The structure of the stress-induced photosystem I-IsiA antenna supercomplex

Dryland Endolithic Chroococcidiopsis and Temperate Fresh Water Synechocystis Have Distinct Membrane Lipid and Photosynthesis Acclimation Strategies upon Desiccation and Temperature Increase

An effect of climate change is the expansion of drylands in temperate regions, predicted to affect microbial biodiversity. Since photosynthetic organisms are at the base of ecosystem's trophic networks, we compared an endolithic desiccation-tolerant Chroococcidiopsis cyanobacteria isolated from gypsum rocks in the Atacama Desert with a freshwater desiccation-sensitive Synechocystis. We sought whether some acclimation traits in response to desiccation and temperature variations were shared, to evaluate the potential of temperate species to possibly become resilient to future arid conditions. When temperature varies, Synechocystis tunes the acyl composition of its lipids, via a homeoviscous acclimation mechanism known to adjust membrane fluidity, whereas no such change occurs in Chroococcidiopsis. Vice versa, a combined study of photosynthesis and pigment content shows that Chroococcidiopsis remodels its photosynthesis components and keeps an optimal photosynthetic capacity at all temperatures, whereas Synechocystis is unable to such adjustment. Upon desiccation on a gypsum surface, Synechocystis is rapidly unable to revive, whereas Chroococcidiopsis is capable to recover after three weeks. Using X-ray diffraction, we found no evidence that Chroococcidiopsis could use water extracted from gypsum crystals in such conditions as a surrogate for missing water. The sulfolipid sulfoquinovosyldiacylglycerol becomes the prominent membrane lipid in both dehydrated cyanobacteria, highlighting an overlooked function for this lipid. Chroococcidiopsis keeps a minimal level of monogalactosyldiacylglycerol, which may be essential for the recovery process. Results support that two independent adaptation strategies have evolved in these species to cope with temperature and desiccation increase and suggest some possible scenarios for microbial biodiversity change triggered by climate change.

Unveiling large charge transfer character of PSII in an iron-deficient cyanobacterial membrane: A Stark fluorescence spectroscopy study

In this work, we applied Stark fluorescence spectroscopy to an iron-stressed cyanobacterial membrane to reveal key insights about the electronic structures and excited state dynamics of the two important pigment-protein complexes, IsiA and PSII, both of which prevail simultaneously within the membrane during iron deficiency and whose fluorescence spectra are highly overlapped and hence often hardly resolved by conventional fluorescence spectroscopy. Thanks to the ability of Stark fluorescence spectroscopy, the fluorescence signatures of the two complexes could be plausibly recognized and disentangled. The systematic analysis of the SF spectra, carried out by employing standard Liptay formalism with a realistic spectral deconvolution protocol, revealed that the IsiA in an intact membrane retains almost identical excited state electronic structures and dynamics as compared to the isolated IsiA we reported in our earlier study. Moreover, the analysis uncovered that the excited state of the PSII subunit of the intact membrane possesses a significantly large CT character. The observed notably large magnitude of the excited state CT character may signify the supplementary role of PSII in regulative energy dissipation during iron deficiency.

Inhomogeneous energy transfer dynamics from iron-stress-induced protein A to photosystem I

Cyanobacteria respond to iron limitation by producing the pigment-protein complex IsiA, forming rings associated with photosystem I (PSI). Initially considered a chlorophyll-storage protein, IsiA is known to act as an auxiliary light-harvesting antenna of PSI, increasing its absorption cross-section and reducing the need for iron-rich PSI core complexes. Spectroscopic studies have demonstrated efficient energy transfer from IsiA to PSI. Here we investigate the room-temperature excitation dynamics in isolated PSI-IsiA, PSI, IsiA monomer complexes and IsiA aggregates using two-dimensional electronic spectroscopy. Cross analyses of the data from these three samples allow us to resolve components of energy transfer between IsiA and PSI with lifetimes of 2-3 ps and around 20 ps. Structure-based Förster theory calculations predict a single major timescale of IsiA-PSI equilibration, that depends on multiple energy transfer routes between different IsiA subunits in the ring. Despite the experimentally observed lifetime heterogeneity, which is attributed to structural heterogeneity of the supercomplexes, IsiA is found to be a unique, highly efficient, membrane antenna complex in cyanobacteria.

