A Protein Blueprint of the Diatom CO2-Fixing Organelle

Abstract

Diatoms are central to the global carbon cycle. At the heart of diatom carbon fixation is an overlooked organelle called the pyrenoid, where concentrated CO2is delivered to densely packed Rubisco. Diatom pyrenoids fix approximately one-fifth of global CO2but virtually nothing is known about this organelle in diatoms. Using large-scale fluorescence protein tagging and affinity purification-mass spectrometry we generate a high-confidence spatially-defined protein-protein interaction network for the diatom pyrenoid. Within our pyrenoid interactome are 10 proteins with no known function. Six form a static shell encapsulating the Rubisco matrix of the pyrenoid, with the shell critical for pyrenoid structural integrity and potentially acting as a CO2diffusion barrier. Although no conservation at a sequence level, the diatom pyrenoid shares some structural similarities to prokaryotic carboxysomes. Collectively, our results support the convergent evolution of pyrenoids across the two main plastid lineages and uncovers a major structural and functional component of global CO2fixation.

A carboxysome‐based CO2 concentrating mechanism for C3 crop chloroplasts: advances and the road ahead

“…A similar concept has been suggested for encapsulins which self-assemble and have been demonstrated to encapsulate specific cargo (Giessen & Silver, 2017). The recent identification of encapsulated pyrenoids provides further models for novel Rubisco compartmentalisation systems (Nam et al, 2023;Shimakawa et al, 2023). Collectively, these examples demonstrate that novel synthetic biology approaches could be considered to transplant a faster Rubisco into plants whilst also providing a localised and optimal CO 2 concentration for the enzyme to operate within.…”

“…Surrounding this Rubisco matrix is a starch sheath that minimises CO 2 leakage (Toyokawa et al, 2020), while tubules also traverse the matrix and are speculated to deliver CO 2 (Engel et al, 2015). In recent analyses of diatom pyrenoids, protein shells have been identified as potential diffusional barriers to substrate entry (Nam et al, 2023;Shimakawa et al, 2023). Similar to carboxysomes, pyrenoid Rubisco phaseseparates with EPYC1 to form a dynamic, flexible matrix (Freeman-Rosenzweig et al, 2017;He et al, 2020He et al, , 2023Wunder et al, 2018), in an interaction mediated by Rubisco small subunit helices (Atkinson et al, 2019;Meyer et al, 2012).…”

Advancing chloroplast synthetic biology through high-throughput plastome engineering ofChlamydomonas reinhardtii

“…20,21 Moreover, several subunits of the light-harvesting and carbon fixation machineries are encoded by the plastome, which makes the direct manipulation of the chloroplast genome central for any efforts that aim at improving photosynthetic yield. One current example are efforts of integrating carboxysome and pyrenoid bases CO2-concentrating mechanism into plant chloroplasts to boost photosynthetic efficiency [22][23][24][25][26][27][28][29][30] These examples emphasize the growing need to develop advanced genetic tools for the direct manipulation of the plastome. However, chloroplast genome engineering offers additional advantages compared to nuclear genome-based engineering strategies of chloroplast functions.…”