Breaking the Red Limit: Efficient Trapping of Long-Wavelength Excitations in Chlorophyll-f-Containing Photosystem I

Recent structural discoveries of photosystems I and II acclimated to absorb far-red light

Photosystems I and II are the photooxidoreductases central to oxygenic photosynthesis and canonically absorb visible light (400-700 nm). Recent investigations have revealed that certain cyanobacteria can acclimate to environments enriched in far-red light (700-800 nm), yet can still perform oxygenic photosynthesis in a process called far-red light photoacclimation, or FaRLiP. During this process, the photosystem subunits and pigment compositions are altered. Here, the current structural understanding of the photosystems expressed during FaRLiP is described. The design principles may be useful for guiding efforts to engineer shade tolerance in organisms that typically cannot utilize far-red light.

Presence of low-energy chlorophylls d in photosystem I trimer and monomer cores isolated from Acaryochloris sp. NBRC 102871

Acaryochloris species belong to a special category of cyanobacteria possessing chlorophyll (Chl) d. One of the photosynthetic characteristics of Acaryochloris marina MBIC11017 is that the absorption spectra of photosystem I (PSI) showed almost no bands and shoulders of low-energy Chls d over 740 nm. In contrast, the absorption spectra of other Acaryochloris species showed a shoulder around 740 nm, suggesting that low-energy Chls d within PSI are diversified among Acaryochloris species. In this study, we purified PSI trimer and monomer cores from Acaryochloris sp. NBRC 102871 and examined their protein and pigment compositions and spectral properties. The protein bands and pigment compositions of the PSI trimer and monomer of NBRC102871 were virtually identical to those of MBIC11017. The absorption spectra of the NBRC102871 PSIs exhibited a shoulder around 740 nm, whereas the fluorescence spectra of PSI trimer and monomer displayed maximum peaks at 754 and 767 nm, respectively. These spectral properties were different from those of MBIC11017, indicating the presence of low-energy Chls d within the NBRC102871 PSIs. Moreover, we analyzed the NBRC102871 genome to identify amino acid sequences of PSI proteins and compared them with those of the A. marina MBIC11017 and MBIC10699 strains whose genomes are available. The results showed that some of the sequences in NBRC102871 were distinct from those in MBIC11017 and MBIC10699. These findings provide insights into the variety of low-energy Chls d with respect to the protein environments of PSI cores among the three Acaryochloris strains.

Oxygenic Photosynthesis in Far-Red Light: Strategies and Mechanisms

Oxygenic photosynthesis, the process that converts light energy into chemical energy, is traditionally associated with the absorption of visible light by chlorophyll molecules. However, recent studies have revealed a growing number of organisms capable of using far-red light (700-800 nm) to drive oxygenic photosynthesis. This phenomenon challenges the conventional understanding of the limits of this process. In this review, we briefly introduce the organisms that exhibit far-red photosynthesis and explore the different strategies they employ to harvest far-red light. We discuss the modifications of photosynthetic complexes and their impact on the delivery of excitation energy to photochemical centers and on overall photochemical efficiency. Finally, we examine the solutions employed to drive electron transport and water oxidation using relatively low-energy photons. The findings discussed here not only expand our knowledge of the remarkable adaptation capacities of photosynthetic organisms but also offer insights into the potential for enhancing light capture in crops.

The use of fluorescence lifetime imaging (FLIM) for in situ microbial detection in complex mineral substrates

The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis, and Bacillus subtilis labelled with SYTO 9 were obtained using two-photon excitation at 730, 750 and 800 nm, identifying characteristic lifetimes of photosynthetic pigments, unpigmented cellular autofluorescence, and SYTO 9. Labelled and unlabelled B. subtilis were seeded onto marble and gypsum samples containing endolithic photosynthetic cyanobacteria and the ability to distinguish cells from mineral autofluorescence and nonspecific dye staining was examined in parallel with ordinary multichannel confocal imaging. It was found that FLIM enabled discrimination of SYTO 9 labelled cells from background, but that the lifetime of SYTO 9 was shorter in cells on minerals than in pure culture under our conditions. Photosynthetic microorganisms were easily observed using both FLIM and confocal. Unlabelled, nonpigmented bacteria showed weak signals that were difficult to distinguish from background when minerals were present, though cellular autofluorescence consistent with NAD(P)H could be seen in pure cultures, and phasor analysis permitted detection on rocks. Gypsum and marble samples showed similar autofluorescence profiles, with little autofluorescence in the yellow-to-red range. Lifetime or time-gated imaging may prove a useful tool for environmental microbiology. LAY DESCRIPTION: The standard method of bacterial enumeration is to label the cells with a fluorescent dye and count them under high-power fluorescence microscopy. However, this can be difficult when the cells are embedded in soil and rock due to fluorescence from the surrounding minerals and dye binding to ambiguous features of the substrate. The use of fluorescence lifetime imaging (FLIM) can disambiguate these signals and allow for improved detection of bacteria in environmental samples.