Investigating the Balance between Structural Conservation and Functional Flexibility in Photosystem I

Photosynthesis, as the primary source of energy for all life forms, plays a crucial role in maintaining the global balance of energy, entropy, and enthalpy in living organisms. Among its various building blocks, photosystem I (PSI) is responsible for light-driven electron transfer, crucial for generating cellular reducing power. PSI acts as a light-driven plastocyanin-ferredoxin oxidoreductase and is situated in the thylakoid membranes of cyanobacteria and the chloroplasts of eukaryotic photosynthetic organisms. Comprehending the structure and function of the photosynthetic machinery is essential for understanding its mode of action. New insights are offered into the structure and function of PSI and its associated light-harvesting proteins, with a specific focus on the remarkable structural conservation of the core complex and high plasticity of the peripheral light-harvesting complexes.

Hypothetical chloroplast reading frame 51 encodes a photosystem I assembly factor in cyanobacteria

Hypothetical chloroplast open reading frames (ycfs) are putative genes in the plastid genomes of photosynthetic eukaryotes. Many ycfs are also conserved in the genomes of cyanobacteria, the presumptive ancestors of present-day chloroplasts. The functions of many ycfs are still unknown. Here, we generated knock-out mutants for ycf51 (sll1702) in the cyanobacterium Synechocystis sp. PCC 6803. The mutants showed reduced photoautotrophic growth due to impaired electron transport between photosystem II (PSII) and PSI. This phenotype results from greatly reduced PSI content in the ycf51 mutant. The ycf51 disruption had little effect on the transcription of genes encoding photosynthetic complex components and the stabilization of the PSI complex. In vitro and in vivo analyses demonstrated that Ycf51 cooperates with PSI assembly factor Ycf3 to mediate PSI assembly. Furthermore, Ycf51 interacts with the PSI subunit PsaC. Together with its specific localization in the thylakoid membrane and the stromal exposure of its hydrophilic region, our data suggest that Ycf51 is involved in PSI complex assembly. Ycf51 is conserved in all sequenced cyanobacteria, including the earliest branching cyanobacteria of the Gloeobacter genus, and is also present in the plastid genomes of glaucophytes. However, Ycf51 has been lost from other photosynthetic eukaryotic lineages. Thus, Ycf51 is a PSI assembly factor that has been functionally replaced during the evolution of oxygenic photosynthetic eukaryotes.

Impact of Peripheral Hydrogen Bond on Electronic Properties of the Primary Acceptor Chlorophyll in the Reaction Center of Photosystem I

Photosystem I (PS I) is a photosynthetic pigment-protein complex that absorbs light and uses the absorbed energy to initiate electron transfer. Electron transfer has been shown to occur concurrently along two (A- and B-) branches of reaction center (RC) cofactors. The electron transfer chain originates from a special pair of chlorophyll a molecules (P700), followed by two chlorophylls and one phylloquinone in each branch (denoted as A-1, A0, A1, respectively), converging in a single iron-sulfur complex Fx. While there is a consensus that the ultimate electron donor-acceptor pair is P700+A0-, the involvement of A-1 in electron transfer, as well as the mechanism of the very first step in the charge separation sequence, has been under debate. To resolve this question, multiple groups have targeted electron transfer cofactors by site-directed mutations. In this work, the peripheral hydrogen bonds to keto groups of A0 chlorophylls have been disrupted by mutagenesis. Four mutants were generated: PsaA-Y692F; PsaB-Y667F; PsaB-Y667A; and a double mutant PsaA-Y692F/PsaB-Y667F. Contrary to expectations, but in agreement with density functional theory modeling, the removal of the hydrogen bond by Tyr → Phe substitution was found to have a negligible effect on redox potentials and optical absorption spectra of respective chlorophylls. In contrast, Tyr → Ala substitution was shown to have a fatal effect on the PS I function. It is thus inferred that PsaA-Y692 and PsaB-Y667 residues have primarily structural significance, and their ability to coordinate respective chlorophylls in electron transfer via hydrogen bond plays a minor role.

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes

Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.

