A practical method for sensitive determination of the fluorescent water-tracer uranine by reversed phase HPLC under alkaline conditions

A stable and highly sensitive HPLC method for uranine has been developed. Because of unstableness of silica-based octadecyl-C18 columns at high pH condition, a reversed phase HPLC analysis under alkaline conditions has not necessarily taken as a usual method. However, the application for uranine seems to be advantageous, since the fluorescence yield of uranine is markedly enhanced at high pH condition. The detection limit of the HPLC system was 0.9 pg. The analytical consideration was also paid for the solid phase extraction (SPE) prior to the HPLC analysis with careful consideration of the recently revised pK(a) values of uranine. The recovery rate of uranine by SPE was found to depend on the sample volume and a few ml of seawater was applied to SPE in order to maintain the recovery rate during SPE. A combination of HPLC and SPE methods achieved detection of uranine at concentrations as low as 0.2 ng l(-1) (0.5 pM), which was comparable to the background concentration of uranine in coastal water off Japan. For the practical use of the detected tracer-uranine concentration values after substantial duration after release, the photodegradation of uranine in surface water was also evaluated in terms of incident solar radiation dose as an exponential rate constant of -0.135 mol photon(-1)m(2).

Photosystem II complex in vivo is a monomer

Photosystem II (PS II) complexes are membrane protein complexes that are composed of >20 distinct subunit proteins. Similar to many other membrane protein complexes, two PS II complexes are believed to form a homo-dimer whose molecular mass is approximately 650 kDa. Contrary to this well known concept, we propose that the functional form of PS II in vivo is a monomer, based on the following observations. Deprivation of lipids caused the conversion of PS II from a monomeric form to a dimeric form. Only a monomeric PS II was detected in solubilized cyanobacterial and red algal thylakoids using blue-native polyacrylamide gel electrophoresis. Furthermore, energy transfer between PS II units, which was observed in the purified dimeric PS II, was not detected in vivo. Our proposal will lead to a re-evaluation of many crystallographic models of membrane protein complexes in terms of their oligomerization status.

Responses to desiccation stress in lichens are different from those in their photobionts

In order to clarify the role of symbiotic association in desiccation tolerance of photosynthetic partners in lichens, responses to air-drying and hypertonic treatments in a green-algal lichen (a chlorolichen, Ramalina yasudae Räsänen) and its green algal photobiont (freshly released and cultured Trebouxia sp.) were studied. Responses to dehydration in the isolated Trebouxia sp. were different from those in the lichen, R. yasudae, i.e. (i) the PSII reaction was totally inhibited in R. yasudae when photosynthesis was completely inhibited by desiccation, but it remained partially active in isolated Trebouxia sp; (ii) dehydration-induced quenching of PSII fluorescence was less in the isolated Trebouxia sp. compared with that in R. yasudae, suggesting that a substance(s) or a mechanism(s) to dissipate absorbed light energy to heat was lost by the isolation of the photobiont; and (iii) the air-dried isolated Trebouxia sp. showed a higher sensitivity to photoinhibition than R. yasudae. These results support the idea that association of the photobionts with the mycobionts increases tolerance to photoinhibition under drying conditions.

slr1923 of Synechocystis sp. PCC6803 is essential for conversion of 3,8-divinyl(proto)chlorophyll(ide) to 3-monovinyl(proto)chlorophyll(ide)

