18O labeling of chlorophyll d in Acaryochloris marina reveals that chlorophyll a and molecular oxygen are precursors

Ecological diversification of a cyanobacterium through divergence of its novel chlorophyll d-based light-harvesting system

The evolution of novel traits can have important consequences for biological diversification. Novelties such as new structures are associated with changes in both genotype and phenotype that often lead to changes in ecological function.1,2 New ecological opportunities provided by a novel trait can trigger subsequent trait modification or niche partitioning3; however, the underlying mechanisms of novel trait diversification are still poorly understood. Here, we report that the innovation of a new chlorophyll (Chl) pigment, Chl d, by the cyanobacterium Acaryochloris marina was followed by the functional divergence of its light-harvesting complex. We identified three major photosynthetic spectral types based on Chl fluorescence properties for a collection of A. marina laboratory strains for which genome sequence data are available,4,5 with shorter- and longer-wavelength types more recently derived from an ancestral intermediate phenotype. Members of the different spectral types exhibited extensive variation in the Chl-binding proteins as well as the Chl energy levels of their photosynthetic complexes. This spectral-type divergence is associated with differences in the wavelength dependence of both growth rate and photosynthetic oxygen evolution. We conclude that the divergence of the light-harvesting apparatus has consequently impacted A. marina ecological diversification through specialization on different far-red photons for photosynthesis.

How to tune the absorption spectrum of chlorophylls to enable better use of the available solar spectrum

Photon capture by chlorophylls and other chromophores in light-harvesting complexes and photosystems is the driving force behind the light reactions of photosynthesis. Excitation of photosystem II allows it to receive electrons from the water-oxidizing oxygen-evolution complex and to transfer them to an electron-transport chain that generates a transmembrane electrochemical gradient and ultimately reduces plastocyanin, which donates its electron to photosystem I. Subsequently, excitation of photosystem I leads to electron transfer to a ferredoxin which can either reduce plastocyanin again (in so-called “cyclical electron-flow”) and release energy for the maintenance of the electrochemical gradient, or reduce NADP+ to NADPH. Although photons in the far-red (700–750 nm) portion of the solar spectrum carry enough energy to enable the functioning of the photosynthetic electron-transfer chain, most extant photosystems cannot usually take advantage of them due to only absorbing light with shorter wavelengths. In this work, we used computational methods to characterize the spectral and redox properties of 49 chlorophyll derivatives, with the aim of finding suitable candidates for incorporation into synthetic organisms with increased ability to use far-red photons. The data offer a simple and elegant explanation for the evolutionary selection of chlorophylls a, b, c, and d among all easily-synthesized singly-substituted chlorophylls, and identified one novel candidate (2,12-diformyl chlorophyll a) with an absorption peak shifted 79 nm into the far-red (relative to chlorophyll a) with redox characteristics fully suitable to its possible incorporation into photosystem I (though not photosystem II). chlorophyll d is shown by our data to be the most suitable candidate for incorporation into far-red utilizing photosystem II, and several candidates were found with red-shifted Soret bands that allow the capture of larger amounts of blue and green light by light harvesting complexes.

The terminal enzymes of (bacterio)chlorophyll biosynthesis

(Bacterio)chlorophylls are modified tetrapyrroles that are used by phototrophic organisms to harvest solar energy, powering the metabolic processes that sustain most of the life on Earth. Biosynthesis of these pigments involves enzymatic modification of the side chains and oxidation state of a porphyrin precursor, modifications that differ by species and alter the absorption properties of the pigments. (Bacterio)chlorophylls are coordinated by proteins that form macromolecular assemblies to absorb light and transfer excitation energy to a special pair of redox-active (bacterio)chlorophyll molecules in the photosynthetic reaction centre. Assembly of these pigment-protein complexes is aided by an isoprenoid moiety esterified to the (bacterio)chlorin macrocycle, which anchors and stabilizes the pigments within their protein scaffolds. The reduction of the isoprenoid 'tail' and its addition to the macrocycle are the final stages in (bacterio)chlorophyll biosynthesis and are catalysed by two enzymes, geranylgeranyl reductase and (bacterio)chlorophyll synthase. These enzymes work in conjunction with photosynthetic complex assembly factors and the membrane biogenesis machinery to synchronize delivery of the pigments to the proteins that coordinate them. In this review, we summarize current understanding of the catalytic mechanism, substrate recognition and regulation of these crucial enzymes and their involvement in thylakoid biogenesis and photosystem repair in oxygenic phototrophs.

Effects of Light and Oxygen on Chlorophyll d Biosynthesis in a Marine Cyanobacterium Acaryochloris marina

A marine cyanobacterium Acaryochloris marina synthesizes chlorophyll (Chl) d as a major Chl. Chl d has a formyl group at its C3 position instead of a vinyl group in Chl a. This modification allows Chl d to absorb far-red light addition to visible light, yet the enzyme catalyzing the formation of the C3-formyl group has not been identified. In this study, we focused on light and oxygen, the most important external factors in Chl biosynthesis, to investigate their effects on Chl d biosynthesis in A. marina. The amount of Chl d in heterotrophic dark-grown cells was comparable to that in light-grown cells, indicating that A. marina has a light-independent pathway for Chl d biosynthesis. Under anoxic conditions, the amount of Chl d increased with growth in light conditions; however, no growth was observed in dark conditions, indicating that A. marina synthesizes Chl d normally even under such “micro-oxic” conditions caused by endogenous oxygen production. Although the oxygen requirement for Chl d biosynthesis could not be confirmed, interestingly, accumulation of pheophorbide d was observed in anoxic and dark conditions, suggesting that Chl d degradation is induced by anaerobicity and darkness.

Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina

The Chlorophyll d-producing cyanobacterium Acaryochloris marina is widely distributed in marine environments enriched in far-red light, but our understanding of its genomic and functional diversity is limited. Here, we take an integrative approach to investigate A. marina diversity for 37 strains, which includes twelve newly isolated strains from previously unsampled locations in Europe and the Pacific Northwest of North America. A genome-wide phylogeny revealed both that closely related A. marina have migrated within geographic regions and that distantly related A. marina lineages can co-occur. The distribution of traits mapped onto the phylogeny provided evidence of a dynamic evolutionary history of gene gain and loss during A. marina diversification. Ancestral genes that were differentially retained or lost by strains include plasmid-encoded sodium-transporting ATPase and bidirectional NiFe-hydrogenase genes that may be involved in salt tolerance and redox balance under fermentative conditions, respectively. The acquisition of genes by horizontal transfer has also played an important role in the evolution of new functions, such as nitrogen fixation. Together, our results resolve examples in which genome content and ecotypic variation for nutrient metabolism and environmental tolerance have diversified during the evolutionary history of this unusual photosynthetic bacterium.

Reacquisition of light-harvesting genes in a marine cyanobacterium confers a broader solar niche

The evolution of phenotypic plasticity, i.e., the environmental induction of alternative phenotypes by the same genotype, can be an important mechanism of biological diversification.^1,2 For example, an evolved increase in plasticity may promote ecological niche expansion as well as the innovation of novel traits;³ however, both the role of phenotypic plasticity in adaptive evolution and its underlying mechanisms are still poorly understood.^4,5 Here, we report that the Chlorophyll d-producing marine cyanobacterium Acaryochloris marina strain MBIC11017 has evolved greater photosynthetic plasticity by reacquiring light-harvesting genes via horizontal gene transfer. The genes, which had been lost by the A. marina ancestor, are involved in the production and degradation of the light-harvesting phycobiliprotein phycocyanin. A. marina MBIC11017 exhibits a high degree of wavelength-dependence in phycocyanin production, and this ability enables it to grow with yellow and green light wavelengths that are inaccessible to other A. marina. Consequently, this strain has a broader solar niche than its close relatives. We discuss the role of horizontal gene transfer for regaining a lost phenotype in light of Dollo's Law⁶ that the loss of a complex trait is irreversible.

Biosynthesis of the modified tetrapyrroles-the pigments of life

Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.

Far-red light allophycocyanin subunits play a role in chlorophyll d accumulation in far-red light

Some terrestrial cyanobacteria acclimate to and utilize far-red light (FRL; λ = 700-800 nm) for oxygenic photosynthesis, a process known as far-red light photoacclimation (FaRLiP). A conserved, 20-gene FaRLiP cluster encodes core subunits of Photosystem I (PSI) and Photosystem II (PSII), five phycobiliprotein subunits of FRL-bicylindrical cores, and enzymes for synthesis of chlorophyll (Chl) f and possibly Chl d. Deletion mutants for each of the five apc genes of the FaRLiP cluster were constructed in Synechococcus sp. PCC 7335, and all had similar phenotypes. When the mutants were grown in white (WL) or red (RL) light, the cells closely resembled the wild-type (WT) strain grown under the same conditions. However, the WT and mutant strains were very different when grown under FRL. Mutants grown in FRL were unable to assemble FRL-bicylindrical cores, were essentially devoid of FRL-specific phycobiliproteins, but retained RL-type phycobilisomes and WL-PSII. The transcript levels for genes of the FaRLiP cluster in the mutants were similar to those in WT. Surprisingly, the Chl d contents of the mutant strains were greatly reduced (~ 60-99%) compared to WT and so were the levels of FRL-PSII. We infer that Chl d may be essential for the assembly of FRL-PSII, which does not accumulate to normal levels in the mutants. We further infer that the cysteine-rich subunits of FRL allophycocyanin may either directly participate in the synthesis of Chl d or that FRL bicylindrical cores stabilize FRL-PSII to prevent loss of Chl d.

Far-red light acclimation in diverse oxygenic photosynthetic organisms

Oxygenic photosynthesis has historically been considered limited to be driven by the wavelengths of visible light. However, in the last few decades, various adaptations have been discovered that allow algae, cyanobacteria, and even plants to utilize longer wavelength light in the far-red spectral range. These adaptations provide distinct advantages to the species possessing them, allowing the effective utilization of shade light under highly filtered light environments. In prokaryotes, these adaptations include the production of far-red-absorbing chlorophylls d and f and the remodeling of phycobilisome antennas and reaction centers. Eukaryotes express specialized light-harvesting pigment-protein complexes that use interactions between pigments and their protein environment to spectrally tune the absorption of chlorophyll a. If these adaptations could be applied to crop plants, a potentially significant increase in photon utilization in lower shaded leaves could be realized, improving crop yields.