Function of iron-stress-induced protein A in cyanobacterial cells with monomeric and trimeric photosystem I

The acclimation of cyanobacteria to iron deficiency is crucial for their survival in natural environments. In response to iron deficiency, many cyanobacterial species induce the production of a pigment-protein complex called iron-stress-induced protein A (IsiA). IsiA proteins associate with photosystem I (PSI) and can function as light-harvesting antennas or dissipate excess energy. They may also serve as chlorophyll storage during iron limitation. In this study, we examined the functional role of IsiA in cells of Synechocystis sp. PCC 6803 grown under iron limitation conditions by measuring the cellular IsiA content and its capability to transfer energy to PSI. We specifically tested the effect of the oligomeric state of PSI by comparing wild-type (WT) Synechocystis sp. PCC 6803 with mutants lacking specific subunits of PSI, namely PsaL/PsaI (PSI subunits XI/VIII) and PsaF/PsaJ (PSI subunits III/IX). Time-resolved fluorescence spectroscopy revealed that IsiA formed functional PSI3-IsiA18 supercomplexes, wherein IsiA effectively transfers energy to PSI on a timescale of 10 ps at room temperature-measured in isolated complexes and in vivo-confirming the primary role of IsiA as an accessory light-harvesting antenna to PSI. However, a notable fraction (40%) remained unconnected to PSI, supporting the notion of a dual functional role of IsiA. Cells with monomeric PSI under iron deficiency contained, on average, only 3 to 4 IsiA complexes bound to PSI. These results show that IsiA can transfer energy to trimeric and monomeric PSI but to varying degrees and that the acclimatory production of IsiA under iron stress is controlled by its ability to perform its light-harvesting function.

Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d-containing cyanobacterium

Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

Phylogenetic and spectroscopic insights on the evolution of core antenna proteins in cyanobacteria

Light harvesting by antenna systems is the initial step in a series of electron-transfer reactions in all photosynthetic organisms, leading to energy trapping by reaction center proteins. Cyanobacteria are an ecologically diverse group and are the simplest organisms capable of oxygenic photosynthesis. The primary light-harvesting antenna in cyanobacteria is the large membrane extrinsic pigment-protein complex called the phycobilisome. In addition, cyanobacteria have also evolved specialized membrane-intrinsic chlorophyll-binding antenna proteins that transfer excitation energy to the reaction centers of photosystems I and II (PSI and PSII) and dissipate excess energy through nonphotochemical quenching. Primary among these are the CP43 and CP47 proteins of PSII, but in addition, some cyanobacteria also use IsiA and the prochlorophyte chlorophyll a/b binding (Pcb) family of proteins. Together, these proteins comprise the CP43 family of proteins owing to their sequence similarity with CP43. In this article, we have revisited the evolution of these chlorophyll-binding antenna proteins by examining their protein sequences in parallel with their spectral properties. Our phylogenetic and spectroscopic analyses support the idea of a common ancestor for CP43, IsiA, and Pcb proteins, and suggest that PcbC might be a distant ancestor of IsiA. The similar spectral properties of CP47 and IsiA suggest a closer evolutionary relationship between these proteins compared to CP43.

Energetic robustness to large scale structural fluctuations in a photosynthetic supercomplex

Photosynthetic organisms transport and convert solar energy with near-unity quantum efficiency using large protein supercomplexes held in flexible membranes. The individual proteins position chlorophylls to tight tolerances considered critical for fast and efficient energy transfer. The variability in protein organization within the supercomplexes, and how efficiency is maintained despite variability, had been unresolved. Here, we report on structural heterogeneity in the 2-MDa cyanobacterial PSI-IsiA photosynthetic supercomplex observed using Cryo-EM, revealing large-scale variances in the positions of IsiA relative to PSI. Single-molecule measurements found efficient IsiA-to-PSI energy transfer across all conformations, along with signatures of transiently decoupled IsiA. Structure based calculations showed that rapid IsiA-to-PSI energy transfer is always maintained, and even increases by three-fold in rare conformations via IsiA-specific chls. We postulate that antennae design mitigates structural fluctuations, providing a mechanism for robust energy transfer in the flexible membrane.

Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens

In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions.

Structural insights into a unique PSI-LHCI-LHCII-Lhcb9 supercomplex from moss Physcomitrium patens

Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.

Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.

Uphill energy transfer mechanism for photosynthesis in an Antarctic alga

Prasiola crispa, an aerial green alga, forms layered colonies under the severe terrestrial conditions of Antarctica. Since only far-red light is available at a deep layer of the colony, P. crispa has evolved a molecular system for photosystem II (PSII) excitation using far-red light with uphill energy transfer. However, the molecular basis underlying this system remains elusive. Here, we purified a light-harvesting chlorophyll (Chl)-binding protein complex from P. crispa (Pc-frLHC) that excites PSII with far-red light and revealed its ring-shaped structure with undecameric 11-fold symmetry at 3.13 Å resolution. The primary structure suggests that Pc-frLHC evolved from LHCI rather than LHCII. The circular arrangement of the Pc-frLHC subunits is unique among eukaryote LHCs and forms unprecedented Chl pentamers at every subunit‒subunit interface near the excitation energy exit sites. The Chl pentamers probably contribute to far-red light absorption. Pc-frLHC's unique Chl arrangement likely promotes PSII excitation with entropy-driven uphill excitation energy transfer.