The deduced amino acid sequence of an slr1923 gene of Synechocystis sp. PCC6803 is homologous to archaean F(420)H(2) dehydrogenase, which acts as a soluble subcomplex of reduced nicotinamide adenine dinucleotide dehydrogenase complex I. In this study, the gene was inactivated and characteristics of the mutant were analyzed. The mutant grew slower than the wild type under 100 microE m(-2) s(-1) but did not grow under high light intensity (300 microE m(-2) s(-1)). The cellular content of chlorophyll was lower in the mutant, and the absorption spectrum showed a shift in the absorption peak of the Soret band to a longer wavelength by about 10 nm compared with the wild type. It was found, by high-performance liquid chromatography analysis, that the retention time of chlorophyll of the mutant is shorter than that of the wild type and that the peak wavelength of the Soret band was also shifted to a longer wavelength by 11 nm. Proton nuclear magnetic resonance analysis of the chlorophyll of the mutant revealed that the ethyl group of position 8 of ring B is replaced with a vinyl group. The spectrum indicates that the chlorophyll of the mutant is not a normal (3-vinyl)chlorophyll a but a 3,8-divinylchlorophyll a. These results strongly suggest that the Slr1923 protein is essential for the conversion from divinylchlorophyll(ide) to normal chlorophyll(ide). We thus designate this gene cvrA (a gene indispensable for cyanobacterial vinyl reductase).

Evidence for a stable association of Psb30 (Ycf12) with photosystem II core complex in the cyanobacterium Synechocystis sp. PCC 6803

Ycf12 (Psb30) is a small hydrophobic subunit of photosystem II (PS II) complexes found in the cyanobacterium, Thermosynechococcus elongatus. However, earlier intense proteomic analysis on the PS II complexes from the cyanobacterium, Synechocystis 6803, could not detect Psb30. In this work, we generated a mutant of Synechocystis 6803 in which a hexa-histidine tag was fused to the C-terminus of Synechocystis Psb30. The mutant accumulated fully functional PS II complexes. Purification of Psb30 by metal affinity chromatography from thylakoid extracts resulted in co-purification of an oxygen-evolving PS II complex with normal subunit composition. This result indicates that Psb30 is expressed and stably associated with the PS II complex in Synechocystis. The histidine-tagged Psb30 in the purified PS II complex was not detected by staining or anti-polyhistidine antibodies. We also generated a mutant in which ycf12 was disrupted. The mutant grew photosynthetically and showed no significant phenotype under moderate growth conditions. Purified PS II complexes from the disruptant showed an oxygen-evolving activity comparable to wild type under low irradiance. However, it showed a remarkably lower activity than wild type under high irradiance. Thus Psb30 is required for the efficient function of PS II complexes, particularly under high irradiance conditions.

Mechanisms to avoid photoinhibition in a desiccation-tolerant cyanobacterium, Nostoc commune

A desiccation-tolerant cyanobacterium, Nostoc commune, shows unique responses to dehydration. These responses are: (i) loss of PSII activity in parallel with the loss of photosynthesis; (ii) loss of PSI activity; and (iii) dissipation of light energy absorbed by pigment-protein complexes. In this study, the deactivation of PSII is shown to be important in avoiding photoinhibition when the Calvin-Benson cycle is repressed by dehydration. Furthermore, our evidence suggests that dissipation of light energy absorbed by PSII blocks photoinhibition under strong light in dehydrated states.

Responses to desiccation stress in bryophytes and an important role of dithiothreitol-insensitive non-photochemical quenching against photoinhibition in dehydrated states

The effects of air drying and hypertonic treatments in the dark on seven bryophytes, which had grown under different water environments, were studied. All the desiccation-tolerant species tested lost most of their PSII photochemical activity when photosynthetic electron transport was inhibited by air drying, while, in all the sensitive species, the PSII photochemical activity remained at a high level even when photosynthesis was totally inhibited. The PSI reaction center remained active under drying conditions in both sensitive and tolerant species, but the activity became non-detectable in the light only in tolerant species due to deactivation of the cyclic electron flow around PSI and of the back reaction in PSI. Light-induced non-photochemical quenching (NPQ) was found to be induced not only by the xanthophyll cycle but also by a DeltapH-induced, dithiothreitol-insensitive mechanism in both the desiccation-tolerant and -intolerant bryophytes. Both mechanisms are thought to have an important role in protecting desiccation-tolerant species from photoinhibition under drying conditions. Fluorescence emission spectra at 77K showed that dehydration-induced quenching of PSII fluorescence was observed only in tolerant species and was due to neither state 1-state 2 transition nor detachment of light-harvesting chlorophyll protein complexes from PSII core complexes. The presence of dehydration-induced quenching of PSI fluorescence was also suggested.

