Search NASA⌕ Search

SEARCH · Search NASA

Results for “thylakoid structure”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

36 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗
DOE OSTI2020

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Abstract Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Small angle neutron scattering and lipidomic analysis of a native, trimeric PSI-SMALP from a thermophilic cyanobacteria

The use of styrene-maleic acid copolymers (SMAs) to produce membrane protein-containing nanodiscs without the initial detergent isolation has gained significant interest over the last decade. We have previously shown that a Photosystem I SMALP from the thermophilic cyanobacterium, Thermosynechococcus elongatus (PSI-SMALP), has much more rapid energy transfer and charge separation in vitro than detergent isolated PSI complexes. In this study, we have utilized small-angle neutron scattering (SANS) to better understand the geometry of these SMALPs. These techniques allow us to investigate the size and shape of these particles in their fully solvated state. Further, the particle's proteolipid core and detergent shell or copolymer belt can be interrogated separately using contrast variation, a capability unique to SANS. Here we report the dimensions of the Thermosynechococcus elongatus PSI-SMALP containing a PSI trimer. At ~1.5 MDa, PSI-SMALP is the largest SMALP to be isolated; our lipidomic analysis indicates it contains ~1300 lipids/per trimeric particle, >40-fold more than the PSI-DDM particle and > 100 fold more than identified in the 1JB0 crystal structure. Interestingly, the lipid composition to the PSI trimer in the PSI-SMALP differs significantly from bulk thylakoid composition, being enriched ~50 % in the anionic sulfolipid, SQDG. Finally, utilizing the contrast match point for the SMA 1440 copolymer, we also can observe the ~1 nm SMA copolymer belt surrounding this SMALP for the first time, consistent with most models of SMA organization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗
DOE OSTI2023

Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins

In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reply to: Is the debate over grana stacking formation finally solved?

In plants, the photosynthetic pigment–protein complexes catalysing energy conversion are harboured in the thylakoid membrane system of chloroplasts. Recent breakthroughs in electron tomography reveal the sophisticated architecture of this unique membrane system with stacked grana as a structural hallmark. Here, a long-standing question has been whether the combination of physicochemical forces alone can explain the strict stacking of grana with an intermembrane separation of 3–4 nm. In our 2017 Nature Plants paper, we argued that the balance between attractive van der Waals (vdW) forces (F vdW ) and repulsive electrostatic (F el ) and hydrostructural (F hydro ) forces could explain grana stacking, in contrast with previous reports. Our finding was challenged in the report by Gudarzi et al. This reply addresses this critique.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Photosynthetic biohybrid systems for solar fuels catalysis

Photosynthetic reaction center (RC) proteins are finely tuned molecular systems optimized for solar energy conversion. RCs effectively capture and convert sunlight with near unity quantum efficiency utilizing light-induced directional electron transfer through a series of molecular cofactors embedded within the protein core to generate a long-lived charge separated state with a useable electrochemical potential. Of current interest are new strategies that couple RC chemistry to the direct synthesis of energy-rich compounds. This Feature Article highlights recent work from our lab on RC and RC-inspired hybrid systems that capture the Sun's energy and convert it to chemical energy in the form of H2, a carbon-neutral energy source derived from water. Further, biohybrids made from the Photosystem I (PSI) RC are among the best photocatalytic H2-producing protein hybrids to date. Targeted self-assembly strategies that couple abiotic catalysts to PSI translate to catalyst incorporation at intrinsic PSI sites within thylakoid membranes to achieve complete solar water-splitting systems. RC-inspired biohybrids interface synthetic photosensitizers and molecular catalysts with small proteins to create photocatalytic systems and enable the spectroscopic discernment of the structural features and electron transfer processes that underpin solar-driven proton reduction. In total, these studies showcase the incredible scientific opportunities photosynthetic biohybrid research provides for harnessing the optimal qualities of both artificial and natural photosynthetic systems and developing materials that capture, convert, and store solar energy as a fuel.

14 SOLAR ENERGY↗
DOE OSTI2025

From cytoplasm to lumen—mapping the free pools of protein subunits of three photosynthetic complexes using quantitative mass spectrometry

The phycobilisome (PBS) captures light energy and transfers it to photosystem I (PSI) and photosystem II (PSII). Which and how many copies of protein subunits in PBSs, PSI, and PSII remain unbound in thylakoids are unknown. Here, quantitative mass spectrometry (QMS) was used to quantify substantial pools of free extrinsic subunits of PSII and PSI. Interestingly, the membrane intrinsic PsaL is 3-fold higher than PsaA/B. This scenario complements the static structures of these complexes as revealed by X-ray crystallography and cryo-EM. Furthermore, the ratios of ApcG and photoprotective OCP over PBS indicate a pool of extra ApcG. The 2.5 ratio of CpcG-PBS over CpcL-PBS improves our understanding of these light-harvesting complexes involved in energy capture and photoprotection in cyanobacteria.

cyanobacteria↗
DOE OSTI2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the “dark complex,” modulate metabolic flux at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.

