Probing the topology of proteins in the chromatophore membrane of Rhodospirillum rubrum G-9 with proteinase K

All the major membrane proteins of isolated chromatophore vesicles are eventually degraded upon incubation with the unspecific proteinase K. These proteins must therefore be exposed at least partially or temporarily on the cytosolic surface of the membrane which is exclusively accessible to the proteinase in intact chromatophore vesicles. That the vesicles are intact during the incubation with proteinase is demonstrated by the finding that cytochrome c₂, which is located in the interior of the vesicles, is protected from proteolytic attack. The degree of degradation of the various chromatophore proteins and the time taken for degradation differ characteristically. From the changes in intensity of the gel bands during the course of digestion it appears that reaction center subunit H is digested first, much faster than are subunits M and L. The near-infrared absorption spectrum of the chromatophores changes only after proteolytic degradation of these two pigment-carrying subunits. Fading of the band of the light-harvesting polypeptide is evident only after prolonged incubation. It seems that this is the most stable component of the chromatophore membrane. The light-harvesting polypeptide appears to be somewhat shortened eventually, leaving the protein conformation necessary for holding the pigments unchanged, as shown by the absorption spectrum. The possible topology of these major membrane components is discussed in the light of these findings.     

Topology and neighbor analysis of the photosynthetic reaction center from Rhodopseudomonas sphaeroides

The subunit arrangement of the reaction center complex (RC) of Rhodopseudomonas sphaeroides was studied by chemical modification with four different cross-linking reagents using purified RC in lauryldimethylamine oxide, RC incorporated into liposomes, and intact chromatophore membranes, from which RCs are isolated. The RC of R. sphaeroides is composed of three polypeptide subunits, H, M, and L, apparent molecular mass as determined in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, of 28,000, 24,000, and 21,000, respectively. The intra-complex products produced, were found to contain the polypeptides H-M-L, H-M, H-L, and M-L linked together. In addition, the cross-linking of cytochrome c to solubilized and membrane-bound RCs was observed with all four reagents. The products were found to be only a cytochrome c linked to either the M or L polypeptide. These results indicate that a portion of the L and M subunits of the RC must be exposed in situ on the periplasmic surface of the membrane near a binding site for cytochrome c on the RC, and all three subunits must be in close proximity to one another.     

Primary structure of the reaction center from Rhodopseudomonas sphaeroides

The reaction center is a pigment-protein complex that mediates the initial photochemical steps of photosynthesis. The amino-terminal sequences of the L, M, and H subunits and the nucleotide and derived amino acid sequences of the L and M structural genes from Rhodopseudomonas sphaeroides have previously been determined. We report here the sequence of the H subunit, completing the primary structure determination of the reaction center from R. sphaeroides. The nucleotide sequence of the gene encoding the H subunit was determined by the dideoxy method after subcloning fragments into single-stranded M13 phage vectors. This information was used to derive the amino acid sequence of the corresponding polypeptide. The termini of the primary structure of the H subunit were established by means of the amino and carboxy terminal sequences of the polypeptide. The data showed that the H subunit is composed of 260 residues, corresponding to a molecular weight of 28,003. A molecular weight of 100,858 for the reaction center was calculated from the primary structures of the subunits and the cofactors. Examination of the genes encoding the reaction center shows that the codon usage is strongly biased towards codons ending in G and C. Hydropathy analysis of the H subunit sequence reveals one stretch of hydrophobic residues near the amino terminus; the L and M subunits contain five such stretches. From a comparison of the sequences of homologous proteins found in bacterial reaction centers and photosystem II of plants, an evolutionary tree was constructed. The analysis of evolutionary relationships showed that the L and M subunits of reaction centers and the D1 and D2 proteins of photosystem II are descended from a common ancestor, and that the rate of change in these proteins was much higher in the first billion years after the divergence of the reaction center and photosystem II than in the subsequent billion years represented by the divergence of the species containing these proteins.     

Photodynamic action of bilirubin on human erythrocyte membranes. Modification of polypeptide constituents.

