BioSciences

Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron microscopy to reveal a unique Fe starvation-dependent arrangement of light-harvesting chlorophyll (LHC) proteins where Fe starvation-induced TIDI1 is found in an additional tetramer of LHC proteins associated with PSI in Dunaliella tertiolecta and Dunaliella salina. These cosmopolitan green algae are resilient to poor Fe nutrition. TIDI1 is a distinct LHC protein that co-occurs in diverse algae with flavodoxin (an Fe-independent replacement for the Fe-containing ferredoxin). The antenna expansion in eukaryotic algae we describe here is reminiscent of the iron-starvation induced (isiA-encoding) antenna ring in cyanobacteria, which typically co-occurs with isiB, encoding flavodoxin. Our work showcases the convergent strategies that evolved after the Great Oxidation Event to maintain PSI capacity.

Photosynthetic organisms coordinate their metabolism and growth with diurnal light, which can range in intensity from limiting to excessive. Little is known about how light intensity impacts the diurnal program in Chlamydomonas reinhardtii, or how diurnal rhythms in gene expression and metabolism shape photoprotective responses at different times of day. To address these questions, we performed a systems analysis of synchronized Chlamydomonas populations acclimated to low, moderate, and high diurnal light. Transcriptomic and proteomic data revealed that the Chlamydomonas rhythmic gene expression program is resilient to limiting and excess light: genome-wide, waves of transcripts, and proteins peak at the same times in populations acclimated to stressful light intensities as in populations acclimated to moderate light. Yet, diurnal photoacclimation gives rise to hundreds of gene expression changes, even at night. Time course measurements of photosynthetic efficiency and pigments responsive to excess light showed that high light-acclimated cells partially overcome photodamage in the latter half of the day prior to cell division. Although gene expression and photodamage are dynamic over the diurnal cycle, Chlamydomonas populations acclimated to low and high diurnal light maintain altered photosystem abundance, thylakoid architecture, and non-photochemical quenching capacity through the night phase. This suggests that cells remember or anticipate the light intensities that they have typically encountered during the day. The integrated data constitute an excellent resource for understanding photoacclimation in eukaryotes under environmentally relevant conditions.

Cu-based oxides and hydroxides represent an important class of materials from a catalytic and corrosion perspective. In this study, we investigate the formation of bulk and surface Cu³⁺ species that are stable under water oxidation catalysis in alkaline media. So far, no direct evidence existed for the presence of hydroxides (CuOOH) or oxides, which were primarily proposed by theory. This work directly places CuOOH in the oxygen evolution reaction (OER) Pourbaix stability region with a calculated free energy of -208.68 kJ/mol, necessitating a revision of known Cu-H₂O phase diagrams. We also predict that the active sites of CuOOH for the OER are consistent with a bridge O* site between the two Cu³⁺ atoms with onset at ≥1.6 V vs the reversible hydrogen electrode (RHE), aligning with experimentally observed Cu^2+/3+ oxidation waves in cyclic voltammetry of Fe-free and Fe-spiked copper in alkaline media. Trace amounts of Fe (2 μg/mL (ppm) to 5 μg/mL) in the solution measurably enhance the catalytic activity of the OER, likely due to the adsorption of Fe species that serve as the active sites . Importantly, modulation excitation X-ray absorption spectroscopy (ME-XAS) of a Cu thin-film electrode shows a distinct Cu³⁺ fingerprint under OER conditions at 1.8 V vs RHE. Additionally, in situ Raman spectroscopy of polycrystalline Cu in 0.1 mol/L (M) KOH revealed features consistent with those calculated for CuOOH in addition to CuO. Overall, this work provides direct evidence of bulk electrochemical Cu³⁺ species under OER conditions and expands our longstanding understanding of the oxidation mechanism and catalytic activity of copper.

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, "pipe strap" conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.

