Overall structure, protein subunits, and cofactors of A. marina PSI
The PSI trimer complex was isolated from A. marina. Detailed methods of sample preparation, data processing, and structural refinement by cryo-EM, and biochemical data, are presented in Supplementary Information (Supplementary Figs. 4–11, Supplementary Tables 1–4). The model of the PSI trimer was refined to give a correlation coefficient and Q-score, which are indices for validating the correctness of a model, of 0.80 and 0.678, respectively (Supplementary Table 4). These index values can be considered reasonable at 2.5 Å resolution (Supplementary Fig. 10).
The PSI trimer has dimensions of 100 Å depth, 200 Å length, and 200 Å width, including the surrounding detergent micelle (Fig. 2). The overall structure resembles those of PSI trimers reported for other cyanobacteria1,22,23,34. The root-mean-square deviations using secondary structure matching between the monomer model (chains A–M) and Protein Data Bank (PDB) structures 1JB0 of Thermosynechococcus elongatus 1, 5OY0 of Synechocystis sp. PCC 6803 34, and 6KMX of Halomicronema hongdechloris 19 are 0.90 Å, 0.90 Å, and 0.87 Å, respectively.
The A. marina PSI monomer contains 11 subunits [PsaA, PsaB, PsaC, PsaD, PsaE, PsaF, PsaJ, PsaK, PsaL, PsaM, and Psa27], all of which could be assigned to the cryo-EM density map (Fig. 2, Supplementary Figs. 5 and 12, and Supplementary Table 1). PsaX (a peripheral subunit in other cyanobacteria such as T. elongatus), PsaG and PsaH (subunits in higher plants) were missing in the density map, consistent with the absence of their genes from the A. marina genome 10. The name Psa27 was given to a novel subunit protein in A. marina that has low sequence identity (29.4%) with PsaI of T. elongatus (Supplementary Table 5) 12. Here, we found that Psa27 is in the same location as PsaI, a transmembrane alpha helix, in T. elongatus. Psa27 also contributes to the structural stabilization of the PSI trimer just as PsaI does in T. elongatus. Thus, we concluded that Psa27 and PsaI are in effect the same subunit.
The loop regions of PsaB (residues 290−320 and 465−510) were not identified due to disorder because of the absence of PsaX, suggesting that PsaX stabilizes these regions in other cyanobacteria. Most of subunits PsaE, PsaF, and PsaK were modeled using polyalanine because of poor regional map quality (Supplementary Figs. 12, 13, and Supplementary Table 1), possibly suggesting that some part of those subunits dissociated during sample preparation.
The cofactors assigned (Supplementary Fig. 15) are 71 Chl d (Supplementary Table 6), one Chl d´ (an epimer of Chl d), 11 α-carotenes (α-Car) but no β-Car (Supplementary Table 7) 10,14, two pheophytins (Pheo) (a derivative of Chl; however, unlike Chl, no Mg2+ ion is coordinated by the tetrapyrrole ring), two phylloquinones (PhyQs), three iron–sulfur clusters, two phosphatidylglycerols, one monogalactosyl diacylglycerol, and 84 water molecules. Two molecules of Pheo were assigned as Pheo a on the basis of pigment analysis (Supplementary Table 7). In addition, a small amount of Chl a (approximately one Chl a per Chl d’) was detected by pigment analysis (Supplementary Table 7). In this study, we assigned the Chls of A. marina-PSI as Chl d. This is because the amount of Chl a in the A. marina PSI is minimal, and it is not possible to distinguish between Chl d and Chl a at 2.5 Å resolution as is described later.