Cyanobacterial Bioenergetics in Relation to Cellular Growth and Productivity

Cyanobacteria, the evolutionary originators of oxygenic photosynthesis, have the capability to convert CO2, water, and minerals into biomass using solar energy. This process is driven by intricate bioenergetic mechanisms that consist of interconnected photosynthetic and respiratory electron transport chains coupled. Over the last few decades, advances in physiochemical analysis, molecular genetics, and structural analysis have enabled us to gain a more comprehensive understanding of cyanobacterial bioenergetics. This includes the molecular understanding of the primary energy conversion mechanisms as well as photoprotective and other dissipative mechanisms that prevent photodamage when the rates of photosynthetic output, primarily in the form of ATP and NADPH, exceed the rates that cellular assimilatory processes consume these photosynthetic outputs. Despite this progress, there is still much to learn about the systems integration and the regulatory circuits that control expression levels for optimal cellular abundance and activity of the photosynthetic complexes and the cellular components that convert their products into biomass. With an improved understanding of these regulatory principles and mechanisms, it should be possible to optimally modify cyanobacteria for enhanced biotechnological purposes.

Native architecture and acclimation of photosynthetic membranes in a fast-growing cyanobacterium

Efficient solar energy conversion is ensured by the organization, physical association, and physiological coordination of various protein complexes in photosynthetic membranes. Here, we visualize the native architecture and interactions of photosynthetic complexes within the thylakoid membranes from a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) using high-resolution atomic force microscopy. In the Syn2973 thylakoid membranes, both photosystem I (PSI)-enriched domains and crystalline photosystem II (PSII) dimer arrays were observed, providing favorable membrane environments for photosynthetic electron transport. The high light (HL)-adapted thylakoid membranes accommodated a large amount of PSI complexes, without the incorporation of iron-stress-induced protein A (IsiA) assemblies and formation of IsiA-PSI supercomplexes. In the iron deficiency (Fe-)-treated thylakoid membranes, in contrast, IsiA proteins densely associated with PSI, forming the IsiA-PSI supercomplexes with varying assembly structures. Moreover, type-I NADH dehydrogenase-like complexes (NDH-1) were upregulated under the HL and Fe- conditions and established close association with PSI complexes to facilitate cyclic electron transport. Our study provides insight into the structural heterogeneity and plasticity of the photosynthetic apparatus in the context of their native membranes in Syn2973 under environmental stress. Advanced understanding of the photosynthetic membrane organization and adaptation will provide a framework for uncovering the molecular mechanisms of efficient light harvesting and energy conversion.

Introduction of cysteine-mediated quenching in the CP43 protein of photosystem II builds resilience to high-light stress in a cyanobacterium

Photosystem (PS) II is prone to photodamage both as a direct consequence of light, and indirectly by producing reactive oxygen species. Engineering high-light tolerance in cyanobacteria with minimal impact on PSII function is desirable in synthetic biology. IsiA, a CP43 homolog found exclusively in cyanobacteria, can dissipate excess light energy. We have recently determined that the sole cysteine residue of IsiA in Synechocystis sp. PCC 6803 has a critical role in non-photochemical quenching. Similar cysteine-mediated energy quenching has also been observed in green‑sulfur bacteria. Sequence analysis of IsiA and CP43 aligns cysteine 260 of IsiA with valine 277 of CP43 in Synechocystis sp. PCC 6803. In the current study, we explore the impact of replacing valine 277 of CP43 to a cysteine on growth, PSII activity and high-light tolerance. Our results imply a decline in the PSII output for the mutant (CP43V277C) presumably due to the dissipation of absorbed light energy by cysteine. Spectroscopic analysis of isolated PSII from this mutant strain also suggests a delayed transfer of excitation energy from CP43-associated chlorophyll a to PSII reaction center. The mutation makes the PSII high-light tolerant and provides a small advantage in growth under high-light conditions. This previously unexplored strategy to engineer high-light tolerance could be a step further towards developing cyanobacterial cells as biofactories.