The photodynamic action of bilirubin on isolated human erythrocyte membranes (ghosts) has been studied. When incorporated into ghosts (pH 8.0,10 degrees) the bile pigment photosensitizes in blue light the peroxidation of unsaturated lipids, as evidenced by a positive color reaction with 2-thiobarbituric acid. Accompanying lipid peroxidation was the disappearance of most of the major membrane proteins (Coomassie Blue staining in sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and appearance of polypeptide photoproducts of greater size (mol wt greater than 250,000). The association of membrane proteins (presumably by cross-linking) was insignificant when bilirubin-ghost suspensions were kept in the dark, or when ghosts were irradiated in the absence of bilirubin. Electrophoretic bands 1 and 2 (Fairbanks, G., Steck, T.L., and Wallach, D. F.H (1971), Biochemistry 10, 2606) diminished rapidly during the photoreaction, whereas band 3 and the three sialoglycoproteins disappeared at a much slower rate. Dispersal of membrane consituents by treatment with sodium dodecyl sulfate prior to irradiation resulted in relatively little peroxidation and no noticeable formation of high molecular weight polypeptide complexes. The possibility that malonaldehyde, a product of lipid peroxidation, is involved in cross-linking during irradiation was studied by incubating ghosts with exogenous malonaldehyde. Although the reagent did cross-link membrane proteins (electrophoretic bands 1, 2, 2.1 2.2, and 4.1 diminished most rapidly and high molecular weight bands appeared), the reaction could only be demonstrated with malonaldehyde concentrations several orders of magnitude greater than those detected in irradiation experiments. If malonaldehyde cross-linking occurs, it does not appeare to be the predominant mechanism of polypeptide association during irradiation of bilirubin-containing ghosts.     

Labeling of chromatophore membranes and reaction centers from the photosynthetic bacterium Rhodospirillum rubrum with the hydrophobic marker 5-[125I]iodonaphthyl-1-azide

Chromatophores of the photosynthetic bacterium Rhodospirillum rubrum and isolated reaction centers were labeled with the lipophilic membrane marker 5-[¹²⁵I]iodonaphthyl-1-azide. The two smaller reaction center proteins L and M bind more label than the larger subunit H, a fact supporting the proposed localisation of the 3 subunits obtained with hydrophilic labels. Besides these integral proteins the lipids, among them mainly the pigments and the quinones, are highly labeled suggesting a hydrophobic environment around these molecules and a preferred reactivity to iodonaphthylazide. Such a hydrophobic environment may be of great importance for the function of the photosynthetic reaction centers especially for the charge separation and the primary reactions in electron transport.     

Amino-terminal sequences of the L, M, and H subunits of reaction centers from the photosynthetic bacterium Rhodopseudomonas sphaeroides R-26

We have determined the sequence of the 25-28 amino-terminal residues of the three subunits, L, M, and H, of the membrane-bound reaction center protein of the photosynthetic bacterium Rhodopseudomonas sphaeroides R-26. The sequences are as follows: L, H2N-Ala-Leu-Leu-Ser-Phe-Glu-Arg-Lys-Tyr-Arg- Val-Pro-Gly-Gly-Thr-Leu-Val-Gly-Gly-Asn-Leu-Phe-Asp-Phe-(His)-Val-; M, H2N-Ala-Glu-Tyr-Gln-Asn-Ile-Phe-Ser-Gln-Val-Gln-Val-Arg-Gly-Pro-Ala-Asp-Leu-Gly-Met-Thr-Glu-Asp-Val-Asn-Leu-Ala-Asn-; H, H2N-Met-Val-Gly-Val-Thr-Ala-Phe-Gly-Asn-Phe-Asp-Leu-Ala-Ser-Leu-Ala-Ile-Tyr-Ser-Phe-Trp-Ile-Phe-Leu-Ala-X-Leu-Ile-. The H sequence, especially after the aspartyl residue at position 11, is rich in hydrophobic residues, consistent with the possibility that this section of the polypeptide chain is located within the membrane. The L sequence is hydrophilic near the amino terminus and then becomes moderately hydrophobic. The M sequence is of average polarity.     