In the A. marina PSI, a large number of Chl d and α-Car harvest light energy and finally transfer the energy to P740. The arrangements of Chl d and α-Car in A. marina resemble those of Chl a and β-Car, respectively, in T. elongatus, as shown in Supplementary Fig. 17. The pigments are numbered according to the nomenclature of Chl a in T. elongatus 36 (Supplementary Table 6). However, there are differences in some amino acid residues surrounding the cofactors, slight gaps in the arrangement of the cofactors, and absence of some Chls in the A. marina PSI compared with those of T. elongatus (Supplementary Table 5, Supplementary Fig. 17 – 19). For example, Phe49/J in A. marina, the counterpart of His39/J that is an axial ligand of Chl a 88 in T. elongatus PSI, explains the absence of the corresponding Chl d (Supplementary Fig. 17D). Owing to the absence of PsaX in A. marina, the Chl d corresponding to Chl a 951,37 in T. elongatus whose axial ligand is Asn23/X is also missing. The absence of Chl a 94 is seen in some other reported PSI structures such as Synechocystis sp. PCC 680334. The arrangements of pigments adjacent to Psa27 (PsaI) and PsaL, whose sequence identity with other cyanobacterial PsaLs is low, are specific to A. marina (Supplementary Fig. 16A, black dashed line region, and Supplementary Fig. 18, and 19). Chl d 38, 52, 53, and the ring (α or ε) of Car4007 near Chl d 53 are set within the surrounding structure differently from those in T. elongatus (Supplementary Fig. 18A). These differences when compared with the structure of T. elongatus help explain the specific features of light harvesting in A. marina. Additionally, the C3-formyl groups of some Chl d in the A. marina PSI form hydrogen bonds with their surrounding amino acid residues (Supplementary Table 6, Supplementary Fig. 19). These unique structural features will be important in future theoretical studies of the light harvesting mechanism in A. marina.
Although the amount of Chl d per Chl d’ determined by pigment analysis (67.0±0.66, n=5 of independently prepared PSI) and assigned by structural analysis (71 including one or two Chl a) is lower in this study than those in previous studies (145±814 and 97.0±11.012), the semi-stoichiometric amount of Phe a at 1.92±0.022 (0.3±0.2 per reaction center in a previous study 12) is consistent with our structural analysis. Notwithstanding the fact that the local resolution of some parts of the outer region is somewhat lower, the PSI was stable enough to keep its integrity for five days (Supplementary Fig. 5). Chls that were unable to be assigned in A. marina PSI compared with those in T. elongatus PSI are shown by marking N/D in the column of the ID number in Supplementary Table 6. Such Chls can be recognized by the chlorins in transparent gray in Supplementary Fig. 17. Chls corresponding to Chl-88 and Chl-94 in T. elongatus appear to be absent in A. marina PSI. The numbers of Chls in the PSI of Chl f-carrying Fischerella thermalis (8922) and H. hongdechloris (9019) are also lower than those of T. elongatus PSI (961). The type I reaction center of Heliobacterium modesticaldum carries a much smaller amount of Chl species; 60 molecules per reaction center35.
Due to the somewhat lower resolutions of the outer regions of the A. marina PSI, we mainly focus on the structure and function of the central part of A. marina PSI at high local resolution, that is, P740 and the electron transfer components.
Electron transfer components
The configuration of the electron transfer chain in A. marina PSI is similar to that of the PSI from T. elongatus (Fig.1), although cofactor compositions are different. The important assigned cofactors involved in electron transfer (Fig. 1B) are four Chls, two Pheos, two PhyQs (A1), and three iron–sulfur clusters (FX, FA, and FB) (Fig. 3A). The Chls and PhyQs are arranged in two branches, the A-branch and the B-branch, which are related by a pseudo-C2 axis as in other type I reaction centers, and are stabilized by amino acid residues of subunits PsaA and PsaB. The Chls of special pair P740 are Chl d´ (PA) and Chl d (PB) (Fig. 4A), which are coordinated by residues His678/A and His657/B, respectively (capitalized letters following the slash (/) indicate the subunit names such as PsaA or PsaB) (Fig. 3B and C). The distance between the ring planes (the π–π interaction distance) of Chl d´ and Chl d is 3.5 Å (Fig. 3D) (3.6 Å in T. elongatus). Two Tyr residues, Tyr601/A and Tyr733/A, are positioned within hydrogen bonding distance of PA as observed in PSI from T. elongatus.
