Harvesting Far-Red Light by Chlorophyll f in Photosystems I and II of Unicellular Cyanobacterium strain KC1

Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light

Although most cyanobacteria use visible light (VL; λ = 400-700 nm) for photosynthesis, some have evolved strategies to use far-red light (FRL; λ = 700-800 nm). These cyanobacteria are defined as far-red light-utilizing cyanobacteria (FRLCyano), including two groups: (1) chlorophyll d-producing Acaryochloris spp. and (2) polyphyletic cyanobacteria that produce chlorophylls d and f in response to FRL. Numerous ecological studies examine pigments, such as chlorophylls d and f, to investigate the presence of FRLCyano in the environment. This method is not ideal because it can only detect FRLCyano that have made chlorophylls d or f. Here we develop a new method, far-red cyanobacteria identification (FRCI), to identify FRLCyano based on 16S rRNA gene sequences. From public databases and published articles, 62 16S rRNA gene sequences of FRLCyano were extracted. Comparing with related lineages, we determined that 97% sequence identity is the optimal cut-off for distinguishing FRLCyano from other cyanobacteria. To test the method experimentally, we collected samples from 17 sites in Taipei, Taiwan, and conducted VL and FRL enrichments. Our results demonstrate that FRCI can detect FRLCyano during FRL enrichments more sensitively than pigment analysis. FRCI can also resolve the composition of FRLCyano at the genus level, which pigment analysis cannot do. In addition, we applied FRCI to published datasets and discovered putative FRLCyano in diverse environments, including soils, hot springs and deserts. Overall, our results indicate that FRCI is a sensitive and high-resolution method using 16S rRNA gene sequences to identify FRLCyano.

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.

Use of Quartz Sand Columns to Study Far-Red Light Photoacclimation (FaRLiP) in Cyanobacteria

Some cyanobacteria can perform far-red light photoacclimation (FaRLiP), which allows them to use far-red light (FRL) for oxygenic photosynthesis. Most of the cyanobacteria able to use FRL were discovered in low visible-light (VL; λ = 400-700 nm) environments that are also enriched in FRL (λ = 700-800 nm). However, these cyanobacteria grow faster in VL than in FRL in laboratory conditions, indicating that FRL is not their preferred light source when VL is available. Therefore, it is interesting to understand why such strains were primarily found in FRL-enriched but not VL-enriched environments. To this aim, we established a terrestrial model system with quartz sand to study the distribution and photoacclimation of cyanobacterial strains. A FaRLiP-performing cyanobacterium, Leptolyngbya sp. JSC-1, and a VL-utilizing model cyanobacterium, Synechocystis sp. PCC 6803, were compared in this study. We found that, although Leptolyngbya sp. JSC-1 can grow well in both VL and FRL, Synechocystis sp. PCC 6803 grows much faster than Leptolyngbya sp. JSC-1 in VL. In addition, the growth was higher in liquid cocultures than in monocultures of Leptolyngbya sp. JSC-1 or Synechocystis sp. PCC 6803. In an artificial terrestrial model system, Leptolyngbya sp. JSC-1 has an advantage when growing in coculture at greater depths by performing FaRLiP. Therefore, strong competition for VL and slower growth rate are possible reasons why FRL-utilizing cyanobacteria are found in environments with low VL intensities. This model system provides a valuable tool for future studies of cyanobacterial ecological niches and interactions in a terrestrial environment. IMPORTANCE This study uses sand columns to establish a terrestrial model system for the investigation of the distribution and acclimation of cyanobacteria to far-red light. Previous studies of this group of cyanobacteria required direct in situ samplings. The variability of conditions and abundances of the cyanobacteria in natural settings impeded detailed analyses and comparisons. Therefore, we established this model system under controlled conditions in the laboratory. In this system, the distribution and acclimation of two cyanobacteria were similar to the situation observed in natural environments, which validates that it can be used to study fundamental questions. Using this approach, we made the unanticipated observation that two cyanobacteria grow faster in coculture than in axenic cultures. This laboratory-based model system can provide a valuable new tool for comparing cyanobacterial strains (e.g., mutants and wild type), exploring interactions between cyanobacterial strains and interactions with other bacteria, and characterizing ecological niches of cyanobacteria.