2-[8-14C]naphthyl 2-diazo-3,3,3-trifluoropropionate, a new carbene generating reagent for probing hydrophobic membrane domains

A new precursor of a lipophilic photolabel, 2-[8-14C]naphthyl 2-diazo-3,3,3-trifluoropropionate (NADIT) has been synthesized. The suitability of the reagent for labeling the hydrophobic core of membranes is demonstrated by studying its reactivity in chromatophores of Rhodospirillum rubrum G-9+. The label binds preferentially to the phospholipids and intrinsic membrane proteins. In isolated reaction centers treated with NADIT the hydrophobic subunits M and L are more labeled than the H subunit. The high reactivity, dark stability and ease of synthesis favors this very lipophilic reagent to identify the intrinsic hydrophobic sections of membrane proteins.     

Topography of reaction center subunits in the membrane of the photosynthetic bacterium, rhodopseudomonas sphaeroides

The localization of the reaction center polypeptides (L, M, and H) in the membranes of both the wild-type, strain 2.4.1, and the carotenoidless mutant, R-26, of Rhodopseudomonas sphaeroides was determined by using affinity-purified antibodies specific for these proteins. Binding of the antibodies to reaction center subunits in spheroplasts was visualized in the electron microscope by immunoferritin labeling. The H and M subunits were labeled at both the cytoplasmic and the periplasmic surfaces of the membrane, whereas the L subunit was labeled only at the periplasmic surface of the membrane. Thus, the reaction center is asymmetrically oriented in the membrane with at least two subunits (H and M) spanning the membrane.     

Nucleotide and deduced polypeptide sequences of the photosynthetic reaction-center, B870 antenna, and flanking polypeptides from R. capsulata

The complete nucleotide sequence (8867 bp) and the deduced polypeptide sequence are given for 11 proteins from the photosynthetic gene cluster of R. capsulata (46 kb), including the photosynthetic reaction-center L, M, and H subunits and the B870 alpha and B870 beta polypeptides (light-harvesting I). These polypeptides bind bacteriochlorophyll, bacteriopheophytin, carotenoids, and quinones that are involved in the primary light reactions of photosynthesis. Hydropathy plots indicate that the L and M subunits are transmembrane proteins that may cross the membrane five times, while the H subunit has only one hydrophobic section near the amino terminus, which may be transmembrane. The L and M subunits are homologous over their entire length and have a high degree of homology with the QB protein from photosystem II of higher plants. An additional six genes were identified that may have some unknown role in bioenergetics since only mutations that affect the differentiation of the photosynthetic apparatus are known to map to this gene cluster.     

Characterisation of reaction centers and their phospholipids from Rhodospirillum rubrum.

1. Reaction centers from Rhodospirillum rubrum have been extracted with the zwitterionic detergent lauryl dimethyl amine oxide. Subsequent purification has been achieved by gel filtration and ion-exchange chromatography. The pure reaction centers are composed of three protein subunits (L, M, H), bacteriocholorophyll and bacteriopheophytin in the ratio 2 : 1 and phospholipids. 2. The phospholipid composition has been found to be similar to that of whole chromatophore membrane, except that diphosphatidyl glycerol is present in higher amount in the isolated complex. When the detergent treatment of the chromatophore membrane is done in the presence of NaCl, a lower phospholipid content in isolated reaction centers has been found together with a lower stability in the association among the protein subunits. In this complex, the largest subunit H is easily split off and a LM complex is obtained. It is concluded that the phospholipids play an important role in the stability of reaction center complexes.     

Localisation of the subunits of the photosynthetic reaction centers in the chromatophore membrane of Rhodospirillum rubrum.

Reaction centers were isolated with the detergent lauryl dimethyl amine oxide from chromatophore membranes of Rhodospirillum rubrum. The subunit composition of these reaction centers is similar to the one obtained from Rhodopseudomonas spheroides: three subunits with the molecular weights of 21 000, 24 000 and 29 000. Reaction centers prepared from chromatophores labeled with 131I were heavely labeled in their large subunit (H). The smaller subunits (L and M) contained only little label. Sonication during labeling yielded a slightly higher incorporation of 131I in subunit H compared to the smaller ones. It is concluded that the H protein is largely exposed at the cytoplasmic side of the membrane but might also be accessible for iodination on the inside of the membrane while the L and M proteins are almost completely embedded in the membrane. Iodination of spheroplasts results in only a slight binding of 131I to chromatophores and reaction centers.     

