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1. Carboxylation and Oxygenation Kinetics and Large Subunit ( rbcL ) DNA Sequences for Rubisco From Two Ecotypes of Plantago lanceolata L. That Are Native to Sites Differing in Atmospheric CO ₂ Levels

   https://doi.org/10.1111/pce.15346  

   Shi, Xiaoxiao; Hannon, Nathan M; Bloom, Arnold J (December 2024, Plant, Cell & Environment)

   ABSTRACT Rubisco, the most prevalent protein on Earth, catalyzes both a reaction that initiates C₃ carbon fixation, and a reaction that initiates photorespiration, which stimulates protein synthesis. Regulation of the balance between these reactions under atmospheric CO₂ fluctuations remains poorly understood. We have hypothesized that vascular plants maintain organic carbon‐to‐nitrogen homeostasis by adjusting the relative activities of magnesium and manganese in chloroplasts to balance carbon fixation and nitrate assimilation rates. The following examined the influence of magnesium and manganese on carboxylation and oxygenation for rubisco purified from two ecotypes of Plantago lanceolataL.: one adapted to the elevated CO₂ atmospheres that occur near a natural CO₂ spring and the other adapted to more typical CO₂ atmospheres that occur nearby. The plastid DNA coding for the large unit of rubisco was similar in both ecotypes. The kinetics of rubiscos from the two ecotypes differed more when associated with manganese than magnesium. Specificity for CO₂over O₂ (S_c/o) for rubisco from both ecotypes was higher when the enzymes were bound to magnesium than manganese. Differences in the responses of rubisco from P. lanceolata to the metals may account for the adaptation of this species to different CO₂ environments. 

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2. Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans

   https://doi.org/10.1111/nph.18835  

   Morley, Stewart A.; Ma, Fangfang; Alazem, Mazen; Frankfater, Cheryl; Yi, Hochul; Burch‐Smith, Tessa; Clemente, Tom Elmo; Veena, Veena; Nguyen, Hanh; Allen, Doug K. (September 2023, New Phytologist)

   Summary Central metabolism produces amino and fatty acids for protein and lipids that establish seed value. Biosynthesis of storage reserves occurs in multiple organelles that exchange central intermediates including two essential metabolites, malate, and pyruvate that are linked by malic enzyme. Malic enzyme can be active in multiple subcellular compartments, partitioning carbon and reducing equivalents for anabolic and catabolic requirements. Prior studies based on isotopic labeling and steady‐state metabolic flux analyses indicated malic enzyme provides carbon for fatty acid biosynthesis in plants, though genetic evidence confirming this role is lacking. We hypothesized that increasing malic enzyme flux would alter carbon partitioning and result in increased lipid levels in soybeans.Homozygous transgenic soybean plants expressing Arabidopsis malic enzyme alleles, targeting the translational products to plastid or outside the plastid during seed development, were verified by transcript and enzyme activity analyses, organelle proteomics, and transient expression assays. Protein, oil, central metabolites, cofactors, and acyl‐acyl carrier protein (ACPs) levels were quantified overdevelopment.Amino and fatty acid levels were altered resulting in an increase in lipids by 0.5–2% of seed biomass (i.e. 2–9% change in oil).Subcellular targeting of a single gene product in central metabolism impacts carbon and reducing equivalent partitioning for seed storage reserves in soybeans. 

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3. Prospects for Engineering Biophysical CO2 Concentrating Mechanisms into Land Plants to Enhance Yields

   https://doi.org/10.1146/annurev-arplant-081519-040100  

   Hennacy, Jessica H; Jonikas, Martin C (March 2020, Annual review of plant biology)

   Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO2 fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO2-fixing enzyme Rubisco using biophysical CO2 concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO2 in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO2 via an organic intermediate, such as malate in the case of C4 CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants. 

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4. Reduced global plant respiration due to the acclimation of leaf dark respiration coupled with photosynthesis

   https://doi.org/10.1111/nph.19355  

   Ren, Yanghang; Wang, Han; Harrison, Sandy P; Prentice, I Colin; Atkin, Owen K; Smith, Nicholas G; Mengoli, Giulia; Stefanski, Artur; Reich, Peter B (January 2024, New Phytologist)

   Summary Leaf dark respiration (R_d) acclimates to environmental changes. However, the magnitude, controls and time scales of acclimation remain unclear and are inconsistently treated in ecosystem models.We hypothesized thatR_dand Rubisco carboxylation capacity (V_cmax) at 25°C (R_d,25,V_cmax,25) are coordinated so thatR_d,25variations supportV_cmax,25at a level allowing full light use, withV_cmax,25reflecting daytime conditions (for photosynthesis), andR_d,25/V_cmax,25reflecting night‐time conditions (for starch degradation and sucrose export). We tested this hypothesis temporally using a 5‐yr warming experiment, and spatially using an extensive field‐measurement data set. We compared the results to three published alternatives:R_d,25declines linearly with daily average prior temperature;R_dat average prior night temperatures tends towards a constant value; andR_d,25/V_cmax,25is constant.Our hypothesis accounted for more variation in observedR_d,25over time (R² = 0.74) and space (R² = 0.68) than the alternatives. Night‐time temperature dominated the seasonal time‐course ofR_d, with an apparent response time scale ofc.2 wk.V_cmaxdominated the spatial patterns.Our acclimation hypothesis results in a smaller increase in globalR_din response to rising CO₂and warming than is projected by the two of three alternative hypotheses, and by current models. 

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5. Pyruvate formate-lyase activating enzyme: The catalytically active 5′-deoxyadenosyl radical caught in the act of H-atom abstraction

   https://doi.org/10.1073/pnas.2314696120  

   Lundahl, Maike N; Yang, Hao; Broderick, William E; Hoffman, Brian M; Broderick, Joan B (November 2023, Proceedings of the National Academy of Sciences)

   Enzymes of the radicalS-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG₇₃₄YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG₇₃₄YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5′C is covalently bound to the unique iron of the [4Fe–4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G₇₃₄• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe–C5′ bond generates the nominally “free” 5′-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5′-dAdo• directly abstracts an H-atom from the peptide to generate the G₇₃₄• peptide radical trapped in the PFL-AE active site. These observations reveal the 5′-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes. 

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