Johnson, Connah G.↗
DOE OSTI2021

Singlet Oxygen Leads to Structural Changes to Chloroplasts during their Degradation in the Arabidopsis thaliana plastid ferrochelatase two Mutant

Abstract During stress, chloroplasts produce large amounts of reactive oxygen species (ROS). Chloroplasts also contain many nutrients, including 80% of a leaf’s nitrogen supply. Therefore, to protect cells from photo-oxidative damage and to redistribute nutrients to sink tissues, chloroplasts are prime targets for degradation. Multiple chloroplast degradation pathways are induced by photo-oxidative stress or nutrient starvation, but the mechanisms by which damaged or senescing chloroplasts are identified, transported to the central vacuole and degraded are poorly defined. Here, we investigated the structures involved with degrading chloroplasts induced by the ROS singlet oxygen (1O2) in the Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant. Under mild 1O2 stress, most fc2 chloroplasts appeared normal, but had reduced starch content. A subset of chloroplasts was degrading, and some protruded into the central vacuole via ‘blebbing’ structures. A 3D electron microscopy analysis demonstrated that up to 35% of degrading chloroplasts contained such structures. While the location of a chloroplast within a cell did not affect the likelihood of its degradation, chloroplasts in spongy mesophyll cells were degraded at a higher rate than those in palisade mesophyll cells. To determine if degrading chloroplasts have unique structural characteristics, allowing them to be distinguished from healthy chloroplasts, we analyzed fc2 seedlings grown under different levels of photo-oxidative stress. A correlation was observed among chloroplast swelling, 1O2 signaling and the state of degradation. Finally, plastoglobule (PG) enzymes involved in chloroplast disassembly were upregulated while PGs increased their association with the thylakoid grana, implicating an interaction between 1O2-induced chloroplast degradation and senescence pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Regulatory Coordination of Photophysical, Photochemical, and Biochemical Reactions in the Photosynthesis of Land Plants

Balance among the sequential photophysical, photochemical, and biochemical reactions of photosynthesis is needed for converting fleeting energy in light to stable energy in chemical bonds. Any imbalance acts as either a bottleneck for limiting photosynthetic efficiency or an agent for inducing structural and functional damage to photosynthetic apparatus. Not only must each reaction be carefully regulated, but regulatory processes must also be coordinated across the reactions. However, regulations of different stages of photosynthesis have rarely been studied jointly. Non-photochemical quenching (NPQ) and stomatal conductance (g s ) are key regulators of photophysical and biochemical reactions, respectively. Existing evidence suggests that the redox state of plastoquinone regulates g s and that the photochemical reactions are partially regulated by the ultrastructural dynamics of thylakoids induced by osmotic water fluxes in chloroplasts of land plants. To examine how these regulations are coordinated and feedback to each other, we simultaneously measured NPQ and gs and inferred the redox state of plastoquinone and the light-induced thylakoid swelling/shrinking on numerous C 3 and C 4 species. For all species measured, NPQ and gs covary with the redox states of the electron transport chain, particularly plastoquinone, and increase as thylakoid swelling is inferred. NPQ has the maximal sensitivity at the light intensity at which thylakoid is inferred to be fully swollen. Our findings suggest that plant energy and water use strategies are intimately linked by evolution, and studying the regulations of different photosynthetic stages as a whole can lead to new insights of the functioning of photosynthetic machinery in dynamic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Rubredoxin 1 promotes the proper folding of D1 and is not required for heme b 559 assembly in Chlamydomonas photosystem II

Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b 559 iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome b 559 , using the RBD1-lacking 2pac mutant from Chlamydomonas reinhardtii, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant 2pac ftsh1-1, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the 2pac ftsh1-1 background and found that α and β cytochrome b 559 subunits are still present and coordinate heme b 559 as in the WT. Interestingly, immunoblot analysis of dark- and low light–grown 2pac ftsh1-1 showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme b 559 assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly via delivery or reduction of the nonheme iron during PSII assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Elucidating mechanisms of Photosystem I assembly and repair (Final Technical Report)