Serial crystallography is an important technique with unique abilities to resolve enzymatic transition states, minimize radiation damage to sensitive metalloenzymes and perform de novo structure determination from micrometre-sized crystals. This technique requires the merging of data from thousands of crystals, making manual identification of errant crystals unfeasible. cctbx.xfel.merge uses filtering to remove problematic data. However, this process is imperfect, and data reduction must be robust to outliers. We add robustness to cctbx.xfel.merge at the step of uncertainty determination for reflection intensities. This step is a critical point for robustness because it is the first step where the data sets are considered as a whole, as opposed to individual lattices. Robustness is conferred by reformulating the error-calibration procedure to have fewer and less stringent statistical assumptions and incorporating the ability to down-weight low-quality lattices. We then apply this method to five macromolecular XFEL data sets and observe the improvements to each. The appropriateness of the intensity uncertainties is demonstrated through internal consistency. This is performed through theoretical CC_1/2 and I/σ relationships and by weighted second moments, which use Wilson's prior to connect intensity uncertainties with their expected distribution. This work presents new mathematical tools to analyze intensity statistics and demonstrates their effectiveness through the often underappreciated process of uncertainty analysis.

Photosynthesis converts solar energy into chemical energy through coordinated energy transfer between light-harvesting complexes and reaction centers (RCs). Understanding exciton motion, particularly the exciton diffusion length, is essential for optimizing energy efficiency in photosystems. In this work, we combine intensity-cycling transient absorption spectroscopy with kinetic Monte Carlo (kMC) simulation to investigate exciton motion in the C2S2 photosystem II supercomplex of spinach. Using exciton-exciton annihilation, revealed in the fifth-order response, we experimentally estimate an exciton diffusion length of 10.9 nm based on a 3D normal diffusion model, suggesting the ability of excitons to traverse the supercomplex. However, kMC simulations reveal that exciton motion is sub-diffusive because of spatial constraints and the strong RC traps. An anomalous diffusion model analysis of the experimental data yields a diffusion length of 9.7 nm, while the simulated diffusion length is 7.4 nm. The variable exciton residence time across subunits, partly influenced by their connectivity to the trap, indicates inhomogeneous annihilation probability and suggests how plants balance efficient light harvesting with photoprotection. We also explore the influence of specific assumptions in the annihilation simulation, which are challenging to access in more complex environments, such as the thylakoid membrane. Our study provides a framework for studying exciton dynamics using exciton-exciton annihilation, which can be extended to understand the light-harvesting efficiencies of larger, more complex photosynthetic assemblies.

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe-S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

Almost every electron microscopy experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive materials. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space movies of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting domains undergoes internal rearrangement as a function of accumulating electron fluence, causing the intensities of some associated Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the isotropic propagation of delocalized radiolytic damage well beyond the direct footprint of the incident beam. We refer to these expanding tides of amorphization as "impact craters."

Antibiotics that operate via multiple mechanisms of action are a promising strategy to combat growing resistance. Previous studies have shown that dual action antifolates formed from a pyrroloquinazolinediamine core can inhibit the growth of bacterial pathogens without developing resistance. In this work, we expand the scope of dual action antifolates by repurposing the 2,4-diamino-1,6-dihydro-1,3,5-triazine (DADHT) cycloguanil scaffold to a variety of derivatives designed to inhibit dihydrofolate reductase (DHFR) and disrupt bacterial membranes. Dual mechanism DADHTs have activity against a variety of target pathogens, including Mycobacterium tuberculosis, Mycobacterium abscessus, and Pseudomonas aeruginosa, among other ESKAPEE organisms. Through X-ray crystallography, we confirmed engagement of the Escherichia coli DHFR target and found that some DADHTs stabilize a previously unobserved conformation of the enzyme but, broadly, bind in the occluded conformation. Using in vitro inhibition of purified E. coli and Staphylococcus aureus DHFR and disruption of E. coli membranes, we determined that alkyl substitution of dihydrotriazine at the 6-position best optimizes the DADHT's two mechanisms of action. By employing both mechanisms, the DADHT spectrum of activity was extended beyond the scope of traditional antifolates. We are optimistic that the dual mechanism approach, particularly through the action of antifolates, offers a unique means of combating hard-to-treat bacterial infections.