Frequency-Domain Spectroscopic Study of the Photosystem I Supercomplexes, Isolated IsiA Monomers, and the Intact IsiA Ring

The PSI₃-IsiA₁₈ supercomplex is one of the largest and most complicated assemblies in photosynthesis. The IsiA ring, composed of 18 IsiA monomers (IsiA₁₈) surrounding the PSI trimer (PSI₃), forms under iron-deficient conditions in cyanobacteria and acts as a peripheral antenna. Based on the supercomplex structure recently determined via cryo-EM imaging, we model various optical spectra of the IsiA monomers and IsiA₁₈ ring. Comparison of the absorption and emission spectra of the isolated IsiA monomers and the full ring reveals that about 2.7 chlorophylls (Chls) are lost in the isolated IsiA monomers. The best fits for isolated monomers spectra are obtained assuming the absence of Chl 508 and Chl 517 and 70% loss of Chl 511. The best model describing all three hexamers and the entire ring suggests that the lowest energy pigments are Chls 511, 514, and 517. Based on the modeling results presented in this work, we conclude that there are most likely three entry points for EET from the IsiA₆ hexamer to the PSI core monomer, with two of these entry points likely being located next to each other (i.e., nine entry points from IsiA₁₈ to the PSI₃ trimer). Finally, we show that excitation energy transfer inside individual monomers is fast (<2 ps at T = 5 K) and at least 20 times faster than intermonomer energy transfer.

Structure, Function, and Variations of the Photosystem I-Antenna Supercomplex from Different Photosynthetic Organisms

Photosystem I (PSI) is a protein complex functioning in light-induced charge separation, electron transfer, and reduction reactions of ferredoxin in photosynthesis, which finally results in the reduction of NAD(P)^- to NAD(P)H required for the fixation of carbon dioxide. In eukaryotic algae, PSI is associated with light-harvesting complex I (LHCI) subunits, forming a PSI-LHCI supercomplex. LHCI harvests and transfers light energy to the PSI core, where charge separation and electron transfer reactions occur. During the course of evolution, the number and sequences of protein subunits and the pigments they bind in LHCI change dramatically depending on the species of organisms, which is a result of adaptation of organisms to various light environments. In this chapter, I will describe the structure of various PSI-LHCI supercomplexes from different organisms solved so far either by X-ray crystallography or by cryo-electron microscopy, with emphasis on the differences in the number, structures, and association patterns of LHCI subunits associated with the PSI core found in different organisms.

Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation

Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that absorb far-red light (FRL). However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core-antenna regions of PSI, and Chl f was not observed among the electron transfer cofactors. This structural analysis also reveals both conserved and nonconserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FRL photoacclimation.

Regulation and Functional Complexity of the Chlorophyll-Binding Protein IsiA

As the oldest known lineage of oxygen-releasing photosynthetic organisms, cyanobacteria play the key roles in helping shaping the ecology of Earth. Iron is an ideal transition metal for redox reactions in biological systems. Cyanobacteria frequently encounter iron deficiency due to the environmental oxidation of ferrous ions to ferric ions, which are highly insoluble at physiological pH. A series of responses, including architectural changes to the photosynthetic membranes, allow cyanobacteria to withstand this condition and maintain photosynthesis. Iron-stress-induced protein A (IsiA) is homologous to the cyanobacterial chlorophyll (Chl)-binding protein, photosystem II core antenna protein CP43. IsiA is the major Chl-containing protein in iron-starved cyanobacteria, binding up to 50% of the Chl in these cells, and this Chl can be released from IsiA for the reconstruction of photosystems during the recovery from iron limitation. The pigment–protein complex (CPVI-4) encoded by isiA was identified and found to be expressed under iron-deficient conditions nearly 30years ago. However, its precise function is unknown, partially due to its complex regulation; isiA expression is induced by various types of stresses and abnormal physiological states besides iron deficiency. Furthermore, IsiA forms a range of complexes that perform different functions. In this article, we describe progress in understanding the regulation and functions of IsiA based on laboratory research using model cyanobacteria.