Isolation and characterization of outer and inner envelope membranes of cyanelles from a glaucocystophyte, Cyanophora paradoxa

Envelope membranes were isolated by sucrose density gradient floatation centrifugation from the homogenate of cyanelles prepared from Cyanophora paradoxa. Two yellow bands were separated after 40 h of centrifugation. The buoyant density of one of the two fractions (fraction Y2) coincided with that of inner envelope membranes of spinach or plasma membranes of cyanobacteria. The other yellow fraction (fraction Y1) migrated to top of sucrose-gradient even at 0% sucrose. Pigment analysis revealed that the heavy yellow fraction was rich in zeaxanthin while the light fraction was rich in beta-carotene, and the both fractions contained practically no chlorophylls. Another yellow fraction (fraction Y3) was isolated from the phycobiliprotein fraction, which was the position where the sample was placed for gradient centrifugation. Its buoyant density and absorption spectra were similar to outer membranes of cyanobacteria. We have assigned fractions Y2 and Y3 as inner and outer envelope membrane fractions of cyanelles, respectively. Protein compositions were rather different between the two envelope membranes indicating little cross-contamination among the fractions.

Preparation of membrane proteins for analysis by two-dimensional gel electrophoresis

In order to separate hydrophobic membrane proteins, we have developed a novel two-dimensional electrophoresis system. For the iso-electric focusing, agarose was used as a supporting matrix and n-dodecyl-beta-D-maltopyranoside was used as a surfactant. In combination with a previously developed Tris/MES electrophoresis system in the second dimension, distinct spots were reproducibly detected from hydrophobic membrane proteins whose grand average hydropathicity (GRAVY) exceed 0.3. In contrast to the immobilized pH gradient system, c-type heme was also visualized in this system.

Chloroplast-encoded Polypeptide PsbT Is Involved in the Repair of Primary Electron Acceptor QA of Photosystem II during Photoinhibition in Chlamydomonas reinhardtii

PsbT is a small chloroplast-encoded hydrophobic polypeptide associated with the D1/D2 heterodimer of the photosystem II (PSII) reaction center and is required for the efficient post-translational repair of photodamaged PSII. Here we addressed that role in detail in Chlamydomonas reinhardtii wild type and DeltapsbT cells by analyzing the activities of PSII, the assembly of PSII proteins, and the redox components of PSII during photoinhibition and repair. Strong illumination of cells for 15 min decreased the activities of electron transfer through PSII and Q(A) photoreduction by 50%, and it reduced the amount of atomic manganese by 20%, but it did not affect the steady-state level of PSII proteins, photoreduction of pheophytin (pheo(D1)), and the amount of bound plastoquinone (Q(A)), indicating that the decrease in PSII activity resulted mainly from inhibition of the electron transfer from pheo(D1) to Q(A). In wild type cells, we observed parallel recovery of electron transfer activity through PSII and Q(A) photoreduction, suggesting that the recovery of Q(A) activity is one of the rate-limiting steps of PSII repair. In DeltapsbT cells, the repairs of electron transfer activity through PSII and of Q(A) photoreduction activity were both impaired, but PSII protein turnover was unaffected. Moreover, about half the Q(A) was lost from the PSII core complex during purification. Since PsbT is intimately associated with the Q(A)-binding region on D2, we propose that this polypeptide enhances the efficient recovery of Q(A) photoreduction by stabilizing the structure of the Q(A)-binding region.