Oxygenic photosynthesis generates the carbohydrates and oxygen that support life on earth. Central to this process are photosystems I and II (PSI and PSII), large protein-pigment complexes that are among the most complex macromolecular structures in nature. Impressive advances have been made in understanding the structure and photochemical mechanisms of PSI and PSII. However, less is known about the mechanisms underlying their biogenesis. The overarching goal of this project was to elucidate mechanisms of photosystem assembly. Several proteins that are not found in mature PSI or PSII are essential for their assembly, but the assembly pathways and the role of each assembly factor are just starting to emerge. During the course of this project, we advanced understanding of this problem in several ways. First, we addressed the spatial organization of photosystem assembly by localizing many known assembly factors to specific subdomains of thylakoid membranes in plant chloroplasts. This work revealed that the "curvature" domain - the highly curved periphery of stacked granal membrane disks - is a center of photosystem assembly. However, whereas some PSI assembly factors localized exclusively to the curvature domain, another was found exclusively in granal margins and unstacked membranes. This spatial partitioning suggests an assembly line along which different assembly intermediates are physically segregated. Most assembly factors localized similarly in dark-adapted and illuminated plants, but one PSII assembly factor shifted from the curvature domain to unstacked membranes upon illumination, suggesting an unanticipated role in the repair of light-induced PSII damage. Whereas most PSII subunits were found primarily in grana stacks (as expected), one PSII subunit, PsbP, was prominent also in the curvature fraction, suggesting that PsbP has functions beyond its role in mature PSII, possibly in biogenesis or repair.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ultrastructure of the green alga Dunaliella salina strain CCAP19/18 (Chlorophyta) as investigated by quick-freeze deep-etch electron microscopy

The single-celled green alga Dunaliella salina is a model system for studies on stress biology, in particular regarding secondary carotenoid accumulation. Under non-stress conditions the cells are green, but under abiotic stress the cells turn orange, because they switch their metabolism and accumulate β-Carotene in globules in the chloroplast. For the first time, Quick-freeze deep-etch electron microscopy was used to visualize cellular structures in green and orange cells of D. salina strain CCAP19/18. This allowed us to present an in-depth analysis of the cellular ultrastructure describing and comparing the features of the two cell types. Our images illustrate the presence of a pericellular matrix for this strain of D. salina. The pericellular matrix was spongy and strands of unknown material anchored it into the plasma membrane. The cytoplasm contained a variety of vesicles, vacuoles, and acidocalcisomes. We could show for strain CCAP19/18 that cytoplasmic lipid bodies were often in close proximity to and sometimes in contact with the outer chloroplast envelope membrane and with the endoplasmic reticulum. Major visible differences between green and orange cells were in the chloroplast: the orange cells have greatly reduced amounts of thylakoid membranes and greatly increased numbers of β-Carotene globules. We showed that the β-Carotene globules often made point contacts with thylakoid membranes, and frequently laid side-by-side along the thylakoid membrane surface, providing support to studies that indicated exchange of molecules between β-Carotene globules and thylakoid membranes. A unique finding was the β-Carotene globule duplets, suggesting intermediate stages in β-Carotene globule morphogenesis. Overall, the β-Carotene globules appear to be similar to plant plastoglobuli. We provide this description of the cellular ultrastructure features as a resource in the context of the recent publication of the genome of D. salina strain CCAP19/18 to expand on the knowledge regarding this novel reference strain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Elements of Life, Photosynthesis and Genomics

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute’s efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets — focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors — that are well-used and appreciated by the community. Finally, a new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true “green yeast” and as a platform for engineering algae to produce useful bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism

The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. merolae 's cellular affinity for CO 2 is stronger than the affinity of its rubisco for CO 2 . This finding provided additional evidence that C. merolae operates a CCM while lacking the structures and functions characteristic of CCMs in other organisms. To test how such a CCM could function, we created a mathematical compartmental model of a simple CCM, distinct from those we have seen previously described in detail. The results of our modeling supported the feasibility of this proposed minimal and non-canonical CCM in C. merolae . To facilitate the robust modeling of this process, we measured and incorporated physiological and enzymatic parameters into the model. Additionally, we trained a surrogate machine-learning model to emulate the mechanistic model and characterized the effects of model parameters on key outputs. This parameter exploration enabled us to identify model features that influenced whether the model met the experimentally derived criteria for functional carbon concentration and efficient energy usage. Such parameters included cytosolic pH, bicarbonate pumping cost and kinetics, cell radius, carboxylation velocity, number of thylakoid membranes, and CO 2 membrane permeability. Our exploration thus suggested that a non-canonical CCM could exist in C. merolae and illuminated the essential features generally necessary for CCMs to function.

Steensma, Anne K. [Michigan State Univ., East Lans↗