Characterization of chlorophyll f synthase heterologously produced in Synechococcus sp. PCC 7002

In diverse terrestrial cyanobacteria, Far-Red Light Photoacclimation (FaRLiP) promotes extensive remodeling of the photosynthetic apparatus, including photosystems (PS)I and PSII and the cores of phycobilisomes, and is accompanied by the concomitant biosynthesis of chlorophyll (Chl) d and Chl f. Chl f synthase, encoded by chlF, is a highly divergent paralog of psbA; heterologous expression of chlF from Chlorogloeopsis fritscii PCC 9212 led to the light-dependent production of Chl f in Synechococcus sp. PCC 7002 (Ho et al., Science 353, aaf9178 (2016)). In the studies reported here, expression of the chlF gene from Fischerella thermalis PCC 7521 in the heterologous system led to enhanced synthesis of Chl f. N-terminally [His]₁₀-tagged ChlF⁷⁵²¹ was purified and identified by immunoblotting and tryptic-peptide mass fingerprinting. As predicted from its sequence similarity to PsbA, ChlF bound Chl a and pheophytin a at a ratio of ~ 3-4:1, bound β-carotene and zeaxanthin, and was inhibited in vivo by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Cross-linking studies and the absence of copurifying proteins indicated that ChlF forms homodimers. Flash photolysis of ChlF produced a Chl a triplet that decayed with a lifetime (1/e) of ~ 817 µs and that could be attributed to intersystem crossing by EPR spectroscopy at 90 K. When the chlF⁷⁵²¹ gene was expressed in a strain in which the psbD1 and psbD2 genes had been deleted, significantly more Chl f was produced, and Chl f levels could be further enhanced by specific growth-light conditions. Chl f synthesized in Synechococcus sp. PCC 7002 was inserted into trimeric PSI complexes.

Spectral signatures of five hydroxymethyl chlorophyll a derivatives chemically derived from chlorophyll b or chlorophyll f

Chlorophylls (Chls) are pigments involved in light capture and light reactions in photosynthesis. Chl a, Chl b, Chl d, and Chl f are characterized by unique absorbance maxima in the blue (Soret) and red (Q_y) regions with Chl b, Chl d, and Chl f each possessing a single formyl group at a unique position. Relative to Chl a the Q_y absorbance maximum of Chl b is blue-shifted while Chl d and Chl f are red-shifted with the shifts attributable to the relative positions of the formyl substitutions. Reduction of a formyl group of Chl b to form 7-hydroxymethyl Chl a, or oxidation of the vinyl group of Chl a into a formyl group to form Chl d was achieved using sodium borohydride (NaBH₄) or β-mercaptoethanol (BME/O₂), respectively. During the consecutive reactions of Chl b and Chl f using a three-step procedure (1. NaBH₄, 2. BME/O₂, and 3. NaBH₄) two new 7-hydroxymethyl Chl a species were prepared possessing the 3-formyl or 3-hydroxymethyl groups and three new 2-hydroxymethyl Chl a species possessing the 3-vinyl, 3-formyl, or 3-hydroxymethyl groups, respectively. Identification of the spectral properties of 2-hydroxymethyl Chl a may be biologically significant for deducing the latter stages of Chl f biosynthesis if the mechanism parallels Chl b biosynthesis. The spectral features and chromatographic properties of these modified Chls are important for identifying potential intermediates in the biosynthesis of Chls such as Chl f and Chl d and for identification of any new Chls in nature.

Global Transcriptional Profiling of the Cyanobacterium Chlorogloeopsis fritschii PCC 9212 in Far-Red Light: Insights Into the Regulation of Chlorophyll d Synthesis

Some terrestrial cyanobacteria can acclimate to and then utilize far-red light (FRL; λ = 700–800 nm) to perform oxygenic photosynthesis through a process called Far-Red Light Photoacclimation (FaRLiP). During FaRLiP, cells synthesize chlorophylls (Chl) d and Chl f and extensively remodel their photosynthetic apparatus by modifying core subunits of photosystem (PS)I, PSII, and the phycobilisome (PBS). Three regulatory proteins, RfpA, RfpB, and RfpC, are encoded in the FaRLiP gene cluster; they sense FRL and control the synthesis of Chl f and expression of the FaRLiP gene cluster. It was previously uncertain if Chl d synthesis and other physiological and metabolic changes to FRL are regulated by RfpABC. In this study we show that Chl d synthesis is regulated by RfpABC; however, most other transcriptional changes leading to the FRL physiological state are not regulated by RfpABC. Surprisingly, we show that erythromycin induces Chl d synthesis in vivo. Transcriptomic and pigment analyses indicate that thiol compounds and/or cysteine proteases could be involved in Chl d synthesis in FRL. We conclude that the protein(s) responsible for Chl d synthesis is/are probably encoded within the FaRLiP gene cluster. Transcriptional responses to FRL help cells to conserve and produce energy and reducing power to overcome implicit light limitation of photosynthesis during the initial acclimation process to FRL.

The C21-formyl group in chlorophyll f originates from molecular oxygen

Chlorophylls (Chls) are the most important cofactors for capturing solar energy to drive photosynthetic reactions. Five spectral types of Chls have been identified to date, with Chl f having the most red-shifted absorption maximum because of a C21-formyl group substitution of Chl f However, the biochemical provenance of this formyl group is unknown. Here, we used a stable isotope labeling technique (18O and 2H) to determine the origin of the C21-formyl group of Chl f and to verify whether Chl f is synthesized from Chl a in the cyanobacterial species Halomicronema hongdechloris. In the presence of either H218O or 18O2, the origin of oxygen atoms in the newly synthesized chlorophylls was investigated. The pigments were isolated with HPLC, followed by MS analysis. We found that the oxygen atom of the C21-formyl group originates from molecular oxygen and not from H2O. Moreover, we examined the kinetics of the labeling of Chl a and Chl f from H. hongdechloris grown in 50% D2O-seawater medium under different light conditions. When cells were shifted from white light D2O-seawater medium to far-red light H2O-seawater medium, the observed deuteration in Chl f indicated that Chl(ide) a is the precursor of Chl f Taken together, our results advance our understanding of the biosynthesis pathway of the chlorophylls and the formation of the formyl group in Chl f.