The PsbQ protein defines cyanobacterial Photosystem II complexes with highest activity and stability

Light-induced conversion of water to molecular oxygen by Photosystem II (PSII) is one of the most important enzymatic reactions in the biosphere. PSII is a multisubunit membrane protein complex with numerous associated cofactors, but it continually undergoes assembly and disassembly due to frequent light-mediated damage as a result of its normal function. Thus, at any instant, there is heterogeneity in the subunit compositions of PSII complexes within the cell. In particular, cyanobacterial PSII complexes have five associated extrinsic proteins, PsbO, PsbP, PsbQ, PsbU, and PsbV. However, little is known about the interactions of the more recently identified PsbQ protein with other components in cyanobacterial PSII. Here we show that PSII complexes can be isolated from the cyanobacterium Synechocystis sp. PCC 6803 on the basis of the presence of a polyhistidine-tagged PsbQ protein. Purification of PSII complexes using a tagged extrinsic protein has not been previously described, and this work conclusively demonstrates that PsbQ is present in combination with the PsbO, PsbU, and PsbV proteins in cyanobacterial PSII. Moreover, PsbQ-associated PSII complexes have higher activity and stability relative to those isolated using histidine-tagged CP47, an integral membrane protein. Therefore, we conclude that the presence of PsbQ defines the fully assembled and optimally active form of the enzyme.

Acclimation to the growth temperature and thermosensitivity of photosystem II in a mesophilic cyanobacterium, Synechocystis sp. PCC6803

Differences in the temperature dependence and thermosensitivities of PSII activities in Synechocystis sp. PCC6803 grown at 25 and 35 degrees C were studied. Hill reactions in cells, thylakoid membranes and purified PSII core complexes were measured at high temperatures or at their growth temperatures after high-temperature treatments. In the presence of 2,5-dichloro-p-benzoquinone as an electron acceptor, which can accept electrons directly from Q(A), the temperature dependence of the oxygen-evolving activity was almost the same in thylakoid membranes and in the purified PSII complexes from cells grown at 25 or 35 degrees C. When duroquinone, which accepts electrons only through Q(B) plastoquinone, was used as an electron acceptor, the temperature dependence was the same for purified PSII core complexes but was different between thylakoids isolated from the cells grown at 25 and 35 degrees C. No remarkable difference was observed in protein compositions between thylakoids and between purified PSII complexes from cells grown at 25 or 35 degrees C. However, the fluidity of thylakoids, measured by electron flow to P700, was affected by the growth temperature. These results suggest that one of the major factors which cause the changes in the thermosensitivity of PSII is the change in the fluidity of thylakoid membranes. As for the acclimation of PSII in thylakoids to high temperatures, one of the main causes is the decrease in the high-temperature-induced formation of non-Q(B) PSII due to the decreased fluidity in the cells grown at 35 degrees C.

Absence of the PsbQ protein results in destabilization of the PsbV protein and decreased oxygen evolution activity in cyanobacterial photosystem II

We have previously reported that cyanobacterial photosystem II (PS II) contains a protein homologous to PsbQ, the extrinsic 17-kDa protein found in higher plant and green algal PS II (Kashino, Y., Lauber, W. M., Carroll, J. A., Wang, Q., Whitmarsh, J., Satoh, K., and Pakrasi, H. B. (2002) Biochemistry 41, 8004-8012) and that it has regulatory role(s) on the water oxidation machinery (Thornton, L. E., Ohkawa, H., Roose, J. L., Kashino, Y., Keren, N., and Pakrasi, H. B. (2004) Plant Cell 16, 2164-2175). In this work, the localization and the function of PsbQ were assessed using the cyanobacterium Synechocystis sp. PCC 6803. From the predicted sequence, cyanobacterial PsbQ is expected to be a lipoprotein on the luminal side of the thylakoid membrane. Indeed, experiments in this work show that upon Triton X-114 fractionation of thylakoid membranes, PsbQ partitioned in the hydrophobic phase, and trypsin digestion revealed that PsbQ was highly exposed to the luminal space of thylakoid membranes. Detailed functional assays were conducted on the psbQ deletion mutant (DeltapsbQ) to analyze its water oxidation machinery. PS II complexes purified from DeltapsbQ mutant cells had impaired oxygen evolution activity and were remarkably sensitive to NH(2)OH, which indicates destabilization of the water oxidation machinery. Additionally, the cytochrome c(550) (PsbV) protein partially dissociated from purified DeltapsbQ PS II complexes, suggesting that PsbQ contributes to the stability of PsbV in cyanobacterial PS II. Therefore, we conclude that the major function of PsbQ is to stabilize the PsbV protein, thereby contributing to the protection of the catalytic Mn(4)-Ca(1)-Cl(x) cluster of the water oxidation machinery.

