy for enhancing photosynthesis but is challenged by the alternate locations of the plastome rbcL gene and nuclear RbcS genes. Here we develop a RNAi-RbcS Nicotiana tabacum (tobacco) master-line, tobRrΔS, amenable to rbcL-rbcS co-engineering by chloroplast transformation. Four tobacco genotypes coding alternative rbcS genes and adjoining 5ˈ-intergenic sequences revealed Rubisco production was highest in the lines incorporating a rbcS gene whose codon use and 5ˈUTR matched rbcL. These lines produced up to 50% the wild-type Rubisco content. Additional tobacco lines coding potato rbcL-rbcS operons examined how the differing mesophyll made small subunits (pS1, pS2, pS3) or the trichome pST-25 subunit influenced Rubisco biogenesis, catalysis, leaf physiology and plant growth. Rubisco levels were ~15% lower in leaves expressing pS3 relative to those producing pS1, pS2, and pST. However, the pS3-subunit increased carboxylation rate (kcatC) by 13% and carboxylation efficiency (CE, kcatC divided by the Km for CO2) by 17% relative to the pS1 and pS2 subunits as a result of the βa-βb loop substitutions Asn-55-His and Lys-57-Ser. By contrast tobacco photosynthesis and growth were most impaired in lines producing the pST-subunit that reduced CE and CO2/O2 specificity of potato Rubisco by 40% and 15% respectively.<br> </p>
Modifying plant photosynthesis and growth via simultaneous chloroplast transformation of Rubisco large and small subunits
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