Structural properties of the D1 and surrounding photosystem II polypeptides as revealed by their interaction with cross-linking reagents

Treatment of Chlamydomonas reinhardtii thylakoids with cross-linking reagents including glutaraldehyde causes polymerization of all thylakoid polypeptides, but not of the reaction center II polypeptide D1 unless the thylakoids are presolubilized by octyl beta-D-glucoside (Adir, N., and Ohad, I. (1986) Biochim. Biophys. Acta 850, 264-274). The results presented here show that this is a general property of D1 as it can be demonstrated in thylakoids of cyanophytes, Dasicladaceae, green algae, and C3 and C4 plants. Solubilization of the membranes by ionic detergents, deoxycholate, lauryl sucrose, or dodecyl beta-D-maltoside is not effective in inducing cross-linking of the D1 polypeptides by glutaraldehyde. The most effective alkyl glucosides were those with 7-9 carbon alkyl chains. The same behavior toward glutaraldehyde was exhibited by the unprocessed D1 precursor and by the palmitoylated D1 protein. Based on the refractility of the D1 protein to cross-linking reagents, a procedure was developed for its isolation from cross-linked thylakoids by lithium dodecyl sulfate-polyacrylamide gel electrophoresis. Isolated D1 retained its behavior toward cross-linking by glutaraldehyde and generated tryptic fragments similar to those obtained following trypsin treatment of intact thylakoids. Denaturation of isolated D1 protein by acetone facilitates cross-linking by glutaraldehyde and extensive degradation by trypsin. The photosystem II polypeptides are differentially cross-linked with increasing concentrations of glutaraldehyde, the most susceptible being the 28- and 23-kDa components of the light-harvesting chlorophyll a-b protein complex and the core complex 44- and 51-kDa polypeptides, and the least affected being the cytochrome b559, the D2 protein, and a 24-kDa component of the light-harvesting chlorophyll a-b protein complex. These results reflect the relative position and interaction of the photosystem II polypeptides within the complex and suggest that strong and specific hydrophobic interactions may be responsible for the tight and stable conformation of D1. This may be based mostly on the conserved amino acid sequences of D1 and possibly plays a role in the process of D1 integration and removal from the reaction center during its light-dependent turnover.     

Transverse topography of the photochemical reaction center polypeptides in the Rhodopseudomonas capsulata membrane.

The exposure of the three polypeptide subunits H, M, and L of the photochemical reaction center (RC) on both surfaces of the membrane of Rhodopseudomonas capsulata was studied by partial proteolysis with proteinase K and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of of degradation products. The possible association of RC subunits with bacteriochlorophyll a and bacteriopheophytin was investigated by spectroscopical measurements. Chromatophores (inside-out oriented) and spheroplasts (right-side-out oriented), as well as purified, detergent-solubilized RCs and RCs reconstituted into phosphatidyl choline liposomes, were used. Subunit H of the RC was degraded to fragments with apparent MrS of 15,000 and 12,500, which were possibly derived from cleavage of a loop exposed on the cytoplasmic surface. Polypeptide M was digested at a comparable rate. The apparent Mr of M decreased by roughly 4,000 upon proteolytic cleavage. Subunit L was relatively insensitive to protease attack, except that a small peptide was clipped off. The primary donor P870 was also found to be only slightly affected proteinase K. All three RC subunits appear to be exposed on the chromatophore surface.     