Coloring Outside the Lines: Exploiting Pigment-Protein Synergy for Far-Red Absorption in Plant Light-Harvesting Complexes

Plants are designed to utilize visible light for photosynthesis. Expanding this light absorption toward the far-red could boost growth in low-light conditions and potentially increase crop productivity in dense canopies. A promising strategy is broadening the absorption of antenna complexes to the far-red. In this study, we investigated the capacity of the photosystem I antenna protein Lhca4 to incorporate far-red absorbing chlorophylls d and f and optimize their spectra. We demonstrate that these pigments can successfully bind to Lhca4, with the protein environment further red-shifting the chlorophyll d absorption, markedly extending the absorption range of this complex above 750 nm. Notably, chlorophyll d substitutes the canonical chlorophyll a red-forms, resulting in the most red-shifted emission observed in a plant light-harvesting complex. Using ultrafast spectroscopy, we show that the introduction of these novel chlorophylls does not interfere with the excited state decay or the energy equilibration processes within the complex. The results demonstrate the feasibility of engineering plant antennae to absorb deeper into the far-red region while preserving their functional and structural integrity, paving the way for innovative strategies to enhance photosynthesis.

Molecular diversity and evolution of far-red light-acclimated photosystem I

The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.

Two-Dimensional Electronic Spectroscopy of the Far-Red-Light Photosystem II Reaction Center

Understanding the role of specific pigments in primary energy conversion in the photosystem II (PSII) reaction center has been impeded by the spectral overlap of its constituent pigments. When grown in far-red light, some cyanobacteria incorporate chlorophyll-f and chlorophyll-d into PSII, relieving the spectral congestion. We employ two-dimensional electronic spectroscopy to study PSII at 77 K from Synechococcus sp. PCC 7335 cells that were grown in far-red light (FRL-PSII). We observe the formation of a radical pair within ∼3 ps that we assign to ChlD1•-PD1•+. While PheoD1 is thought to act as the primary electron acceptor in PSII from cells grown in visible light, we see no evidence of its involvement, which we attribute to its reduction by dithionite treatment in our samples. Our work demonstrates that primary charge separation occurs between ChlD1 and PD1 in FRL-PSII, suggesting that PD1/PD2 may play an underappreciated role in PSII's charge separation mechanism.

Energy transfer and trapping in photosystem I with and without chlorophyll-f

We establish a general kinetic scheme for energy transfer and trapping in the photosystem I (PSI) of cyanobacteria grown under white light (WL) or far-red light (FRL) conditions. With the help of simultaneous target analysis of all emission and transient absorption datasets measured in five cyanobacterial strains, we resolved the spectral and kinetic properties of the different species present in PSI. WL-PSI can be described by Bulk Chl a, two Red Chl a, and a reaction center compartment (WL-RC). The FRL-PSI contains two additional Chl f compartments. The lowest excited state of the FRL-RC is downshifted by ≈ 29 nm. The rate of charge separation drops from ≈900 ns-1 in WL-RC to ≈300 ns-1 in FRL-RC. The delayed trapping in the FRL-PSI (≈130 ps) is explained by uphill energy transfer from the Chl f compartments with Gibbs free energies of ≈kBT below that of the FRL-RC.

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light

Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400-700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700-800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL-PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.

The antenna of far-red absorbing cyanobacteria increases both absorption and quantum efficiency of Photosystem II

Cyanobacteria carry out photosynthetic light-energy conversion using phycobiliproteins for light harvesting and the chlorophyll-rich photosystems for photochemistry. While most cyanobacteria only absorb visible photons, some of them can acclimate to harvest far-red light (FRL, 700-800 nm) by integrating chlorophyll f and d in their photosystems and producing red-shifted allophycocyanin. Chlorophyll f insertion enables the photosystems to use FRL but slows down charge separation, reducing photosynthetic efficiency. Here we demonstrate with time-resolved fluorescence spectroscopy that on average charge separation in chlorophyll-f-containing Photosystem II becomes faster in the presence of red-shifted allophycocyanin antennas. This is different from all known photosynthetic systems, where additional light-harvesting complexes increase the overall absorption cross section but slow down charge separation. This remarkable property can be explained with the available structural and spectroscopic information. The unique design is probably important for these cyanobacteria to efficiently switch between visible and far-red light.