In A. marina PSI, we identified three water molecules (W1−W3) around PA. They form hydrogen bonds with surrounding amino acid residues (Tyr601/A, Ser605/A, Asn608/A, Ser741/A, and Try745/A) and one Chl d (Chl d 32) (Fig. 3B and C). For the T. elongatus PA, only one water molecule forms hydrogen bonds with surrounding amino acid residues (Tyr603/A, Ser607/A, Ile610/A, Thr743/A, and Phe747/A) and Chl a´ (PA). There are no water molecules around PB in A. marina, but some water molecules surround PB in T. elongatus without forming hydrogen bonds. This difference around PB may come from the difference in two amino acid residues: Val594/B in A. marina vs. Thr597/B in T. elongatus, and Asn598/B in A. marina vs. His601/B in T. elongatus. The hydrogen bonding pattern around PA probably contributes to the charge distribution ratio (PA˙+/PB˙+) 1,38, and therefore, is likely different in the two organisms. The midpoint potential values, Em (PA) and Em (PB), are influenced by the protein environment, in particular by the presence of charged residues. The Em difference, Em (PA) − Em (PB) (= ΔEm), is an important factor in determining the PA˙+/PB˙+ ratio 39.
The orientations of the formyl group in PA (Chl d´) and PB (Chl d) were identified by considering the distribution of the cryo-EM density (Fig. 5A and B). No amino acid residues and pigments capable of forming hydrogen bonds with these formyl groups were found in the vicinity of PA and PB. This suggests that these formyl groups form hydrogen bonds with the C5 H atom in Chl d´ and Chl d, respectively. Similarly, there were no amino acid residues and pigments capable of forming a hydrogen bond around the formyl group of Acc (AccA and AccB) (Fig. 5C and D). However, the orientations of the formyl group of Acc (AccA and AccB) were altered by the hydrophobic environment caused by Trp (Trp585/B and Trp599/A) when compared with P740.
Previous studies have suggested that the primary electron acceptor A0 in A. marina PSI (Fig. 1A) is Chl a 13,40, in line with other species 1,41. However, we found that there was no Mg2+-derived density at the center of the tetrapyrrole rings of A0A and A0B, but rather a hole in the cryo-EM density map (Fig. 4A; Fig. 5E, F). This indicates, when combined with the result of pigment analysis (Supplementary Table 7 and Supplementary Fig. 16), that A0 is actually Pheo a, a derivative of Chl a. Furthermore, the position of Leu665/B (Supplementary Fig. 20B) 42 pointing to A0B, supports Pheo a as A0B in A. marina, because Leu cannot serve as a ligand to Mg2+ in Chl. Thus, surprisingly, A0A and A0B are assigned as Pheo a in A. marina PSI (Fig. 1B; Fig. 3A; Fig. 4A–C). The present study reveals that the axial amino acid residues at the A0A and A0B sites are Met686/A and Leu665/B, respectively. In comparison, the A0A and A0B sites in T. elongatus PSI are both occupied by Chl a molecules whose central Mg2+ ions are both coordinated by Met residues 1,42. At present, it is unclear how the A. marina PSI selectively binds Pheo a at the A0 sites instead of other pigments (Chl a or Chl d). However, the switch from Chl a to Pheo a in the A0A and A0B sites of A. marina PSI is probably not entirely dependent on the difference in its central ligand.
The amino acid residue nearest to A0A in A. marina is Met (Met686/A) (Supplementary Fig. 20A) 42 and the identity of close amino acid residues may modify the reduction potentials of the two A0 sites and their absorption peak wavelength(s). Two mechanisms have been proposed for electron transfer in PSI reaction centers, one using both A- and B-branches 43,44, and the other using the A-branch preferentially 45,46. Only the A-branch may be active in A. marina PSI 42. Two previous studies have reported different mechanisms for the delocalization of the charge distribution in P74047,48. Future theoretical studies using the A. marina PSI structure may throw more light on the details of the electron transfer mechanism in relation to the PA˙+/PB˙+ ratio.