Theoretical isotopic fractionation of magnesium between chlorophylls

Magnesium is the metal at the center of all types of chlorophyll and is thus crucial to photosynthesis. When an element is involved in a biosynthetic pathway its isotopes are fractionated based on the difference of vibrational frequency between the different molecules. With the technical advance of multi-collectors plasma-mass-spectrometry and improvement in analytical precision, it has recently been found that two types of chlorophylls (a and b) are isotopically distinct. These results have very significant implications with regards to the use of Mg isotopes to understand the biosynthesis of chlorophyll. Here we present theoretical constraints on the origin of these isotopic fractionations through ab initio calculations. We present the fractionation factor for chlorphyll a, b, d, and f. We show that the natural isotopic variations among chlorophyll a and b are well explained by isotopic fractionation under equilibrium, which implies exchanges of Mg during the chlorophyll cycle. We predict that chlorophyll d and f should be isotopically fractionated compared to chlorophyll a and that this could be used in the future to understand the biosynthesis of these molecules.

Photosynthesis at the far-red region of the spectrum in Acaryochloris marina

Acaryochloris marina is an oxygenic cyanobacterium that utilizes far-red light for photosynthesis. It has an expanded genome, which helps in its adaptability to the environment, where it can survive on low energy photons. Its major light absorbing pigment is chlorophyll d and it has α-carotene as a major carotenoid. Light harvesting antenna includes the external phycobilin binding proteins, which are hexameric rods made of phycocyanin and allophycocyanins, while the small integral membrane bound chlorophyll binding proteins are also present. There is specific chlorophyll a molecule in both the reaction center of Photosystem I (PSI) and PSII, but majority of the reaction center consists of chlorophyll d. The composition of the PSII reaction center is debatable especially the role and position of chlorophyll a in it. Here we discuss the photosystems of this bacterium and its related biology.

The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.

Chlorophylls d and f and Their Role in Primary Photosynthetic Processes of Cyanobacteria

The finding of unique Chl d- and Chl f-containing cyanobacteria in the last decade was a discovery in the area of biology of oxygenic photosynthetic organisms. Chl b, Chl c, and Chl f are considered to be accessory pigments found in antennae systems of photosynthetic organisms. They absorb energy and transfer it to the photosynthetic reaction center (RC), but do not participate in electron transport by the photosynthetic electron transport chain. However, Chl d as well as Chl a can operate not only in the light-harvesting complex, but also in the photosynthetic RC. The long-wavelength (Qy) Chl d and Chl f absorption band is shifted to longer wavelength (to 750 nm) compared to Chl a, which suggests the possibility for oxygenic photosynthesis in this spectral range. Such expansion of the photosynthetically active light range is important for the survival of cyanobacteria when the intensity of light not exceeding 700 nm is attenuated due to absorption by Chl a and other pigments. At the same time, energy storage efficiency in photosystem 2 for cyanobacteria containing Chl d and Chl f is not lower than that of cyanobacteria containing Chl a. Despite great interest in these unique chlorophylls, many questions related to functioning of such pigments in primary photosynthetic processes are still not elucidated. This review describes the latest advances in the field of Chl d and Chl f research and their role in primary photosynthetic processes of cyanobacteria.

Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410

Acaryochloris species are a genus of cyanobacteria that utilize chlorophyll (chl) d as their primary chlorophyll molecule during oxygenic photosynthesis. Chl d allows Acaryochloris to harvest red-shifted light, which gives them the ability to live in filtered light environments that are depleted in visible light. Although genomes of multiple Acaryochloris species have been sequenced, their analysis has not revealed how chl d is synthesized. Here, we demonstrate that Acaryochloris sp. CCMEE 5410 cells undergo chlorosis by nitrogen depletion and exhibit robust regeneration of chl d by nitrogen repletion. We performed a time course RNA-Seq experiment to quantify global transcriptomic changes during chlorophyll recovery. We observed upregulation of numerous known chl biosynthesis genes and also identified an oxygenase gene with a similar transcriptional profile as these chl biosynthesis genes, suggesting its possible involvement in chl d biosynthesis. Moreover, our data suggest that multiple prochlorophyte chlorophyll-binding homologs are important during chlorophyll recovery, and light-independent chl synthesis genes are more dominant than the light-dependent gene at the transcription level. Transcriptomic characterization of this organism provides crucial clues toward mechanistic elucidation of chl d biosynthesis.

