Membraneless organelles containing the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are a common feature of organisms utilizing CO
2 concentrating mechanisms to enhance photosynthetic carbon acquisition. In cyanobacteria and proteobacteria, the Rubisco condensate is encapsulated in a proteinaceous shell, collectively termed a carboxysome, while some algae and hornworts have evolved Rubisco condensates known as pyrenoids. In both cases, CO
2 fixation is enhanced compared with the free enzyme. Previous mathematical models have attributed the improved function of carboxysomes to the generation of elevated CO
2 within the organelle via a colocalized carbonic anhydrase (CA) and inwardly diffusing HCO
3−, which have accumulated in the cytoplasm via dedicated transporters. Here, we present a concept in which we consider the net of two
protons produced in every Rubisco carboxylase reaction. We evaluate this in a reaction–diffusion compartment model to investigate functional advantages these
protons may provide Rubisco condensates and carboxysomes, prior to the evolution of HCO
3− accumulation. Our model highlights that diffusional resistance to reaction species within a condensate allows Rubisco-derived
protons to drive the conversion of HCO
3− to CO
2 via colocalized CA, enhancing both condensate [CO
2] and Rubisco rate. Protonation of Rubisco substrate (RuBP) and product (phosphoglycerate) plays an important role in modulating internal pH and CO
2 generation. Application of the model to putative evolutionary ancestors, prior to contemporary cellular HCO
3− accumulation, revealed photosynthetic enhancements along a logical sequence of advancements, via Rubisco condensation, to fully formed carboxysomes. Our model suggests that evolution of Rubisco condensation could be favored under low CO
2 and low light environments.Carbon dioxide (CO
2) fixation into the biosphere has been primarily dependent upon action of the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) over geological timescales. Rubisco is distinguished by the competitive inhibition of its carboxylation activity by the alternative substrate molecular oxygen (O
2), leading to loss of CO
2 and metabolic energy via a photorespiratory pathway in most phototrophs (
1). Almost certainly the most abundant enzyme on the planet (
2), Rubisco’s competing catalytic activities have required evolution of the enzyme, and/or its associated machinery, to maintain capture of sufficient carbon into organic molecules to drive life on Earth. In concert with geological weathering, the evolution of oxygenic photosynthesis ∼2.4 billion years ago has transformed the atmosphere from one rich in CO
2 and low in O
2 to one in which the relative abundances of these gases has overturned (
3). Under these conditions, the Rubisco oxygenation reaction has increased, to the detriment of CO
2 capture. This catalytic paradox has led to different adaptive solutions to ensure effective rates of photosynthetic CO
2 fixation including the evolution of the kinetic properties of the enzyme (
4), increases in Rubisco abundance in the leaves of many terrestrial C
3 plants (
5), and the evolution of diverse and complex CO
2 concentrating mechanisms (CCMs) in many cyanobacteria, algae, and more recently hornworts, CAM, and C
4 plants (
6,
7).A defining characteristic of contemporary cyanobacteria is the encapsulation of their Rubisco enzymes within specialized, protein-encased microcompartments called carboxysomes (
8). These microbodies are central to the cyanobacterial CCM, in which cellular bicarbonate (HCO
3−) is elevated by a combination of membrane-associated HCO
3− pumps and CO
2-to-HCO
3− converting complexes (
9–
11), to drive CO
2 production within the carboxysome by an internal carbonic anhydrase (CA;
12,
13). This process results in enhanced CO
2 fixation, with a concomitant decrease in oxygenation, and is a proposed evolutionary adaptation to a low CO
2 atmosphere (
14,
15).An analogous CCM operates in many algal and hornwort species, which contain chloroplastic Rubisco condensates called pyrenoids (
16,
17). Pyrenoids are liquid–liquid phase separated Rubisco aggregates, which lack the protein shell of a carboxysome (
18). These CCMs accumulate HCO
3− and convert it to CO
2 within the pyrenoid to maximize CO
2 fixation. Common to cyanobacterial and algal systems is the presence of unique Rubisco-binding proteins, enabling condensation of Rubisco from the bulk cytoplasm (
18–
25). Condensation of proteins to form aggregates within the cell is increasingly recognized as a means by which cellular processes can be segregated and organized, across a broad range of biological systems (
26–
28). The commonality of pyrenoid and carboxysome function (
29) despite their disparate evolutionary histories (
6), suggests a convergence of function driven by Rubisco condensation. In addition, dependency of functional CCMs on their pyrenoids or carboxysomes (
30,
31) has led to the speculation that the evolution of Rubisco organization into membraneless organelles likely preceded systems which enabled elevated cellular HCO
3− (
14), raising the possibility that Rubisco condensation and encapsulation may have been the first steps in modern aquatic CCM evolution.We consider here that, in a primordial model system without active HCO
3− accumulation, co-condensation of Rubisco and CA enzymes is beneficial for the elevation of internal CO
2 because Rubisco carboxylation produces a net of two
protons for every reaction turnover (
SI Appendix, Fig. S1;
32,
33). These
protons can be used within the condensate to convert HCO
3− to CO
2, with pH lowered and CO
2 elevated as a result of restricted outward diffusion due to the high concentration of protein in the condensate and surrounding cell matrix acting as a barrier to diffusion. We propose that proton release within a primordial Rubisco condensate enabled the evolution of carboxysomes with enhanced carboxylation rates, prior to advancements which enabled cellular HCO
3− accumulation.
相似文献