PsbU Provides a Stable Architecture for the Oxygen-Evolving System in Cyanobacterial Photosystem II

PsbU is a lumenal peripheral protein in the photosystem II (PS II) complex of cyanobacteria and red algae. It is thought that PsbU is replaced functionally by PsbP or PsbQ in plant chloroplasts. After the discovery of PsbP and PsbQ homologues in cyanobacterial PS II [Thornton et al. (2004) Plant Cell 16, 2164-2175], we investigated the function of PsbU using a psbU deletion mutant (DeltaPsbU) of Synechocystis 6803. In contrast to the wild type, DeltaPsbU did not grow when both Ca2+ and Cl- were eliminated from the growth medium. When only Ca2+ was eliminated, DeltaPsbU grew well, whereas when Cl- was eliminated, the growth rate was highly suppressed. Although DeltaPsbU grew normally in the presence of both ions under moderate light, PS II-related disorders were observed as follows. (1) The mutant cells were highly susceptible to photoinhibition. (2) Both the efficiency of light utilization under low irradiance and the chlorophyll-specific maximum rate of oxygen evolution in DeltaPsbU cells were 60% lower than those of the wild type. (3) The decay of the S2 state in DeltaPsbU cells was decelerated. (4) In isolated PS II complexes from DeltaPsbU cells, the amounts of the other three lumenal extrinsic proteins and the electron donation rate were drastically decreased, indicating that the water oxidation system became significantly labile without PsbU. Furthermore, oxygen-evolving activity in DeltaPsbU thylakoid membranes was highly suppressed in the absence of Cl-, and 60% of the activity was restored by NO3- but not by SO4(2-), indicating that PsbU had functions other than stabilizing Cl-. On the basis of these results, we conclude that PsbU is crucial for the stable architecture of the water-splitting system to optimize the efficiency of the oxygen evolution process.

Inactivation of ycf33 Results in an Altered Cyclic Electron Transport Pathway Around Photosystem I in Synechocystis sp. PCC6803

ycf33 encodes a small protein with a molecular mass of 7.5 kDa and is found from cyanobacteria to higher plants. A ycf33 deletion mutant was constructed in Synechocystis sp. PCC6803 and characterized. The mutant showed a higher phycobilisome/chlorophyll ratio than the wild type and a higher photosystem II/photosystem I fluorescence ratio measured at 77 K. Under photoautotrophic conditions, the growth rates were not much different from those of the wild type. Cyclic electron transport activities around photosystem I were not much different between the wild type and the mutant. However, the effects of diphenyleneiodonium, an inhibitor of flavoprotein, on cyclic electron transport in the mutant were different from those in the wild type; it was severely inhibited in the wild type but not much in the mutant. Together with the effects of nitrite, which accepts electrons from ferredoxin via nitrite reductase and those of HgCl2, it was suggested that the pathway of cyclic electron transport is altered in the mutant.

