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Effects of mutations of D1-R323, D1-N322, D1-D319, D1-H304 on the functioning of photosystem II in Thermosynechococcus vulcanus

Abstract

Photosystem II (PSII) has a number of hydrogen-bonding networks connecting the manganese cluster with the lumenal bulk solution. The structure of PSII from Thermosynechococcus vulcanus (T. vulcanus) showed that D1-R323, D1-N322, D1-D319 and D1-H304 are involved in one of these hydrogen-bonding networks located in the interfaces between the D1, CP43 and PsbV subunits. In order to investigate the functions of these residues in PSII, we generated seven site-directed mutants D1-R323A, D1-R323E, D1-N322R, D1-D319L, D1-D319R, D1-D319Y and D1-H304D of T. vulcanus and examined the effects of these mutations on the growth and functions of the oxygen-evolving complex. The photoautotrophic growth rates of these mutants were similar to that of the wild type, whereas the oxygen-evolving activities of the mutant cells were decreased differently to 63–91% of that of the wild type at pH 6.5. The mutant cells showed a higher relative activity at higher pH region than the wild type cells, suggesting that higher pH facilitated proton egress in the mutants. In addition, oxygen evolution of thylakoid membranes isolated from these mutants showed an apparent decrease compared to that of the cells. This is due to the loss of PsbU during purification of the thylakoid membranes. Moreover, PsbV was also lost in the PSII core complexes purified from the mutants. Taken together, D1-R323, D1-N322, D1-D319 and D1-H304 are vital for the optimal function of oxygen evolution and functional binding of extrinsic proteins to PSII core, and may be involved in the proton egress pathway mediated by YZ.

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Abbreviations

CmR :

Chloramphenicol-resistant gene cassette

StrR :

Streptomycin-resistant gene cassette

DCBQ:

2,6-Dichloro-p-benzoquinone

DCMU:

3-(3,4-Dichlorophenyl)-1,1-dimethylurea

PCR:

Polymerase chain reaction

PCET:

Proton-coupled electron transfer

Q A :

PSII primary quinone electron acceptor

Q B :

PSII secondary quinone electron acceptor

References

  • Banerjee G, Ghosh I, Kim CJ, Debus RJ, Brudvig GW (2018) Substitution of the D1 Asn87 site in photosystem II of cyanobacteria mimics the chloride-binding characteristics of spinach photosystem II. J Biol Chem 293:2487–2497

    CAS  Article  PubMed  Google Scholar 

  • Bao H, Burnap DPL (2013) Proton transport facilitating water-oxidation: the role of second sphere ligands surrounding the catalytic metal cluster. Photosynth Res 116:215–229

    CAS  Article  PubMed  Google Scholar 

  • Bao H, Burnap RL (2015) Structural rearrangements preceding dioxygen formation by the water oxidation complex of photosystem II. Proc Natl Acad Sci USA 112:6139–6147

    Article  CAS  Google Scholar 

  • Chu HA, Nguyen AP, Debus RJ (1994) Site-directed photosystem II mutants with perturbed oxygen-evolving properties. 2. Increased binding or photooxidation of manganese in the absence of the extrinsic 33-kDa polypeptide in vivo. Biochemistry 33:6150–6157

    CAS  Article  PubMed  Google Scholar 

  • Chu HA, Nguyen AP, Debus RJ (1995) Amino acid residues that influence the binding of manganese or calcium to photosystem II. 1. The lumenal interhelical domains of the D1 polypeptide. Biochemistry 34:5839–5858

    CAS  Article  PubMed  Google Scholar 

  • Dau H, Zaharieva I, Haumann M (2012) Recent developments in research on water oxidation by photosystem II. Curr Opin Chem Biol 16:3–10

    CAS  Article  PubMed  Google Scholar 

  • Deák Z, Vass I (2008) Oscillating yield of fash-induced chlorophyll fuorescence decay in intact cells of Thermosynechococcus elongatus. In: Allen JF, Gantt E, Golbeck JH, Osmond B (eds) Photosynthesis, energy from the sun. Springer, Dordrecht, pp 573–576

    Chapter  Google Scholar 

  • Deák Z, Sass L, Kiss E, Vass I (2014) Characterization of wave phenomena in the relaxation of flash-induced chlorophyll fluorescence yield in cyanobacteria. Biochim Biophys Acta 1837:1522–1532

    Article  CAS  PubMed  Google Scholar 

  • Dilbeck PL, Bao H, Neveu CL, Burnap RL (2013) Perturbing the water cavity surrounding the manganese cluster by mutating the residue D1-valine 185 has a strong effect on the water oxidation mechanism of photosystem II. Biochemistry 52:6824–6833