Plant LHC-like proteins show robust folding and static non-photochemical quenching

Life on Earth depends on photosynthesis, the conversion of light energy into chemical energy. Plants collect photons by light harvesting complexes (LHC)-abundant membrane proteins containing chlorophyll and xanthophyll molecules. LHC-like proteins are similar in their amino acid sequence to true LHC antennae, however, they rather serve a photoprotective function. Whether the LHC-like proteins bind pigments has remained unclear. Here, we characterize plant LHC-like proteins (LIL3 and ELIP2) produced in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). Both proteins were associated with chlorophyll a (Chl) and zeaxanthin and LIL3 was shown to be capable of quenching Chl fluorescence via direct energy transfer from the Chl Q_y state to zeaxanthin S₁ state. Interestingly, the ability of the ELIP2 protein to quench can be acquired by modifying its N-terminal sequence. By employing Synechocystis carotenoid mutants and site-directed mutagenesis we demonstrate that, although LIL3 does not need pigments for folding, pigments stabilize the LIL3 dimer.

The Plasticity of Photosystem I

Most of life's energy comes from sunlight, and thus, photosynthesis underpins the survival of virtually all life forms. The light-driven electron transfer at photosystem I (PSI) is certainly the most important generator of reducing power at the cellular level and thereby largely determines the global amount of enthalpy in living systems (Nelson 2011). The PSI is a light-driven plastocyanin:ferredoxin oxidoreductase, which is embedded into thylakoid membranes of cyanobacteria and chloroplasts of eukaryotic photosynthetic organism. Structural determination of complexes of the photosynthetic machinery is vital for the understanding of its mode of action. Here, we describe new structural and functional insights into PSI and associated light-harvesting proteins, with a focus on the plasticity of PSI.

Characterizing the supercomplex association of photosynthetic complexes in cyanobacteria

The light reactions of photosynthesis occur in thylakoid membranes that are densely packed with a series of photosynthetic complexes. The lateral organization and close association of photosynthetic complexes in native thylakoid membranes are vital for efficient light harvesting and energy transduction. Recently, analysis of the interconnections between photosynthetic complexes to form supercomplexes has garnered great interest. In this work, we report a method integrating immunoprecipitation, mass spectrometry and atomic force microscopy to identify the inter-complex associations of photosynthetic complexes in thylakoid membranes from the cyanobacterium Synechococcus elongatus PCC 7942. We characterize the preferable associations between individual photosynthetic complexes and binding proteins involved in the complex-complex interfaces, permitting us to propose the structural models of photosynthetic complex associations that promote the formation of photosynthetic supercomplexes. We also identified other potential binding proteins with the photosynthetic complexes, suggesting the highly connecting networks associated with thylakoid membranes. This study provides mechanistic insight into the physical interconnections of photosynthetic complexes and potential partners, which are crucial for efficient energy transfer and physiological acclimatization of the photosynthetic apparatus. Advanced knowledge of the protein organization and interplay of the photosynthetic machinery will inform rational design and engineering of artificial photosynthetic systems to supercharge energy production.

Time-resolved comparative molecular evolution of oxygenic photosynthesis

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.

A Novel Mode of Photoprotection Mediated by a Cysteine Residue in the Chlorophyll Protein IsiA

Oxygenic photosynthetic organisms have evolved a multitude of mechanisms for protection against high-light stress. IsiA, a chlorophyll a-binding cyanobacterial protein, serves as an accessory antenna complex for photosystem I. Intriguingly, IsiA can also function as an independent pigment protein complex in the thylakoid membrane and facilitate the dissipation of excess energy, providing photoprotection. The molecular basis of the IsiA-mediated excitation quenching mechanism remains poorly understood. In this study, we demonstrate that IsiA uses a novel cysteine-mediated process to quench excitation energy. The single cysteine in IsiA in the cyanobacterium Synechocystis sp. strain PCC 6803 was converted to a valine. Ultrafast fluorescence spectroscopic analysis showed that this single change abolishes the excitation energy quenching ability of IsiA, thus providing direct evidence of the crucial role of this cysteine residue in energy dissipation from excited chlorophylls. Under stress conditions, the mutant cells exhibited enhanced light sensitivity, indicating that the cysteine-mediated quenching process is critically important for photoprotection.

Restoration of photosynthetic activity and supercomplexes from severe iron starvation in Chlamydomonas reinhardtii