Kovacikia minuta sp. nov. (Leptolyngbyaceae, Cyanobacteria), a new freshwater chlorophyll f-producing cyanobacterium

A few groups of cyanobacteria have been characterized as having far-red light photoacclimation (FaRLiP) that results from chlorophyll f (Chl f) production. In this study, using a polyphasic approach, we taxonomically transferred the Cf. Leptolyngbya sp. CCNUW1 isolated from a shaded freshwater pond, which produces Chl f under far-red light, to the genus Kovacikia and named this taxon Kovacikia minuta sp. nov. This strain was morphologically similar to Leptolyngbya-like strains. The thin filaments were purplish-brown under white light but became grass green under far-red light. The 31-gene phylogeny grouped K. minuta CCNU0001 into order Synechococcales and family Leptolyngbyaceae. Phylogenetic analysis based on 16S rRNA gene sequences further showed that K. minuta CCNU0001 was clustered into Kovacikia with similarities of 97.2-97.4% to the recently reported type species of Kovacikia muscicola HA7619-LM3. Additionally, the internal transcribed spacer region between 16S-23S rRNA genes had a unique sequence and secondary structure compared with other Kovacikia strains and phylogenetically related taxa. Draft genome sequences of K. minuta CCNU0001 (8,564,336 bp) were assembled into one circular chromosome and two circular plasmids. A FaRLiP 20-gene cluster comprised two operons with the unique organization. In sum, K. minuta was established as a new species, and it is the first species reported to produce Chl f and for which a draft genome was produced in genus Kovacikia. This study expanded our knowledge regarding the diversity of Chl f-producing cyanobacteria in far-red light-enriched environments and provides important foundational information for future investigations of FaRLiP evolution in cyanobacteria.

Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f

Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the ChlD1 position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth.

Far-red absorption and light-use efficiency trade-offs in chlorophyll f photosynthesis

Plants and cyanobacteria use the chlorophylls embedded in their photosystems to absorb photons and perform charge separation, the first step of converting solar energy to chemical energy. While oxygenic photosynthesis is primarily based on chlorophyll a photochemistry, which is powered by red light, a few cyanobacterial species can harness less energetic photons when growing in far-red light. Acclimatization to far-red light involves the incorporation of a small number of molecules of red-shifted chlorophyll f in the photosystems, whereas the most abundant pigment remains chlorophyll a. Due to its different energetics, chlorophyll f is expected to alter the excited-state dynamics of the photosynthetic units and, ultimately, their performances. Here we combined time-resolved fluorescence measurements on intact cells and isolated complexes to show that chlorophyll f insertion slows down the overall energy trapping in both photosystems. While this marginally affects the efficiency of photosystem I, it substantially decreases that of photosystem II. Nevertheless, we show that despite the lower energy output, the insertion of red-shifted chlorophylls in the photosystems remains advantageous in environments that are enriched in far-red light and therefore represents a viable strategy for extending the photosynthetically active spectrum in other organisms, including plants. However, careful design of the new photosynthetic units will be required to preserve their efficiency.

Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis

Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light color niches. The recent discoveries of several new CA types suggest that additional CA systems involving additional light colors and molecular mechanisms will be revealed in coming years. Here we provide a comprehensive overview of the currently known types of CA and summarize the molecular details that underpin CA regulation.