Chlorophylls: A Personal Snapshot

Chlorophylls provide the basis for photosynthesis and thereby most life on Earth. Besides their involvement in primary charge separation in the reaction center, they serve as light-harvesting and light-sensing pigments, they also have additional functions, e.g., in inter-system electron transfer. Chlorophylls also have a wealth of applications in basic science, medicine, as colorants and, possibly, in optoelectronics. Considering that there has been more than 200 years of chlorophyll research, one would think that all has been said on these pigments. However, the opposite is true: ongoing research evidenced in this Special Issue brings together current work on chlorophylls and on their carotenoid counterparts. These introductory notes give a very brief and in part personal account of the history of chlorophyll research and applications, before concluding with a snapshot of this year’s publications.

Identification and Comprehensive Evaluation of Resistant Weeds Using Unmanned Aerial Vehicle-Based Multispectral Imagery

Atrazine is one of the most widely used herbicides in weed management. However, the widespread use of atrazine has concurrently accelerated the evolution of weed resistance mechanisms. Resistant weeds were identified early to contribute to crop protection in precision agriculture before visible symptoms of atrazine application to weeds in actual field environments. New developments in unmanned aerial vehicle (UAV) platforms and sensor technologies promote cost-effective data collection by collecting multi-modal data at very high spatial and spectral resolution. In this study, we obtained multispectral and RGB images using UAVs, increased available information with the help of image fusion technology, and developed a weed spectral resistance index, WSRI = (RE-R)/(RE-B), based on the difference between susceptible and resistant weed biotypes. A deep convolutional neural network (DCNN) was applied to evaluate the potential for identifying resistant weeds in the field. Comparing the WSRI introduced in this study with previously published vegetation indices (VIs) shows that the WSRI is better at classifying susceptible and resistant weed biotypes. Fusing multispectral and RGB images improved the resistance identification accuracy, and the DCNN achieved high field accuracies of 81.1% for barnyardgrass and 92.4% for velvetleaf. Time series and weed density influenced the study of weed resistance, with 4 days after application (4DAA) identified as a watershed timeframe in the study of weed resistance, while different weed densities resulted in changes in classification accuracy. Multispectral and deep learning proved to be effective phenotypic techniques that can thoroughly analyze weed resistance dynamic response and provide valuable methods for high-throughput phenotyping and accurate field management of resistant weeds.

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.

Electrostatic profiling of photosynthetic pigments: implications for directed spectral tuning

Photosynthetic pigment-protein complexes harvest solar energy with a high quantum efficiency. Protein scaffolds are known to tune the spectral properties of embedded pigments principally through structured electrostatic environments. Although the physical nature of electrostatic tuning is straightforward, the precise spatial principles of electrostatic preorganization remain poorly explored for different protein matrices and incompletely characterized with respect to the intrinsic properties of different photosynthetic pigments. In this work, we study the electronic structure features associated with the lowest excited state of a series of eight naturally occurring (bacterio)chlorophylls and pheophytins to describe the precise topological differences in electrostatic potentials and hence determine intrinsic differences in the expected mode and impact of electrostatic tuning. The difference electrostatic potentials between the ground and first excited states are used as fingerprints. Both the spatial profile and the propensity for spectral tuning are found to be unique for each pigment, indicating spatially and directionally distinct modes of electrostatic tuning. The results define a specific partitioning of the protein matrix around each pigment as an aid to identify regions with a maximal impact on spectral tuning and have direct implications for dimensionality reduction in protein design and engineering. Thus, a quantum mechanical basis is provided for understanding, predicting, and ultimately designing sequence-modified or pigment-exchanged biological systems, as suggested for selected examples of pigment-reconstituted proteins.

Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light

Chlorophyll cofactors are vital for the metabolism of photosynthetic organisms. Cryo-electron microscopy (cryo-EM) has been used to elucidate molecular structures of pigment-protein complexes, but the minor structural differences between multiple types of chlorophylls make them difficult to distinguish in cryo-EM maps. This is exemplified by inconsistencies in the assignments of chlorophyll f molecules in structures of photosystem I acclimated to far-red light (FRL-PSI). A quantitative assessment of chlorophyll substituents in cryo-EM maps was used to identify chlorophyll f-binding sites in structures of FRL-PSI from two cyanobacteria. The two cryo-EM maps provide direct evidence for chlorophyll f-binding at two and three binding sites, respectively, and three more sites in each structure exhibit strong indirect evidence for chlorophyll f-binding. Common themes in chlorophyll f-binding are described that clarify the current understanding of the molecular basis for FRL photoacclimation in photosystems.