    CAS  Article  PubMed  Google Scholar 

  • Diner BA, Rappaport F (2002) Structure, dynamics, and energetics of the primary photochemistry of photosystem II of oxygenic photosynthesis. Ann Rev Plant Biol 53:551–580

    CAS  Article  Google Scholar 

  • Forbush B, Kok B, McGloin MP (1971) Cooperation of charges in photosynthetic O2 evolution-II. Damping of flash yield oscillation, deactivation. Photochem Photobiol 14:307–321

    CAS  Article  Google Scholar 

  • Ghosh I, Banerjee G, Kim CJ, Reiss K, Batista VS, Debus RJ, Brudvig GW (2019a) D1–S169A substitution of photosystem II perturbs water oxidation. Biochemistry 58:1379–1387

    CAS  Article  PubMed  Google Scholar 

  • Ghosh I, Khan S, Banerjee G, Dziarski A, Vinyard DJ, Debus RJ, Brudvig GW (2019b) Insights into proton transfer pathways during water oxidation in photosystem II. J Phys Chem B 123:8195–8202

    CAS  Article  PubMed  Google Scholar 

  • Ghosh I, Banerjee G, Reiss K, Kim CJ, Batista DRJ, VS, Brudvig GW (2020) D1–S169A substitution of photosystem II reveals a novel S2-state structure. Biochim Biophys Acta 1861:148301

    CAS  Article  Google Scholar 

  • Goussias C, Boussac A, Rutherford AW (2002) Photosystem II and photosynthetic oxidation of water: an overview. Philos Trans R Soc Lond B 357:1369–1381

    CAS  Article  Google Scholar 

  • Haumann M, Liebisch P, Muller C, Barra M, Grabolle M, Dau H (2005) Photosynthetic O2 formation tracked by time resolved X-ray experiments. Science 310:1019–1021

    CAS  Article  PubMed  Google Scholar 

  • Hays AM, Vassiliev IR, Golbeck JH, Debus RJ (1998) Role of D1-His190 in proton-coupled electron transfer reactions in photosystem II: a chemical complementation study. Biochemistry 37:11352–11365

    CAS  Article  PubMed  Google Scholar 

  • Ho FM (2012) Structural and mechanistic investigations of photosystem II through computational methods. Biochim Biophys Acta 1817:106–120

    CAS  Article  PubMed  Google Scholar 

  • Hoganson CW, Babcock GT (1997) A metalloradical mechanism for the generation of oxygen from water in photosynthesis. Science 277:1953–1956

    CAS  Article  PubMed  Google Scholar 

  • Holzwarth AR, Muller MG, Reus M, Nowaczyk M, Sander J, Rogner M (2006) Kinetics and mechanism of electron transfer in intact photosystem II and in the isolated reaction center: pheophytin is the primary electron acceptor. Proc Natl Acad Sci USA 103:6895–6900

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Huang G, Xiao Y, Pi X, Zhao L, Zhu Q, Wang W, Kuang T, Han G, Sui SF, Shen J-R (2021) Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus. Proc Natl Acad Sci USA 118:e2018053118

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Ikeuchi M, Inoue Y (1988) A new photosystem II reaction center component (4.8 kDa protein) encoded by chloroplast genome. FEBS Lett 241:99–104

    CAS  Article  PubMed  Google Scholar 

  • Junge W, Haumann M, Ahlbrink R, Mulkidjanian A, Clausen J (2002) Electrostatics and proton transfer in photosynthetic water oxidation. Philos Trans R Soc Lond B 357:1407–1420

    CAS  Article  Google Scholar 

  • Katoh H, Itoh S, Shen JR, Ikeuchi M (2001) Functional analysis of psbV and a novel c-type cytochrome gene psbV2 of the thermophilic cyanobacterium Thermosynechococcus elongatus strain BP-1. Plant Cell Physiol 42:599–607

    CAS  Article  PubMed  Google Scholar 

  • Kawakami K, Umena Y, Kamiya N, Shen JR (2011) Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 Å resolution. J Photochem Photobiol B 104:9–18

    CAS  Article  PubMed  Google Scholar 

  • Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK (2018) Structures of the intermediates of Kok’s photosynthetic water oxidation clock. Nature 563:421–425

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Kim CJ, Debus RJ (2020) Roles of D1-Glu189 and D1-Glu329 in O2 formation by the water-splitting Mn4Ca Cluster in photosystem II. Biochemistry 59:3902–3917