Light-dependent chlorophyll f synthase is a highly divergent paralog of PsbA of photosystem II

Chlorophyll f (Chl f) permits some cyanobacteria to expand the spectral range for photosynthesis by absorbing far-red light. We used reverse genetics and heterologous expression to identify the enzyme for Chl f synthesis. Null mutants of "super-rogue" psbA4 genes, divergent paralogs of psbA genes encoding the D1 core subunit of photosystem II, abolished Chl f synthesis in two cyanobacteria that grow in far-red light. Heterologous expression of the psbA4 gene, which we rename chlF, enables Chl f biosynthesis in Synechococcus sp. PCC 7002. Because the reaction requires light, Chl f synthase is probably a photo-oxidoreductase that employs catalytically useful Chl a molecules, tyrosine YZ, and plastoquinone (as does photosystem II) but lacks a Mn4Ca1O5 cluster. Introduction of Chl f biosynthesis into crop plants could expand their ability to use solar energy.

Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina

The major photopigment of the cyanobacterium Acaryochloris marina is chlorophyll d, while its direct biosynthetic precursor, chlorophyll a, is also present in the cell. These pigments, along with the majority of chlorophylls utilized by oxygenic phototrophs, carry an ethyl group at the C-8 position of the molecule, having undergone reduction of a vinyl group during biosynthesis. Two unrelated classes of 8-vinyl reductase involved in the biosynthesis of chlorophylls are known to exist, BciA and BciB. The genome of Acaryochloris marina contains open reading frames (ORFs) encoding proteins displaying high sequence similarity to BciA or BciB, although they are annotated as genes involved in transcriptional control (nmrA) and methanogenesis (frhB), respectively. These genes were introduced into an 8-vinyl chlorophyll a-producing ΔbciB strain of Synechocystis sp. strain PCC 6803, and both were shown to restore synthesis of the pigment with an ethyl group at C-8, demonstrating their activities as 8-vinyl reductases. We propose that nmrA and frhB be reassigned as bciA and bciB, respectively; transcript and proteomic analysis of Acaryochloris marina reveal that both bciA and bciB are expressed and their encoded proteins are present in the cell, possibly in order to ensure that all synthesized chlorophyll pigment carries an ethyl group at C-8. Potential reasons for the presence of two 8-vinyl reductases in this strain, which is unique for cyanobacteria, are discussed.

IMPORTANCE The cyanobacterium Acaryochloris marina is the best-studied phototrophic organism that uses chlorophyll d for photosynthesis. Unique among cyanobacteria sequenced to date, its genome contains ORFs encoding two unrelated enzymes that catalyze the reduction of the C-8 vinyl group of a precursor molecule to an ethyl group. Carrying a reduced C-8 group may be of particular importance to organisms containing chlorophyll d. Plant genomes also contain orthologs of both of these genes; thus, the bacterial progenitor of the chloroplast may also have contained both bciA and bciB.

Hydroxylation of the C132 and C18 carbons of chlorophylls by heme and molecular oxygen

Following extraction from photosynthetic organisms, chlorophylls are prone to reactions including demetalation, dephytylation and specific oxidations of the exocyclic ring E, termed allomerizations. Allomerization of chlorophylls has been well-characterized in methanol and to a lesser extent in aqueous solution. Here we detail novel allomerization-like reactions of chlorophyll a and chlorophyll b. In the presence of heme, detergent-solubilized chlorophyll a is hydroxylated at its C 132 position in ring E and, surprisingly, the C 18 position in ring D. Two major oxidation products are synthesized — a C 132- OH and a C 132- OH , C 18- OH derivative of chlorophyll a. We track the origin of the oxygen atoms added in these hydroxylated chlorophylls using 18 O 2 labeling and demonstrate that the additional oxygen atoms are derived from molecular oxygen. A similar heme-catalyzed reaction is also observed using chlorophyll b as a substrate. These results highlight the need for care when dealing with extracted chlorophylls and demonstrate an unusual hydroxylation of the C 18 position of chlorophylls in the presence of heme.

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

Cells of a unicellular cyanobacterium strain KC1, which were collected from Japanese fresh water Lake Biwa, formed chlorophyll (Chl) f at 6.7%, Chl a' at 2.0% and pheophytin a at 0.96% with respect to Chl a after growth under 740 nm light. The far-red-acclimated cells (Fr cells) formed extra absorption bands of Chl f at 715 nm in addition to the major Chl a band. Fluorescence lifetimes were measured. The 405-nm laser flash, which excites mainly Chl a in photosystem I (PSI), induced a fast energy transfer to multiple fluorescence bands at 720-760 and 805 nm of Chl f at 77 K in Fr cells with almost no PSI-red-Chl a band. The 630-nm laser flash, which mainly excited photosystem II (PSII) through phycocyanin, revealed fast energy transfer to another set of Chl f bands at 720-770 and 810 nm as well as to the 694-nm Chl a fluorescence band. The 694-nm band did not transfer excitation energy to Chl f. Therefore, Chl a in PSI, and phycocyanin in PSII of Fr cells transferred excitation energy to different sets of Chl f molecules. Multiple Chl f forms, thus, seem to work as the far-red antenna both in PSI and PSII. A variety of cyanobacterial species, phylogenically distant from each other, seems to use a Chl f antenna in far-red environments, such as under dense biomats, in colonies, or under far-red LED light.