Separation methods in the analysis of protein membrane complexes

The separation of membrane protein complexes can be divided into two categories. One category, which is operated on a relatively large scale, aims to purify the membrane protein complex from membrane fractions while retaining its native form, mainly to characterize its nature. The other category aims to analyze the constituents of the membrane protein complex, usually on a small scale. Both of these face the difficulty of isolating the membrane protein complex without interference originating from the hydrophobic nature of membrane proteins or from the close association with membrane lipids. To overcome this difficulty, many methods have been employed. Crystallized membrane protein complexes are the most successful example of the former category. In these purification methods, special efforts are made in the steps prior to the column chromatography to enrich the target membrane protein complexes. Although there are specific aspects for each complex, the most popular method for isolating these membrane protein complexes is anion-exchange column chromatography, especially using weak anion-exchange columns. Another remarkable trend is metal affinity column chromatography, which purifies the membrane protein complex as an intact complex in one step. Such protein complexes contain subunit proteins which are genetically engineered so as to include multiple-histidine tags at carboxyl- or amino-termini. The key to these successes for multi-subunit complex isolation is the idea of keeping the expression at its physiological level, rather than overexpression. On the other hand, affinity purification using the Fv fragment, in which a Strep tag is genetically introduced, is ideal because this method does not introduce any change to the target protein. These purification methods supported by affinity interaction can be applied to minor membrane protein complexes in the membrane system. Isoelectric focusing (IEF) and blue native (BN) electrophoresis have also been employed to prepare membrane protein complexes. Generally, a combination of two or more chromatographic and/or electrophoretic methods is conducted to separate membrane protein complexes. IEF or BN electrophoresis followed by 2nd dimension electrophoresis serve as useful tools for analytical demand. However, some problems still exist in the 2D electrophoresis using IEF. To resolve such problems, many attempts have been made, e.g. introduction of new chaotropes, surfactants, reductants or supporting matrices. This review will focus in particular on two topics: the preparative methods that achieved purification of membrane protein complexes in the native (intact) form, and the analytical methods oriented to resolve the membrane proteins. The characteristics of these purification and analytical methods will be discussed along with plausible future developments taking into account the nature of membrane protein complexes.

Homologs of plant PsbP and PsbQ proteins are necessary for regulation of photosystem ii activity in the cyanobacterium Synechocystis 6803

The mechanism of oxygen evolution by photosystem II (PSII) has remained highly conserved during the course of evolution from ancestral cyanobacteria to green plants. A cluster of manganese, calcium, and chloride ions, whose binding environment is optimized by PSII extrinsic proteins, catalyzes this water-splitting reaction. The accepted view is that in plants and green algae, the three extrinsic proteins are PsbO, PsbP, and PsbQ, whereas in cyanobacteria, they are PsbO, PsbV, and PsbU. Our previous proteomic analysis established the presence of a PsbQ homolog in the cyanobacterium Synechocystis 6803. The current study additionally demonstrates the presence of a PsbP homolog in cyanobacterial PSII. Both psbP and psbQ inactivation mutants exhibited reduced photoautotrophic growth as well as decreased water oxidation activity under CaCl(2)-depleted conditions. Moreover, purified PSII complexes from each mutant had significantly reduced activity. In cyanobacteria, one PsbQ is present per PSII complex, whereas PsbP is significantly substoichiometric. These findings indicate that both PsbP and PsbQ proteins are regulators that are necessary for the biogenesis of optimally active PSII in Synechocystis 6803. The new picture emerging from these data is that five extrinsic PSII proteins, PsbO, PsbP, PsbQ, PsbU, and PsbV, are present in cyanobacteria, two of which, PsbU and PsbV, have been lost during the evolution of green plants.