    CAS  Article  PubMed  Google Scholar 

  • Kim CJ, Bao H, Burnap RL, Debus RJ (2018) Impact of D1–V185 on the water molecules that facilitate O2 formation by the catalytic Mn4CaO5 cluster in photosystem II. Biochemistry 57:4299–4311

    CAS  Article  PubMed  Google Scholar 

  • Kirilovsky D, Roncel M, Boussac A, Wilson A, Zurita JL, Ducruet JM, Bottin H, Sugiura M, Ortega JM, Rutherford AW (2004) Cytochrome c550 in the cyanobacterium Thermosynechococcus elongatus: study of redox mutants. J Biol Chem 279:52869–52880

    CAS  Article  PubMed  Google Scholar 

  • Kok B, Forbush B, McGloin M (1970) Cooperation of charges in photosynthetic O2 evolution-I. A linear four step mechanism. Photochem Photobiol 11:457–475

    CAS  Article  PubMed  Google Scholar 

  • Krishna PS, Morello G, Mamedov F (2019) Characterization of the transient fluorescence wave phenomenon that occurs during H2 production in Chlamydomonas reinhardtii. J Exp Bot 70:6321–6336

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Kuroda H, Kodama N, Sun XY, Ozawa S, Takahashi Y (2014) Requirement for Asn298 on D1 protein for oxygen evolution: analyses by exhaustive amino acid substitution in the green alga Chlamydomonas reinhardtii. Plant Cell Physiol 55:1266–1275

    CAS  Article  PubMed  Google Scholar 

  • Lavergne J, Junge W (1993) Proton release during the redox cycle of the water oxidase. Photosynth Res 38:279–296

    CAS  Article  PubMed  Google Scholar 

  • Lichtenberg CD, Avramov AP, Zhang M, Mamedov F, Burnap RL, Messinger J (2021) The D1–V185N mutation alters substrate water exchange by stabilizing alternative structures of the Mn4Ca-cluster in photosystem II. Biochim Biophys Acta 1862:148319

    Article  CAS  Google Scholar 

  • Lubitz W, Chrysina M, Cox N (2019) Water oxidation in photosystem II. Photosynth Res 142:105–125

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Makarova VV, Kosourov S, Krendeleva TE, Semin BK, Kukarskikh GP, Rubin AB, Sayre RT, Ghirardi ML, Seibert M (2007) Photoproduction of hydrogen by sulfur-deprived C. reinhardtii mutants with impaired photosystem II photochemical activity. Photosynth Res 94:79–89

    CAS  Article  PubMed  Google Scholar 

  • Mamedov F, Sayre RT, Styring S (1998) Involvement of histidine 190 on the D1 protein in electron/proton transfer reactions on the donor side of photosystem II. Biochemistry 37:14245–14256

    CAS  Article  PubMed  Google Scholar 

  • Muhlenhoff U, Chauvat F (1996) Gene transfer and manipulation in the thermophilic cyanobacterium Synechococcus elongatus. Mol Gen Genet 252:93–100

    CAS  Article  PubMed  Google Scholar 

  • Nagao R, Ueoka-Nakanishi H, Noguchi T (2017) D1-Asn-298 in photosystem II is involved in a hydrogen-bond network near the redox-active tyrosine YZ for proton exit during water oxidation. J Biol Chem 292:20046–20057

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Najafpour MM, Renger G, Holyńska M, Moghaddam A, Aro EM, Carpentier R, Nishihara H, Eaton-Rye JJ, Shen JR, Allakhverdiev SI (2016) Manganese compounds as water-oxidizing catalysts: from the natural water-oxidizing complex to nano-sized manganese oxide structures. Chem Rev 116:2886–2936

    CAS  Article  PubMed  Google Scholar 

  • Najafpour MM, Zaharieva I, Zand Z, Hosseini SM, Kouzmanova M, Hołynska M, Tranca I, Larkum AW, Shen J-R, Allakhverdiev SI (2020) Water-oxidizing complex in photosystem II: its structure and relation to manganese-oxide based catalysts. Coord Chem Rev 409:213183

    CAS  Article  Google Scholar 

  • Nixon PJ, Diner BA (1992) Aspartate 170 of the photosystem II reaction center polypeptide D1 is involved in the assembly of the oxygen-evolving manganese cluster. Biochemistry 31:942–948

    CAS  Article  PubMed  Google Scholar 

  • Nowaczyk MM, Hebeler R, Schlodder E, Meyer HE, Warscheid B, Rogner M (2006) Psb27, a cyanobacterial lipoprotein, is involved in the repair cycle of photosystem II. Plant Cell 18:3121–3131