Turnover rates in microorganisms by laser ablation electrospray ionization mass spectrometry and pulse-chase analysis

Biochemical processes rely on elaborate networks containing thousands of compounds participating in thousands of reaction. Rapid turnover of diverse metabolites and lipids in an organism is an essential part of homeostasis. It affects energy production and storage, two important processes utilized in bioengineering. Conventional approaches to simultaneously quantify a large number of turnover rates in biological systems are currently not feasible. Here we show that pulse-chase analysis followed by laser ablation electrospray ionization mass spectrometry (LAESI-MS) enable the simultaneous and rapid determination of metabolic turnover rates. The incorporation of ion mobility separation (IMS) allowed an additional dimension of analysis, i.e., the detection and identification of isotopologs based on their collision cross sections. We demonstrated these capabilities by determining metabolite, lipid, and peptide turnover in the photosynthetic green algae, Chlamydomonas reinhardtii, in the presence of (15)N-labeled ammonium chloride as the main nitrogen source. Following the reversal of isotope patterns in the chase phase by LAESI-IMS-MS revealed the turnover rates and half-lives for biochemical species with a wide range of natural concentrations, e.g., chlorophyll metabolites, lipids, and peptides. For example, the half-lives of lyso-DGTS(16:0) and DGTS(18:3/16:0), t1/2 = 43.6 ± 4.5 h and 47.6 ± 2.2 h, respectively, provided insight into lipid synthesis and degradation in this organism. Within the same experiment, half-lives for chlorophyll a, t1/2 = 24.1 ± 2.2 h, and a 2.8 kDa peptide, t1/2 = 10.4 ± 3.6 h, were also determined.

Establishment of the forward genetic analysis of the chlorophyll d-dominated cyanobacterium Acaryochloris marina MBIC 11017 by applying in vivo transposon mutagenesis system

Acaryochloris marina MBIC 11017 possesses chlorophyll (Chl) d as a major Chl, which enables this organism to utilize far-red light for photosynthesis. Thus, the adaptation mechanism of far-red light utilization, including Chl d biosynthesis, has received much attention, though a limited number of reports on this subject have been published. To identify genes responsible for Chl d biosynthesis and adaptation to far-red light, molecular genetic analysis of A. marina was required. We developed a transformation system for A. marina and introduced expression vectors into A. marina. In this study, the high-frequency in vivo transposon mutagenesis system recently established by us was applied to A. marina. As a result, we obtained mutants with the transposon in their genomic DNA at various positions. By screening transposon-tagged mutants, we isolated a mutant (Y1 mutant) that formed a yellow colony on agar medium. In the Y1 mutant, the transposon was inserted into the gene encoding molybdenum cofactor biosynthesis protein A (MoaA). The Y1 mutant was functionally complemented by introducing the moaA gene or increasing the ammonium ion in the medium. These results indicate that the mutation of the moaA gene reduced nitrate reductase activity, which requires molybdenum cofactor, in the Y1 mutant. This is the first successful forward genetic analysis of A. marina, which will lead to the identification of genes responsible for adaptation to far-red light.

In vitro conversion of vinyl to formyl groups in naturally occurring chlorophylls

The chemical structural differences distinguishing chlorophylls in oxygenic photosynthetic organisms are either formyl substitution (chlorophyll b, d, and f) or the degree of unsaturation (8-vinyl chlorophyll a and b) of a side chain of the macrocycle compared with chlorophyll a. We conducted an investigation of the conversion of vinyl to formyl groups among naturally occurring chlorophylls. We demonstrated the in vitro oxidative cleavage of vinyl side groups to yield formyl groups through the aid of a thiol-containing compound in aqueous reaction mixture at room temperature. Heme is required as a catalyst in aqueous solution but is not required in methanolic reaction mixture. The conversion of vinyl- to formyl- groups is independent of their position on the macrocycle, as we observed oxidative cleavages of both 3-vinyl and 8-vinyl side chains to yield formyl groups. Three new chlorophyll derivatives were synthesised using 8-vinyl chlorophyll a as substrate: 8-vinyl chlorophyll d, [8-formyl]-chlorophyll a, and [3,8-diformyl]-chlorophyll a. The structural and spectral properties will provide a signature that may aid in identification of the novel chlorophyll derivatives in natural systems. The ease of conversion of vinyl- to formyl- in chlorophylls demonstrated here has implications regarding the biosynthetic mechanism of chlorophyll din vivo.

Chlorophyll modifications and their spectral extension in oxygenic photosynthesis

Chlorophylls are magnesium-tetrapyrrole molecules that play essential roles in photosynthesis. All chlorophylls have similar five-membered ring structures, with variations in the side chains and/or reduction states. Formyl group substitutions on the side chains of chlorophyll a result in the different absorption properties of chlorophyll b, chlorophyll d, and chlorophyll f. These formyl substitution derivatives exhibit different spectral shifts according to the formyl substitution position. Not only does the presence of various types of chlorophylls allow the photosynthetic organism to harvest sunlight at different wavelengths to enhance light energy input, but the pigment composition of oxygenic photosynthetic organisms also reflects the spectral properties on the surface of the Earth. Two major environmental influencing factors are light and oxygen levels, which may play central roles in the regulatory pathways leading to the different chlorophylls. I review the biochemical processes of chlorophyll biosynthesis and their regulatory mechanisms.

Chlorophyll d and Acaryochloris marina: current status

The discovery of the chlorophyll d-containing cyanobacterium Acaryochloris marina in 1996 precipitated a shift in our understanding of oxygenic photosynthesis. The presence of the red-shifted chlorophyll d in the reaction centre of the photosystems of Acaryochloris has opened up new avenues of research on photosystem energetics and challenged the unique status of chlorophyll a in oxygenic photosynthesis. In this review, we detail the chemistry and role of chlorophyll d in photosynthesis and summarise the unique adaptations that have allowed the proliferation of Acaryochloris in diverse ecological niches around the world.