Deactivation of Photosynthetic Activities is Triggered by Loss of a Small Amount of Water in a Desiccation-Tolerant Cyanobacterium, Nostoc commune

Changes in photosynthetic activities under hypertonic conditions were studied in a terrestrial, highly desiccation-tolerant cyanobacterium, Nostoc commune, and in some desiccation-sensitive cyanobacteria. The amounts of water sustained in the colony matrix outside the N. commune cells and the cellular solute concentration were estimated by measuring the water potential, and the solute concentration was supposed to correspond to around 0.22 M sorbitol. Incubation of the colonies in 0.8 M sorbitol solution inhibited the energy transfer from the phycobilisome (PBS) anchor to PSII core complexes. At higher sorbitol concentrations, light energy absorbed by PSI, PSII, and PBS was dissipated to heat. PSI and cyclic electron flow around PSI was also deactivated by hypertonic treatment. Fv/Fm and (Fm'-F)/Fm' values started to decrease at 0.6 and 0.3 M sorbitol and reached zero at 1.0 and 0.8 M, respectively. Decreases in these two fluorescence parameters corresponded to the decreases in PSII fluorescence (F695) and photosynthetic CO2 fixation, respectively. The intensity of delayed light emission started to decrease at 1.0 M sorbitol and became negligible at 4.0 M. Comparing these changes in N. commune with those in desiccation-sensitive species, we found that N. commune cells actively deactivates photosynthetic systems on sensing water loss.

Low-molecular-mass polypeptide components of a photosystem II preparation from the thermophilic cyanobacterium Thermosynechococcus vulcanus

Using a recently introduced electrophoresis system [Kashino et al. (2001) Electrophoresis 22: 1004], components of low-molecular-mass polypeptides were analyzed in detail in photosystem II (PSII) complexes isolated from a thermophilic cyanobacterium, Thermosynechococcus vulcanus (formerly, Synechococcus vulcanus). PsbE, the large subunit polypeptide of cytochrome b(559), showed an apparent molecular mass much lower than the expected one. The unusually large mobility could be attributed to the large intrinsic net electronic charge. All other Coomassie-stained polypeptides were identified by N-terminal sequencing. In addition to the well-known cyanobacterial PSII polypeptides, such as PsbE, F, H, I, L, M, U, V and X, the presence of PsbY, PsbZ and Psb27 was also confirmed in the isolated PSII complexes. Furthermore, the whole amino acid sequence was determined for the polypeptide which was known as PsbN. The whole amino acid sequence revealed that this polypeptide was identical to PsbTc which has been found in higher plants and green algae. These results strongly suggest that PsbN is not a member of the PSII complex. It is also shown that cyanobacteria have cytochrome b(559) in the high potential form as in higher plants.

Proteomic analysis of a highly active photosystem II preparation from the cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel polypeptides

A highly active oxygen-evolving photosystem II (PSII) complex was purified from the HT-3 strain of the widely used cyanobacterium Synechocystis sp. PCC 6803, in which the CP47 polypeptide has been genetically engineered to contain a polyhistidine tag at its carboxyl terminus [Bricker, T. M., Morvant, J., Masri, N., Sutton, H. M., and Frankel, L. K. (1998) Biochim. Biophys. Acta 1409, 50-57]. These purified PSII centers had four manganese atoms, one calcium atom, and two cytochrome b(559) hemes each. Optical absorption and fluorescence emission spectroscopy as well as western immunoblot analysis demonstrated that the purified PSII preparation was devoid of any contamination with photosystem I and phycobiliproteins. A comprehensive proteomic analysis using a system designed to enhance resolution of low-molecular-weight polypeptides, followed by MALDI mass spectrometry and N-terminal amino acid sequencing, identified 31 distinct polypeptides in this PSII preparation. We propose a new nomenclature for the polypeptide components of PSII identified after PsbZ, which proceeds sequentially from Psb27. During this study, the polypeptides PsbJ, PsbM, PsbX, PsbY, PsbZ, Psb27, and Psb28 proteins were detected for the first time in a purified PSII complex from Synechocystis 6803. Five novel polypeptides were also identified in this preparation. They included the Sll1638 protein, which shares significant sequence similarity to PsbQ, a peripheral protein of PSII that was previously thought to be present only in chloroplasts. This work describes newly identified proteins in a highly purified cyanobacterial PSII preparation that is being widely used to investigate the structure, function, and biogenesis of this photosystem.