The eukaryotic alga Chlamydomonas (C.) reinhardtii is used as a model organism to study photosynthetic efficiency. We studied the organization and protein profile of thylakoid membranes under severe iron (Fe²⁺) deficiency condition and iron supplement for their restoration. Chlorophyll (Chl) a fluorescence fast OJIP transients were decreased in the severe Fe²⁺ deficient cells resulting in the reduction of the photochemical efficiency. The circular dichroism (CD) results from Fe²⁺ deficient thylakoid membranes show a significant change in pigment-pigment and pigment-protein excitonic interactions. The organization of super-complexes was also affected significantly. Furthermore, super-complexes of photosystem (PS) II and PSI, along with its dimers, were severely reduced. The complexes separated using sucrose gradient centrifugation shows that loss of super-complexes and excitonic pigment-pigment interactions were restored in the severely Fe²⁺ deficient cells upon Fe supplementation for three generations. Additionally, the immunoblots demonstrated that both PSII, PSI core, and their light-harvesting complex antenna proteins were differentially decreased. However, reduced core proteins were aggregated, which in turn proteins were unfold and destabilized the supercomplexes and its function. Interestingly, the aggregated proteins were insoluble after n-Dodecyl β-D-maltoside solubilization. Further, they were identified in the pellet form. When Fe²⁺ was added to the severely deficient cells, the photosynthetic activity, pigment-proteins complexes, and proteins were restored to the level of control after 3^rd generation.

The structure of a red-shifted photosystem I reveals a red site in the core antenna

Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structure⁻function relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency.

Cyanobacterial photosystem I has a highly conserved core antenna consisting of eleven subunits and more than 90 chlorophylls. Here via CryoEM and spectroscopy, the authors determine the location of a red-shifted low-energy chlorophyll that allows harvesting of longer wavelengths of light.

Molecular organizations and function of iron-stress-induced-A protein family in Anabaena sp. PCC 7120

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions, and surround photosystem I (PSI) trimer with a ring formation. A cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, it is unknown how the IsiAs are associated with PSI. Here we report on molecular organizations and function of the IsiAs in this cyanobacterium. A deletion mutant of the isiA1 gene was constructed, and the four types of thylakoids were prepared from the wild-type (WT) and ΔisiA1 cells under iron-replete (+Fe) and iron-deficient (-Fe) conditions. Immunoblotting analysis exhibits a clear expression of the IsiA1 in the WT-Fe. The PSI-IsiA1 supercomplex is found in the WT-Fe, and excitation-energy transfer from IsiA1 to PSI is verified by time-resolved fluorescence analyses. Instead of the IsiA1, both IsiA2 and IsiA3 are bound to PSI monomer in the ΔisiA1-Fe. These findings provide insights into multiple-expression system of the IsiA family in this cyanobacterium.

Light harvesting in oxygenic photosynthesis: Structural biology meets spectroscopy

Oxygenic photosynthesis is the main process that drives life on earth. It starts with the harvesting of solar photons that, after transformation into electronic excitations, lead to charge separation in the reaction centers of photosystems I and II (PSI and PSII). These photosystems are large, modular pigment-protein complexes that work in series to fuel the formation of carbohydrates, concomitantly producing molecular oxygen. Recent advances in cryo-electron microscopy have enabled the determination of PSI and PSII structures in complex with light-harvesting components called "supercomplexes" from different organisms at near-atomic resolution. Here, we review the structural and spectroscopic aspects of PSI and PSII from plants and algae that directly relate to their light-harvesting properties, with special attention paid to the pathways and efficiency of excitation energy transfer and the regulatory aspects.

Current limits of structural biology: The transient interaction between cytochrome c 6 and photosystem I

Trimeric photosystem I from the cyanobacterium Thermosynechococcus elongatus (TePSI) is an intrinsic membrane protein, which converts solar energy into electrical energy by oxidizing the soluble redox mediator cytochrome c 6 (Cyt c 6 ) and reducing ferredoxin. Here, we use cryo-electron microscopy and small angle neutron scattering (SANS) to characterize the transient binding of Cyt c 6 to TePSI. The structure of TePSI cross-linked to Cyt c 6 was solved at a resolution of 2.9 Å and shows additional cofactors as well as side chain density for 84% of the peptide chain of subunit PsaK, revealing a hydrophobic, membrane intrinsic loop that enables binding of associated proteins. Due to the poor binding specificity, Cyt c 6 could not be localized with certainty in our cryo-EM analysis. SANS measurements confirm that Cyt c 6 does not bind to TePSI at protein concentrations comparable to those for cross-linking. However, SANS data indicate a complex formation between TePSI and the non-native mitochondrial cytochrome from horse heart (Cyt c HH ). Our study pinpoints the difficulty of identifying very small binding partners (less than 5% of the overall size) in EM structures when binding affinities are poor. We relate our results to well resolved co-structures with known binding affinities and recommend confirmatory methods for complexes with K M values higher than 20 μM.