Formyl group modification of chlorophyll a: a major evolutionary mechanism in oxygenic photosynthesis

We discuss recent advances in chlorophyll research in the context of chlorophyll evolution and conclude that some derivations of the formyl side chain arrangement of the porphyrin ring from that of the Chl a macrocycle can extend the photosynthetic active radiation (PAR) of these molecules, for example, Chl d and Chl f absorb light in the near-infrared region, up to ∼750 nm. Derivations such as this confer a selective advantage in particular niches and may, therefore, be beneficial for photosynthetic organisms thriving in light environments with particular light signatures, such as red- and near-far-red light-enriched niches. Modelling of formyl side chain substitutions of Chl a revealed yet unidentified but theoretically possible Chls with a distinct shift of light absorption properties when compared to Chl a.

Extending the limits of natural photosynthesis and implications for technical light harvesting

Photosynthetic organisms provide, directly or indirectly, the energy that sustains life on earth by harvesting light from the sun. The amount of light impinging on the surface of the earth vastly surpasses the energy needs of life including man. Harvesting the sun is, therefore, an option for a sustainable energy source: directly by improving biomass production, indirectly by coupling it to the production of hydrogen for fuel or, conceptually, by using photosynthetic strategies for technological solutions based on non-biological or hybrid materials. In this review, we summarize the various light climates on earth, the primary reactions responsible for light harvesting and transduction to chemical energy in photosynthesis, and the mechanisms of competitively adapting the photosynthetic apparatus to the ever-changing light conditions. The focus is on oxygenic photosynthesis, its adaptation to the various light-climates by specialized pigments and on the extension of its limits by the evolution of red-shifted chlorophylls. The implications for potential technical solutions are briefly discussed.

A cyanobacterium that contains chlorophyll f--a red-absorbing photopigment

A Chl f-containing filamentous cyanobacterium was purified from stromatolites and named as Halomicronema hongdechloris gen., sp. nov. after its phylogenetic classification and the morphological characteristics. Hongdechloris contains four main carotenoids and two chlorophylls, a and f. The ratio of Chl f to Chl a is reversibly changed from 1:8 under red light to an undetectable level of Chl f under white-light culture conditions. Phycobiliproteins were induced under white light growth conditions. A fluorescence emission peak of 748 nm was identified as due to Chl f. The results suggest that Chl f is a red-light inducible chlorophyll.

Non-enzymatic conversion of chlorophyll-a into chlorophyll-d in vitro: a model oxidation pathway for chlorophyll-d biosynthesis

Chlorophyll-a (Chl-a) was readily converted into Chl-d under mild conditions without any enzymes. Treatment of Chl-a dissolved in dry tetrahydrofuran (THF) with thiophenol and acetic acid at room temperature successfully produced Chl-d in 31% yield. During the acidic oxidation, removal of the central magnesium, pheophytinization, was sufficiently suppressed. This mild pathway can give insights into the yet unidentified Chl-d biosynthesis.

Biofilm growth and near-infrared radiation-driven photosynthesis of the chlorophyll d-containing cyanobacterium Acaryochloris marina

The cyanobacterium Acaryochloris marina is the only known phototroph harboring chlorophyll (Chl) d. It is easy to cultivate it in a planktonic growth mode, and A. marina cultures have been subject to detailed biochemical and biophysical characterization. In natural situations, A. marina is mainly found associated with surfaces, but this growth mode has not been studied yet. Here, we show that the A. marina type strain MBIC11017 inoculated into alginate beads forms dense biofilm-like cell clusters, as in natural A. marina biofilms, characterized by strong O(2) concentration gradients that change with irradiance. Biofilm growth under both visible radiation (VIS, 400 to 700 nm) and near-infrared radiation (NIR, ∼700 to 730 nm) yielded maximal cell-specific growth rates of 0.38 per day and 0.64 per day, respectively. The population doubling times were 1.09 and 1.82 days for NIR and visible light, respectively. The photosynthesis versus irradiance curves showed saturation at a photon irradiance of E(k) (saturating irradiance) >250 μmol photons m(-2) s(-1) for blue light but no clear saturation at 365 μmol photons m(-2) s(-1) for NIR. The maximal gross photosynthesis rates in the aggregates were ∼1,272 μmol O(2) mg Chl d(-1) h(-1) (NIR) and ∼1,128 μmol O(2) mg Chl d(-1) h(-1) (VIS). The photosynthetic efficiency (α) values were higher in NIR-irradiated cells [(268 ± 0.29) × 10(-6) m(2) mg Chl d(-1) (mean ± standard deviation)] than under blue light [(231 ± 0.22) × 10(-6) m(2) mg Chl d(-1)]. A. marina is well adapted to a biofilm growth mode under both visible and NIR irradiance and under O(2) conditions ranging from anoxia to hyperoxia, explaining its presence in natural niches with similar environmental conditions.