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Pokhrel R, Debus RJ, Brudvig GW (2015) Probing the effect of mutations of Asparagine 181 in the D1 subunit of photosystem II. Biochemistry 14:1663–1672

    Article  CAS  Google Scholar 

  • Pokhrel R, Service RJ, Debus RJ (2013) Mutation of lysine 317 in the D2 subunit of photosystem II alters chloride binding and proton transport. Biochemistry 52:4758–4773

    Article  CAS  PubMed  Google Scholar 

  • Porra RJ, Thompson WA, Kriedemann PE (1989) Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochim Biophys Acta 975:384–394

    CAS  Article  Google Scholar 

  • Renger G (2011) Light induced oxidative water splitting in photosynthesis: energetics, kinetics and mechanism. J Photochem Photobiol 104:35–43

    CAS  Article  Google Scholar 

  • Roose JL, Pakrasi HB (2008) The Psb27 protein facilitates manganese cluster assembly in photosystem II. J Biol Chem 283:4044–4050

    CAS  Article  PubMed  Google Scholar 

  • Schlodder E, Witt HT (1999) Stoichiometry of proton release from the catalytic center in photosynthetic water oxidation. Reexamination by a glass electrode study at pH 5.5-7.2. J Biol Chem 274:30387–30392

    CAS  Article  PubMed  Google Scholar 

  • Service RJ, Hillier W, Debus RJ (2010) Evidence from FTIR difference spectroscopy of an extensive network of hydrogen bonds near the oxygen-evolving Mn4Ca cluster of photosystem II involving D1-Glu 65, D2-Glu312, and D1-Glu329. Biochemistry 49:6655–6669

    Article  CAS  PubMed  Google Scholar 

  • Service RJ, Hillier W, Debus RJ (2014) Network of hydrogen bonds near the oxygen-evolving Mn4CaO5 cluster of photosystem II probed with FTIR difference spectroscopy. Biochemistry 53:1001–1017

    Article  CAS  PubMed  Google Scholar 

  • Shen JR (2015) The structure of photosystem II and the mechanism of water oxidation in photosynthesis. Annu Rev Plant Biol 66:23–48

    CAS  Article  PubMed  Google Scholar 

  • Shen JR, Inoue Y (1993) Binding and functional properties of two new extrinsic components, cytochrome c-550 and a 12-kDa protein, in cyanobacterial photosystem II. Biochemistry 32:1825–1832

    CAS  Article  PubMed  Google Scholar 

  • Shen JR, Kamiya N (2000) Crystallization and the crystal properties of the oxygen-evolving photosystem II from Synechococcus vulcanus. Biochemistry 39:14739–14744

    CAS  Article  PubMed  Google Scholar 

  • Shen JR, Ikeuchi M, Inoue Y (1992) Stoichiometric association of extrinsic cytochrome c550 and 12 kDa protein with a highly purifed oxygen-evolving photosystem II core complex from Synechococcus vulcanus. FEBS Lett 301:145–149

    CAS  Article  PubMed  Google Scholar 

  • Shimada Y, Kitajima-Ihara T, Ryo N, Noguchi T (2020) Role of the O4 channel in photosynthetic water oxidation as revealed by fourier transform infrared difference and time-resolved infrared analysis of the D1–S169A mutant. J Phys Chem B 124:1470–1480

    CAS  Article  PubMed  Google Scholar 

  • Styring S, Rutherford AW (1988) Deactivation kinetics and temperature dependence of the S-states transition in the oxygen-evolving system of photosystem II measured by EPR spectroscopy. Biochim Biophys Acta 933:378–387

    CAS  Article  Google Scholar 

  • Styring S, Sjoholm J, Mamedov F (2012) Two tyrosines that changed the world: interfacing the oxidizing power of photochemistry to water splitting in photosystem II. Biochim Biophys Acta 1817:76–87

    CAS  Article  PubMed  Google Scholar 

  • Suga A, Akita F, Hirata K, Ueno G, Murakami H, Nakajima Y, Shimizu T, Yamashita K, Yamamoto M, Ago H, Shen JR (2015) Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. Nature 517:99–103

    CAS  Article  PubMed  Google Scholar 

  • Suga M, Akita F, Yamashita K, Nakajima Y, Ueno G, Li H, Yamane T, Hirata K, Umena Y, Yonekura S, Yu LJ, Murakami H, Nomura T, Kimura T, Kubo M, Baba S, Kumasaka T, Tono K, Yabashi M, Isobe H, Yamaguchi K, Yamamoto M, Ago H, Shen JR (2019) An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser. Science 366:334–338