Structure-based Hamiltonian model for IsiA uncovers a highly robust pigment-protein complex

The iron stress-induced protein A (IsiA) is a source of interest and debate in biological research. The IsiA supercomplex, binding over 200 chlorophylls, assembles in multimeric rings around photosystem I (PSI). Recently, the IsiA-PSI structure from Synechocystis sp. PCC 6803 was resolved to 3.48 Å. Based on this structure, we created a model simulating a single excitation event in an IsiA monomer. This model enabled us to calculate the fluorescence and the localization of the excitation in the IsiA structure. To further examine this system, noise was introduced to the model in two forms-thermal and positional. Introducing noise highlights the functional differences in the system between cryogenic temperatures and biologically relevant temperatures. Our results show that the energetics of the IsiA pigment-protein complex are very robust at room temperature. Nevertheless, shifts in the position of specific chlorophylls lead to large changes in their optical and fluorescence properties. Based on these results, we discuss the implication of highly robust structures, with potential for serving different roles in a context-dependent manner, on our understanding of the function and evolution of photosynthetic processes.

Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

In this Perspective, Christopher Gisriel et al. discuss the challenges in accurate assignment of co-factors in cryo-EM, particularly for chlorophylls. They explore the factors that lead to misassignment and offer suggestions for improving reliability of cryo-EM-based assignments.

Structural variability, coordination and adaptation of a native photosynthetic machinery

Cyanobacterial thylakoid membranes represent the active sites for both photosynthetic and respiratory electron transport. We used high-resolution atomic force microscopy to visualize the native organization and interactions of photosynthetic complexes within the thylakoid membranes from the model cyanobacterium Synechococcus elongatus PCC 7942. The thylakoid membranes are heterogeneous and assemble photosynthetic complexes into functional domains to enhance their coordination and regulation. Under high light, the chlorophyll-binding proteins IsiA are strongly expressed and associate with Photosystem I (PSI), forming highly variable IsiA-PSI supercomplexes to increase the absorption cross-section of PSI. There are also tight interactions of PSI with Photosystem II (PSII), cytochrome b₆f, ATP synthase and NAD(P)H dehydrogenase complexes. The organizational variability of these photosynthetic supercomplexes permits efficient linear and cyclic electron transport as well as bioenergetic regulation. Understanding the organizational landscape and environmental adaptation of cyanobacterial thylakoid membranes may help inform strategies for engineering efficient photosynthetic systems and photo-biofactories.

Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins

Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI–IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI–IsiA supercomplex.

Akita et al. present the latest approach to solve IsiA–PSI supercomplex molecular structure with increased resolution using cryo-EM and time-resolved fluorescence studies. With 2.7 Å resolution, they reveal molecular interactions between PSI and IsiA subunits and that IsiA functions as an energy donor in the supercomplex.

Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly

Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding.

Structural basis for energy and electron transfer of the photosystem I-IsiA-flavodoxin supercomplex

Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), and upregulate the expression of iron-stress-induced proteins A and B (IsiA and flavodoxin (Fld)). Multiple IsiAs function as the peripheral antennae that encircle the PSI core, whereas Fld replaces Fd as the electron receptor of PSI. Here, we report the structures of the PSI₃-IsiA₁₈-Fld₃ and PSI₃-IsiA₁₈ supercomplexes from Synechococcus sp. PCC 7942, revealing features that are different from the previously reported PSI structures, and a sophisticated pigment network that involves previously unobserved pigment molecules. Spectroscopic results demonstrated that IsiAs are efficient light harvesters for PSI. Three Flds bind symmetrically to the trimeric PSI core-we reveal the detailed interaction and the electron transport path between PSI and Fld. Our results provide a structural basis for understanding the mechanisms of light harvesting, energy transfer and electron transport of cyanobacterial PSI under stressed conditions.

The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis

Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria overcome this challenge by expressing paralogous photosynthetic proteins and by synthesizing and incorporating ~8% chlorophyll f into their Photosystem I (PSI) complexes, enabling them to grow under far-red light (FRL). We solved the structure of FRL-acclimated PSI from the cyanobacterium Fischerella thermalis PCC 7521 by single-particle, cryo-electron microscopy to understand its structural and functional differences. Four binding sites occupied by chlorophyll f are proposed. Subtle structural changes enable FRL-adapted PSI to extend light utilization for oxygenic photosynthesis to nearly 800 nm. This structure provides a platform for understanding FRL-driven photosynthesis and illustrates the robustness of adaptive and acclimation mechanisms in nature.