Interaction of cytochrome c with reaction centers of Rhodopseudomonas sphaeroides R-26: localization of the binding site by chemical cross-linking and immunochemical studies

The location of the cytochrome binding site on the reaction center of Rhodopseudomonas sphaeroides was studied by two different approaches. In one, cross-linking agents, principally dithiobis(propionimidate) and dimethyl suberimidate, were used to link cytochrome c and cytochrome c2 to reaction centers; in the other, the inhibition of electron transfer by antibodies against the subunits was investigated. Cytochrome c (horse) cross-linked to the L and M subunits, whereas cytochrome c2 (R. sphaeroides) cross-linked only to the L subunit. The cross-linked reaction center-cytochrome complexes were isolated by affinity chromatography. The rate of electron transfer in the cross-linked cytochrome c2 complex was the same as that in the un-cross-linked complex. However, when cytochrome c was used, the rate in the cross-linked complex was about 15 times slower than that in the un-cross-linked complex. Fab fragments of antibodies specific against the L and M subunits blocked electron transfer from both cytochrome c (horse) and cytochrome c2 (R. sphaeroides). Antibodies specific for the H subunit did not block either reaction. We conclude that the cytochrome binding site on the reaction center is close (approximately 10 A) to both the L and M subunits, possibly in a cleft between them.     

Molecular aspects of photosystem I

Photosystem I (PSI) in higher plants consists of 17 polypeptide subunits. Cofactors are chlorophyll a and b , β-carotene, phylloquinone and iron-sulfur clusters. Eight subunits are specific for higher plants while the remaining ones are also present in cyanobacteria. Two 80-kDa subunits (PSI-A and -B) constitute the major part of PSI and bind most of the pigments and electron donors and acceptors. The 9-kDa PSI-C carries the remaining electron acceptors which are [4Fe-4S] iron sulfur clusters. PSI-D, -E and -H have importance for integrity and function at the stromal face of PSI while PSI-F has importance for function at the lumenal face. PSI-N is localized at the lumenal side, but its function is unknown. Four subunits are light-harvesting chlorophyll a/b -binding proteins. The remaining subunits are integral membrane proteins with poorly understood function. Subunit interactions have been studied in reconstitution experiments and by cross-linking studies. Based on these data, it is concluded that iron-sulfur cluster F_B is proximal to F_X and that F_A is the terminal acceptor in PSI. Similarities between PSI and the reaction center from green sulfur bacteria are discussed.     

Deficiencies of Chromatophore Proteins in Some Mutants of Rhodopseudomonas spheroides with Altered Carotenoids

Chromatophore proteins of a wild type and three mutant strains of Rhodopseudomonas spheroides were examined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The mutants consisted of a green and a blue-green one, whose phenotypes were essentially the same as those of known mutants, and a brown one, which may be a double mutant and represents a new phenotype. Wild-type chromatophores contained at least six major and seven minor protein bands, with molecular weights ranging from 10,000 to 65,000. The green mutant contained the same protein bands in the same relative quantities. The brown mutant had one protein completely missing and no other alterations. The blue-green mutant was deficient in a different protein, and had reduced quantities of all proteins with molecular weights less than 25,000. Chromatophores were separated into a fraction containing the reaction centers and a fraction containing the light-harvesting bacteriochlorophyll by treatment with sodium dodecyl sulfate. Eight of the proteins were found only in the reaction center fraction, one was only in the light-harvesting fraction, and the remainder were present in both fractions. The protein missing from the brown mutant was found to be a component of the reaction center fraction, whereas the proteins which were missing from the blue-green mutant were all components of the light-harvesting fraction. Some implications for the structure and biogenesis of chromatophores are discussed.     

Structure of a bacterial photosynthetic membrane. Isolation, polypeptide composition, and selective proteolysis

A procedure for the isolation of highly purified bacterial photosynthetic membranes from Rhodopseudomonas viridis is described. The purity of the final membrane fraction has been confirmed by electron microscopy. Seven major polypeptide bands are associated with the photosynthetic membranes, and all seven are resistant to solubilization in Triton X-100 detergent. Two pigmented bands with apparent molecular weights of 44K and 41K are thought to be cytochromes. The three polypeptides with apparent molecular weights of 38K, 32K, and 28K have been reported in reaction center preparations of other laboratories. Two low-molecular-weight (16K and 11K) bands bind bacteriochlorophyll b and may represent light-harvesting bacteriochlorophyll-protein complexes. The structures that were isolated seem to represent complete photosynthetic membranes, consisting of reaction center, electron transport, and light-harvesting components, all arranged in the regular lattice characteristic of viridis. Selective proteolysis of these membranes indicates that all membrane components are accessible to digestion by trypsin and pronase, except for the light-harvesting complexes.