Substantial near-infrared radiation-driven photosynthesis of chlorophyll f-containing cyanobacteria in a natural habitat

Far-red absorbing chlorophylls are constitutively present as chlorophyll (Chl) d in the cyanobacterium Acaryochloris marina, or dynamically expressed by synthesis of Chl f, red-shifted phycobiliproteins and minor amounts of Chl d via far-red light photoacclimation in a range of cyanobacteria, which enables them to use near-infrared-radiation (NIR) for oxygenic photosynthesis. While the biochemistry and molecular physiology of Chl f-containing cyanobacteria has been unraveled in culture studies, their ecological significance remains unexplored and no data on their in situ activity exist. With a novel combination of hyperspectral imaging, confocal laser scanning microscopy, and nanoparticle-based O₂ imaging, we demonstrate substantial NIR-driven oxygenic photosynthesis by endolithic, Chl f-containing cyanobacteria within natural beachrock biofilms that are widespread on (sub)tropical coastlines. This indicates an important role of NIR-driven oxygenic photosynthesis in primary production of endolithic and other shaded habitats.

Extensive remodeling of the photosynthetic apparatus alters energy transfer among photosynthetic complexes when cyanobacteria acclimate to far-red light

Some cyanobacteria remodel their photosynthetic apparatus by a process known as Far-Red Light Photoacclimation (FaRLiP). Specific subunits of the phycobilisome (PBS), photosystem I (PSI), and photosystem II (PSII) complexes produced in visible light are replaced by paralogous subunits encoded within a conserved FaRLiP gene cluster when cells are grown in far-red light (FRL; λ = 700-800 nm). FRL-PSII complexes from the FaRLiP cyanobacterium, Synechococcus sp. PCC 7335, were purified and shown to contain Chl a, Chl d, Chl f, and pheophytin a, while FRL-PSI complexes contained only Chl a and Chl f. The spectroscopic properties of purified photosynthetic complexes from Synechococcus sp. PCC 7335 were determined individually, and energy transfer kinetics among PBS, PSII, and PSI were analyzed by time-resolved fluorescence (TRF) spectroscopy. Direct energy transfer from PSII to PSI was observed in cells (and thylakoids) grown in red light (RL), and possible routes of energy transfer in both RL- and FRL-grown cells were inferred. Three structural arrangements for RL-PSI were observed by atomic force microscopy of thylakoid membranes, but only arrays of trimeric FRL-PSI were observed in thylakoids from FRL-grown cells. Cells grown in FRL synthesized the FRL-specific complexes but also continued to synthesize some PBS and PSII complexes identical to those produced in RL. Although the light-harvesting efficiency of photosynthetic complexes produced in FRL might be lower in white light than the complexes produced in cells acclimated to white light, the FRL-complexes provide cells with the flexibility to utilize both visible and FRL to support oxygenic photosynthesis. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.

The amazing phycobilisome

Cyanobacteria and red-algae share a common light-harvesting complex which is different than all other complexes that serve as photosynthetic antennas - the Phycobilisome (PBS). The PBS is found attached to the stromal side of thylakoid membranes, filling up most of the gap between individual thylakoids. The PBS self assembles from similar homologous protein units that are soluble and contain conserved cysteine residues that covalently bind the light absorbing chromophores, linear tetra-pyrroles. Using similar construction principles, the PBS can be as large as 16.8 MDa (68×45×39nm), as small as 1.2 MDa (24 × 11.5 × 11.5 nm), and in some unique cases smaller still. The PBS can absorb light between 450 nm to 650 nm and in some cases beyond 700 nm, depending on the species, its composition and assembly. In this review, we will present new observations and structures that expand our understanding of the distinctive properties that make the PBS an amazing light harvesting system. At the end we will suggest why the PBS, for all of its excellent properties, was discarded by photosynthetic organisms that arose later in evolution such as green algae and higher plants.