Extinction coefficient for red-shifted chlorophylls: chlorophyll d and chlorophyll f

Both chlorophyll f and chlorophyll d are red-shifted chlorophylls in oxygenic photosynthetic organisms, which extend photon absorbance into the near infrared region. This expands the range of light that can be used to drive photosynthesis. Quantitative determination of chlorophylls is a crucial step in the investigation of chlorophyll-photosynthetic reactions in the field of photobiology and photochemistry. No methods have yet been worked out for the quantitative determination of chlorophyll f. There is also no method available for the precise quantitative determination of chlorophyll d although it was discovered in 1943. In order to obtain the extinction coefficients (ε) of chlorophyll f and chlorophyll d, the concentrations of chlorophylls were determined by Inductive Coupled Plasma Mass Spectrometry according to the fact that each chlorophyll molecule contains one magnesium (Mg) atom. Molar extinction coefficient ε(chl f) is 71.11×10(3)Lmol(-1)A(707nm)cm(-1) and ε(chl d) is 63.68×10(3)Lmol(-1)A(697nm)cm(-1) in 100% methanol. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Evolution of a divinyl chlorophyll-based photosystem in Prochlorococcus

Acquisition of new photosynthetic pigments has been a crucial process for the evolution of photosynthesis and photosynthetic organisms. In this process, pigment-binding proteins must evolve to fit new pigments. Prochlorococcus is a unique photosynthetic organism that uses divinyl chlorophyll (DVChl) instead of monovinyl chlorophyll. However, cyanobacterial mutants that accumulate DVChl immediately die even under medium-light conditions, suggesting that chlorophyll (Chl)-binding proteins had to evolve to fit to DVChl concurrently with Prochlorococcus evolution. To elucidate the coevolutionary process of Chl and Chl-binding proteins during the establishment of DVChl-based photosystems, we first compared the amino acid sequences of Chl-binding proteins in Prochlorococcus with those in other photosynthetic organisms. Two amino acid residues of the D1 protein, V205 and G282, are conserved in monovinyl chlorophyll-based photosystems; however, in Prochlorococcus, they are substituted with M205 and C282, respectively. According to the solved photosystem II structure, these amino acids are not involved in Chl binding. To mimic Prochlorococcus, V205 was mutated to M205 in the D1 protein from Synechocystis sp. PCC6803 and Synechocystis dvr mutant was transformed with this construct. Although these transgenic cells could not grow under high-light conditions, they acquired light tolerance and grew under medium-light conditions, whereas untransformed dvr mutants could not survive. Substitution of G282 for C282 contributed additional light tolerance, suggesting that the amino acid substitutions in the D1 protein played an essential role in the development of DVChl-based photosystems. Here, we discuss the coevolution of a photosynthetic pigment and its binding protein.

Expanding the solar spectrum used by photosynthesis

A limiting factor for photosynthetic organisms is their light-harvesting efficiency, that is the efficiency of their conversion of light energy to chemical energy. Small modifications or variations of chlorophylls allow photosynthetic organisms to harvest sunlight at different wavelengths. Oxygenic photosynthetic organisms usually utilize only the visible portion of the solar spectrum. The cyanobacterium Acaryochloris marina carries out oxygenic photosynthesis but contains mostly chlorophyll d and only traces of chlorophyll a. Chlorophyll d provides a potential selective advantage because it enables Acaryochloris to use infrared light (700-750 nm) that is not absorbed by chlorophyll a. Recently, an even more red-shifted chlorophyll termed chlorophyll f has been reported. Here, we discuss using modified chlorophylls to extend the spectral region of light that drives photosynthetic organisms.

Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche

Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.

Evolution of photosynthesis

Energy conversion of sunlight by photosynthetic organisms has changed Earth and life on it. Photosynthesis arose early in Earth's history, and the earliest forms of photosynthetic life were almost certainly anoxygenic (non-oxygen evolving). The invention of oxygenic photosynthesis and the subsequent rise of atmospheric oxygen approximately 2.4 billion years ago revolutionized the energetic and enzymatic fundamentals of life. The repercussions of this revolution are manifested in novel biosynthetic pathways of photosynthetic cofactors and the modification of electron carriers, pigments, and existing and alternative modes of photosynthetic carbon fixation. The evolutionary history of photosynthetic organisms is further complicated by lateral gene transfer that involved photosynthetic components as well as by endosymbiotic events. An expanding wealth of genetic information, together with biochemical, biophysical, and physiological data, reveals a mosaic of photosynthetic features. In combination, these data provide an increasingly robust framework to formulate and evaluate hypotheses concerning the origin and evolution of photosynthesis.

Adventures with cyanobacteria: a personal perspective

Cyanobacteria, or the blue-green algae as they used to be called until 1974, are the oldest oxygenic photosynthesizers. We summarize here adventures with them since the early 1960s. This includes studies on light absorption by cyanobacteria, excitation energy transfer at room temperature down to liquid helium temperature, fluorescence (kinetics as well as spectra) and its relationship to photosynthesis, and afterglow (or thermoluminescence) from them. Further, we summarize experiments on their two-light reaction - two-pigment system, as well as the unique role of bicarbonate (hydrogen carbonate) on the electron-acceptor side of their photosystem II, PSII. This review, in addition, includes a discussion on the regulation of changes in phycobilins (mostly in PSII) and chlorophyll a (Chl a; mostly in photosystem I, PSI) under oscillating light, on the relationship of the slow fluorescence increase (the so-called S to M rise, especially in the presence of diuron) in minute time scale with the so-called state-changes, and on the possibility of limited oxygen evolution in mixotrophic PSI (minus) mutants, up to 30 min, in the presence of glucose. We end this review with a brief discussion on the position of cyanobacteria in the evolution of photosynthetic systems.