    CAS  Article  PubMed  Google Scholar 

  • Sugiura M, Tibiletti T, Takachi I, Hara Y, Kanawaku S, Sellés J, Boussac A (2018) Probing the role of valine 185 of the D1 protein in the photosystem II oxygen evolution. Biochim Biophys Acta 1859:1259–1273

    CAS  Article  Google Scholar 

  • Sugiura M, Taniguchi T, Tango N, Nakamura M, Sellés J, Boussac A (2021) Probing the role of arginine 323 of the D1 protein in photosystem II function. Physiol Plantarum 171:183–199

    CAS  Article  Google Scholar 

  • Suzuki H, Yu J, Kobayashi T, Nakanishi H, Nixon PJ, Noguchi T (2013) Functional roles of D2-Lys317 and the interacting chloride ion in the water oxidation reaction of photosystem II as revealed by fourier transform infrared analysis. Biochemistry 52:4748–4757

    CAS  Article  PubMed  Google Scholar 

  • Umena Y, Kawakami K, Shen JR, Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature 473:55–60

    CAS  Article  PubMed  Google Scholar 

  • Vass I, Kirilovsky D, Etienne AL (1999) UV-B radiation-induced donor and acceptor side modifications of photosystem II in the cyanobacterium Synechocystis sp. PCC 6803. Biochemistry 38:12786–12794

    CAS  Article  PubMed  Google Scholar 

  • Vinyard DJ, Brudvig GW (2017) Progress toward a molecular mechanism of water oxidation in photosystem II. Annul Rev Phys Chem 68:101–116

    CAS  Article  Google Scholar 

  • Vinyard DJ, Ananyev GM, Dismukes GC (2013) Photosystem II: the reaction center of oxygenic photosynthesis. Annu Rev Biochem 82:577–606

    CAS  Article  PubMed  Google Scholar 

  • Vogt L, Vinyard DJ, Khan S, Brudvig GW (2015) Oxygen-evolving complex of photosystem II: an analysis of second-shell residues and hydrogen-bonding networks. Curr Opin Chem Biol 25:152–158

    CAS  Article  PubMed  Google Scholar 

  • Xiao Y, Zhu Q, Yang Y, Wang W, Kuang T, Shen JR, Han G (2020) Role of PsbV-Tyr137 in photosystem II studied by site-directed mutagenesis in the thermophilic cyanobacterium Thermosynechococcus vulcanus. Photosynth Res 146:41–54

    CAS  Article  PubMed  Google Scholar 

  • Xiao Y, Huang G, You X, Zhu Q, Wang W, Kuang T, Han G, Sui SF, Shen JR (2021) Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063. Nat Plants 7:1132–1142

    CAS  Article  PubMed  Google Scholar 

  • Zabret J, Bohn S, Schuller SK, Arnolds O, Möller M, Meier-Credo J, Liauw P, Chan A, Tajkhorshid E, Langer JD, Stoll R, Krieger-Liszkay A, Engel BD, Rudack T, Schuller JM, Nowaczyk MM (2021) Structural insights into photosystem II assembly. Nat Plants 7:524–538

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Zaharieva I, Dau H, Haumann M (2016) Sequential and coupled proton and electron transfer events in the S2 → S3 transition of photosynthetic water oxidation revealed by time-resolved X-ray absorption spectroscopy. Biochemistry 55:6996–7004

    CAS  Article  PubMed  Google Scholar 

  • Zhu Q, Yang Y, Xiao Y, Wang W, Kuang T, Shen JR, Han G (2020) Function of PsbO- Asp158 in photosystem II: effects of mutation of this residue on the binding of PsbO and function of PSII in Thermosynechococcus vulcanus. Photosynth Res 146:29–40

    CAS  Article  PubMed  Google Scholar 

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Funding

Funding was provided by National Natural Science Foundation of China (31470339), National Key R&D Program of China (2017YFA0503700, 2020YFA0907600), CAS Project for Young Scientists in Basic Research (YSBR-004), CAS Interdisciplinary Innovation Team (JCTD-2020-06), and A Strategic Priority Research Program of CAS (XDA26050402).

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Zhu, Q., Yang, Y., Xiao, Y. et al. Effects of mutations of D1-R323, D1-N322, D1-D319, D1-H304 on the functioning of photosystem II in Thermosynechococcus vulcanus. Photosynth Res (2022). https://doi.org/10.1007/s11120-022-00920-z

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Keywords

  • Photosystem II
  • Site-directed mutagenesis
  • Water oxidation
  • Hydrogen-bond networks
  • Functional binding