Photosynthesis supported by a chlorophyll f-dependent, entropy-driven uphill energy transfer in Halomicronema hongdechloris cells adapted to far-red light

The phototrophic cyanobacterium Halomicronema hongdechloris shows far-red light-induced accumulation of chlorophyll (Chl) f, but the involvement of the pigment in photosynthetic energy harvesting by photosystem (PS) II is controversially discussed. While H. hongdechloris contains negligible amounts of Chl f in white-light culture conditions, the ratio of Chl f to Chl a is reversibly changed up to 1:8 under illumination with far-red light (720-730 nm). We performed UV-Vis absorption spectroscopy, time-integrated and time-resolved fluorescence spectroscopy for the calculation of decay-associated spectra (DAS) to determine excitation energy transfer (EET) processes between photosynthetic pigments in intact H. hongdechloris filaments. In cells grown under white light, highly efficient EET occurs from phycobilisomes (PBSs) to Chl a with an apparent time constant of about 100 ps. Charge separation occurs with a typical apparent time constant of 200-300 ps from Chl a. After 3-4 days of growth under far-red light, robust Chl f content was observed in H. hongdechloris and EET from PBSs reached Chl f efficiently within 200 ps. It is proposed based on mathematical modeling by rate equation systems for EET between the PBSs and PSII and subsequent electron transfer (ET) that charge separation occurs from Chl a and excitation energy is funneled from Chl f to Chl a via an energetically uphill EET driven by entropy, which is effective because the number of Chl a molecules coupled to Chl f is at least eight- to tenfold larger than the corresponding number of Chl f molecules. The long lifetime of Chl f molecules in contact to a tenfold larger pool of Chl a molecules allows Chl f to act as an intermediate energy storage level, from which the Gibbs free energy difference between Chl f and Chl a can be overcome by taking advantage from the favorable ratio of degeneracy coefficients, which formally represents a significant entropy gain in the Eyring formulation of the Arrhenius law. Direct evidence for energetically uphill EET and charge separation in PSII upon excitation of Chl f via anti-Stokes fluorescence in far-red light-adapted H. hongdechloris cells was obtained: Excitation by 720 nm laser light resulted in robust Chl a fluorescence at 680 nm that was distinctly temperature-dependent and, notably, increased upon DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) treatment in far-red light-adapted cells. Thus, rather than serving as an excitation energy trap, Chl f in far-red light-adapted H. hongdechloris cells is directly contributing to oxygenic photosynthesis at PSII.

Photochemistry beyond the red limit in chlorophyll f-containing photosystems

Photosystems I and II convert solar energy into the chemical energy that powers life. Chlorophyll a photochemistry, using red light (680 to 700 nm), is near universal and is considered to define the energy "red limit" of oxygenic photosynthesis. We present biophysical studies on the photosystems from a cyanobacterium grown in far-red light (750 nm). The few long-wavelength chlorophylls present are well resolved from each other and from the majority pigment, chlorophyll a. Charge separation in photosystem I and II uses chlorophyll f at 745 nm and chlorophyll f (or d) at 727 nm, respectively. Each photosystem has a few even longer-wavelength chlorophylls f that collect light and pass excitation energy uphill to the photochemically active pigments. These photosystems function beyond the red limit using far-red pigments in only a few key positions.

Light regulation of pigment and photosystem biosynthesis in cyanobacteria

Most cyanobacteria are obligate oxygenic photoautotrophs, and thus their growth and survival is highly dependent on effective utilization of incident light. Cyanobacteria have evolved a diverse set of phytochromes and cyanobacteriochromes (CBCRs) that allow cells to respond to light in the range from ∼300nm to ∼750nm. Together with associated response regulators, these photosensory proteins control many aspects of cyanobacterial physiology and metabolism. These include far-red light photoacclimation (FaRLiP), complementary chromatic acclimation (CCA), low-light photoacclimation (LoLiP), photosystem content and stoichiometry (long-term adaptation), short-term acclimation (state transitions), circadian rhythm, phototaxis, photomorphogenesis/development, and cellular aggregation. This minireview highlights some discoveries concerning phytochromes and CBCRs as well as two acclimation processes that improve light harvesting and energy conversion under specific irradiance conditions: FaRLiP and CCA.