Why is Pheo a the primary acceptor, A0, in A. marina PSI? According to the midpoint potential value (Em), it seems reasonable for the Chl d-driven PSI to use Pheo a as A0, since the energy gap is sufficient for the primary electron transfer step as is estimated below. The Em of P740 vs. the standard hydrogen electrode (SHE) is 439 mV12,13,18,49, which is comparable with that of P700 (470 mV 50). While the special pair P740, which are Chl d/d’, use low-energy far-red light of 740 nm (1.68 eV), it generates reducing power almost equivalent to that of the P700 (Chl a/a', 1.77 eV) in plants and most cyanobacteria 12. The produced reducing power of the excited state of P740 (P740*) is weaker by 0.09 eV than that of P700* (i.e., 1.77 – 1.68 eV). This could result in a slower electron transfer rate to A0 and an increase in reverse reaction without a change in Em of A0, due to the smaller driving force. It is reported that the rates of electron transfer from P740* to A0, and to PhyQ are actually comparable to those from P700* to A0 and to PhyQ 40. Then, Em of A0 has to change for a proper forward reaction. Because most of the amino acid residues around A0 in A. marina PSI are similar to those in T. elongatus, it is unlikely that the protein structure around A0 influences the Em value. Therefore, we looked at the Em value of the cofactor molecule itself, and obtained Em (vs. SHE) values of purified Chl a, Chl d, and Pheo a in acetonitrile of −1,100, −910, and −750 mV, respectively (Supplementary Fig. 21) 50,51. The Em of Pheo a is the highest. Accordingly, Pheo a as A0 should achieve the same electron transfer efficiency as the Chl a-type PSI. Then, reinvestigation of a possible effect on rate of the following A0 to PhyQ (A1) step may be warranted as the charge recombination kinetics between P740+ and A1- has been reported to be comparable to those between P700+ and A1- of Chl a-type PSI49.
A. marina contains a limited but distinct amount of Chl a 12,14,42, and we found a small amount in the PSI (1–2 Chl a per PSI monomer) (Supplementary Table 7). It was once assumed that A0 is Chl a40, but we now know this to be incorrect. One possible place for Chl a is as the accessory Chls, AccA and AccB (Figs. 1 and 4). Unfortunately, the functional group containing C31 of Acc Chl could not be precisely defined from the cryo-EM density map. While quantum mechanical/molecular mechanical calculations show that the formyl group of Chl d adopts two orientations (Supplementary Fig. 1C, D) 52, the oxygen atom of the formyl group on the Chl d molecule in a vacuum is more stable when oriented towards the C5 H atom, suggesting the conformer in Supplementary Fig. 1C. In contrast, the vinyl group of Chl a can adopt either orientation. Therefore, Acc could not be conclusively identified as Chl d or Chl a at the present resolution, and we assigned Accs as Chl d in this study. The Mg2+ in AccA and AccB are coordinated by water molecules forming hydrogen bonds with Asn588/B and Asn602/A, respectively (Fig. 4B and C). In T. elongatus PSI, the methyl ester groups of the Chl a in AccA and AccB affect the charge and spin distributions on P700 39,53–55. In A. marina PSI, these distances were estimated to be 6.2 Å (AccA−PA) and 6.6 Å (AccB−PB), respectively (Fig. 4D), in the present structure.
The amino acid residues surrounding PhyQ (A1A and A1B) are switched compared with those in T. elongatus PSI - Met720/A and Leu665/B in A. marina vs. Leu722/A and Met668/B in T. elongatus (Supplementary Fig. 22A, B). The arrangement of the phytol chain of A1B is also different from that in other cyanobacteria (Supplementary Fig. 22B). These structural differences may suggest that the protein environment within A. marina PSI containing Chl d is modified to support forward electron transfer by suppressing the reverse electron transfer from PhyQ to A0. However, cofactors FX, FA, and FB and their surrounding structures in A. marina PSI are nearly identical to those in other cyanobacteria (Fig. 3A and Supplementary Fig. 22). This indicates that the reduction potentials are likely at the same level, although the three Fe/S clusters, Fx, FA, FB, transfer electrons from PhyQ (A1) to ferredoxin and the environment does not need to be conserved as long as the overall energy trajectory is downhill.
A. marina PSI is a trimer as the other cyanobacterial PSIs, but the amino acid sequence identity of each protein subunit is low, and, not unexpectedly, the divergence is most pronounced around the pigments specifically observed in A. marina PSI, for example Chl d, α-Car, and Pheo a-A0 (Supplementary Table 5). Again, the alterations must reflect optimization to drive efficient photochemistry utilizing low-energy light.
In conclusion, the structure and identification of electron carriers and key light-harvesting pigments provide a basis for understanding how low-energy far-red light is utilized by A. marina PSI. However, the full picture must wait for the structure of A. marina PSII, the system responsible for oxygen evolution through water-splitting, to be elucidated 3.